U.S. patent application number 17/723280 was filed with the patent office on 2022-08-11 for tube lens design for improved depth-of-field.
The applicant listed for this patent is Element Biosciences, Inc.. Invention is credited to Steve Xiangling CHEN, Derek FULLER, Minghao GUO, Michael PREVITE, Chunhong ZHOU.
Application Number | 20220251644 17/723280 |
Document ID | / |
Family ID | 1000006284814 |
Filed Date | 2022-08-11 |
United States Patent
Application |
20220251644 |
Kind Code |
A1 |
CHEN; Steve Xiangling ; et
al. |
August 11, 2022 |
TUBE LENS DESIGN FOR IMPROVED DEPTH-OF-FIELD
Abstract
Imaging systems and methods comprising imaging a first interior
surface and a second interior surface of a flow cell are described.
In some embodiments, the imaging systems may comprise: a) an
objective lens; b) at least one image sensor; and c) at least one
tube lens disposed in an optical path between the objective lens
and the at least one image sensor; wherein the at least one tube
lens is configured to correct imaging performance such that images
of the first interior surface of the flow cell and the second
interior surface of the flow cell have substantially the same
optical resolution.
Inventors: |
CHEN; Steve Xiangling; (San
Diego, CA) ; GUO; Minghao; (San Diego, CA) ;
PREVITE; Michael; (San Diego, CA) ; ZHOU;
Chunhong; (San Diego, CA) ; FULLER; Derek;
(San Diego, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Element Biosciences, Inc. |
San Diego |
CA |
US |
|
|
Family ID: |
1000006284814 |
Appl. No.: |
17/723280 |
Filed: |
April 18, 2022 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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17016350 |
Sep 9, 2020 |
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17723280 |
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63076361 |
Sep 9, 2020 |
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62962723 |
Jan 17, 2020 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 21/6428 20130101;
C12Q 1/6806 20130101; G01N 2021/6463 20130101; G01N 15/147
20130101; G01N 2021/6441 20130101; C12Q 1/6869 20130101; G01N
2015/144 20130101; C12N 15/1006 20130101; G01N 21/6456 20130101;
G01N 21/6486 20130101; G01N 2201/0612 20130101; G01N 2021/6439
20130101; G01N 15/1484 20130101; G01N 21/6458 20130101; G01N
21/6402 20130101; G01N 15/1436 20130101 |
International
Class: |
C12Q 1/6869 20060101
C12Q001/6869; G01N 21/64 20060101 G01N021/64; G01N 15/14 20060101
G01N015/14; C12N 15/10 20060101 C12N015/10; C12Q 1/6806 20060101
C12Q001/6806 |
Claims
1. An imaging system configured to image a first interior surface
and a second interior surface of a flow cell, the imaging system
comprising: a) an objective lens; b) at least one image sensor; and
c) at least one tube lens disposed in an optical path between the
objective lens and the at least one image sensor; wherein said
optical system has a numerical aperture (NA) of less than 0.6 and a
field-of-view (FOV) of greater than 1.0 mm.sup.2; and wherein the
at least one tube lens is configured to correct imaging performance
such that images of the first interior surface of the flow cell and
the second interior surface of the flow cell have substantially the
same optical resolution.
2. The imaging system of claim 1, wherein the flow cell has a wall
thickness of at least 700 .mu.m and a fluid-filled gap between the
first interior surface and the second interior surface of at least
50 .mu.m.
3. The imaging system of claim 1, wherein the images of the first
interior surface and the second interior surface are acquired
without moving an optical compensator into an optical path between
said objective lens and said at least one image sensor.
4. The imaging system of claim 1, wherein the imaging system has a
numerical aperture (NA) of less than 0.6.
5. The imaging system of claim 1, wherein the imaging system has a
numerical aperture (NA) of greater than 0.3.
6. The imaging system of claim 1, wherein the imaging system has a
field-of-view (FOV) of greater than 1.5 mm.sup.2.
7. The imaging system of claim 6, wherein the optical resolution of
images of the first interior surface and the second interior
surface are diffraction-limited across the entire field-of-view
(FOV).
8. The imaging system of claim 1, wherein the at least one tube
lens comprises, in order, an asymmetric convex-convex lens, a
convex-plano lens, an asymmetric concave-concave lens, and an
asymmetric convex-concave lens.
9. The imaging system of claim 1, wherein the imaging system
comprises two or more tube lenses which are designed to provide
optimal imaging performance for the first interior surface and the
second interior surface at two or more fluorescence
wavelengths.
10. The imaging system of claim 1, further comprising a focusing
mechanism configured to refocus the optical system between
acquiring images of the first interior surface and the second
interior surface.
11. The imaging system of claim 1, wherein the imaging system is
configured to image two or more fields-of-view on at least one of
the first interior surface or the second interior surface.
12. The imaging system of claim 1, wherein the first interior
surface and second interior surface of the flow cell are coated
with a hydrophilic coating layer, and wherein said hydrophilic
coating layer further comprises labeled nucleic acid colonies
disposed thereon at a surface density of >10,000 nucleic acid
colonies/mm.sup.2.
13. The imaging system of claim 12, wherein an image of the first
interior surface or second interior surface acquired using the
imaging system shows a contrast to noise ratio (CNR) of at least 5
when the nucleic acid colonies are labeled with cyanine dye 3
(Cy3), the imaging system comprises a dichroic mirror and bandpass
filter set optimized for Cy3 emission, and the image is acquired
under non-signal saturating conditions while the surface is
immersed in 25 mM ACES, pH 7.4 buffer.
14. The imaging system of claim 12, wherein said imaging system
comprises 1, 2, 3, or 4 imaging channels configured to detect
nucleic acid colonies disposed on at least one of said two distinct
surfaces that have been labeled with 1, 2, 3, or 4 distinct
detectable labels.
15. The imaging system of claim 12, wherein the imaging system is
used to monitor a sequencing-by-avidity, sequencing-by-nucleotide
base-pairing, sequencing-by-nucleotide binding, or
sequencing-by-nucleotide incorporation reaction on at least one of
the first interior surface and the second interior surface and
detect a bound or incorporated nucleotide base.
16. The imaging system of claim 12, wherein the imaging system is
used to perform nucleic acid sequencing.
17. The imaging system of claim 12, wherein the imaging system is
used to determine a genotype of a sample, wherein determining the
genotype of the sample comprises preparing a nucleic acid molecule
extracted from the sample for sequencing, and then sequencing the
nucleic acid molecule.
18. The imaging system of claim 1, wherein the at least one image
sensor comprises pixels having a pixel dimension chosen such that a
spatial sampling frequency for the imaging system is at least twice
an optical resolution of the imaging system.
19. The imaging system of claim 1, wherein a combination of the
objective lens and the at least one tube lens is configured to
optimize a modulation transfer function in the spatial frequency
range from 700 cycles per mm to 1100 cycles per mm in the sample
plane.
20. The imaging system of claim 1, wherein the at least one tube
lens is designed to correct modulation transfer function (MTF) at
one or more specified spatial frequencies, defocus, spherical
aberration, chromatic aberration, coma, astigmatism, field
curvature, image distortion, image contrast-to-noise ratio (CNR),
or any combination thereof, for a combination of the objective lens
and the at least one tube lens.
Description
[0001] This application is a continuation application of U.S.
application Ser. No. 17/016,350, filed Sep. 9, 2020, which claims
the benefit of U.S. Provisional Application No. 63/076,361, filed
Sep. 9, 2020 and U.S. Provisional Application No. 62/962,723, filed
Jan. 17, 2020, each of which is incorporated herein by reference in
its entirety.
BACKGROUND
[0002] In typical fluorescence-based genomic testing assays, e.g.,
genotyping or nucleic acid sequencing (using either real time,
cyclic, or stepwise reaction schemes), dye molecules that are
attached to nucleic acid molecules tethered on a substrate are
excited using an excitation light source, a fluorescence photon
signal is generated in one or more spatially-localized positions on
the substrate, and the fluorescence is subsequently imaged through
an optical system onto an image sensor. An analysis process is then
used to analyze the images, find the positions of labeled molecules
(or clonally amplified clusters of molecules) on the substrate, and
quantify the fluorescence photon signal in terms of wavelength and
spatial coordinates, which may then be correlated with the degree
to which a specific chemical reaction, e.g., a hybridization event
or base addition event, occurred in the specified locations on the
substrate. Imaging-based methods provide large scale parallelism
and multiplexing capabilities, which help to drive down the cost
and accessibility of such technologies. However, detection errors
that arise from, for example, overly dense packing of labeled
molecules (or clonally-amplified clusters of molecules) within a
small region of the substrate surface, or due to low
contrast-to-noise ratio (CNR) in the image, may lead to errors in
attributing the fluorescence signal to the correct molecules (or
clonally amplified clusters of molecules).
SUMMARY
[0003] Disclosed herein are imaging systems configured to image a
first interior surface and a second interior surface of a flow
cell, the imaging systems comprising: a) an objective lens; b) at
least one image sensor; and c) at least one tube lens disposed in
an optical path between the objective lens and the at least one
image sensor; wherein said optical system has a numerical aperture
(NA) of less than 0.6 and a field-of-view (FOV) of greater than 1.0
mm.sup.2; and wherein the at least one tube lens is configured to
correct imaging performance such that images of the first interior
surface of the flow cell and the second interior surface of the
flow cell have substantially the same optical resolution.
[0004] In some embodiments, the flow cell has a wall thickness of
at least 700 .mu.m and a fluid-filled gap between the first
interior surface and the second interior surface of at least 50
.mu.m. In some embodiments, the images of the first interior
surface and the second interior surface are acquired without moving
an optical compensator into an optical path between said objective
lens and said at least one image sensor. In some embodiments, the
imaging system has a numerical aperture (NA) of less than 0.6. In
some embodiments, the imaging system has a numerical aperture (NA)
of greater than 0.3. In some embodiments, the imaging system has a
field-of-view (FOV) of greater than 1.5 mm.sup.2. In some
embodiments, the optical resolution of images of the first interior
surface and the second interior surface are diffraction-limited
across the entire field-of-view (FOV). In some embodiments, the at
least one tube lens comprises, in order, an asymmetric
convex-convex lens, a convex-plano lens, an asymmetric
concave-concave lens, and an asymmetric convex-concave lens. In
some embodiments, the imaging system comprises two or more tube
lenses which are designed to provide optimal imaging performance
for the first interior surface and the second interior surface at
two or more fluorescence wavelengths. In some embodiments, the
imaging system further comprises a focusing mechanism configured to
refocus the optical system between acquiring images of the first
interior surface and the second interior surface. In some
embodiments, the imaging system is configured to image two or more
fields-of-view on at least one of the first interior surface or the
second interior surface. In some embodiments, the first interior
surface and second interior surface of the flow cell are coated
with a hydrophilic coating layer, and wherein said hydrophilic
coating layer further comprises labeled nucleic acid colonies
disposed thereon at a surface density of >10,000 nucleic acid
colonies/mm.sup.2. In some embodiments, an image of the first
interior surface or second interior surface acquired using the
imaging system shows a contrast to noise ratio (CNR) of at least 5
when the nucleic acid colonies are labeled with cyanine dye 3
(Cy3), the imaging system comprises a dichroic mirror and bandpass
filter set optimized for Cy3 emission, and the image is acquired
under non-signal saturating conditions while the surface is
immersed in 25 mM ACES, pH 7.4 buffer. In some embodiments, said
imaging system comprises 1, 2, 3, or 4 imaging channels configured
to detect nucleic acid colonies disposed on at least one of said
two distinct surfaces that have been labeled with 1, 2, 3, or 4
distinct detectable labels. In some embodiments, the imaging system
is used to monitor a sequencing-by-avidity,
sequencing-by-nucleotide base-pairing, sequencing-by-nucleotide
binding, or sequencing-by-nucleotide incorporation reaction on at
least one of the first interior surface and the second interior
surface and detect a bound or incorporated nucleotide base. In some
embodiments, the imaging system is used to perform nucleic acid
sequencing. In some embodiments, the imaging system is used to
determine a genotype of a sample, wherein determining the genotype
of the sample comprises preparing a nucleic acid molecule extracted
from the sample for sequencing, and then sequencing the nucleic
acid molecule. In some embodiments, the at least one image sensor
comprises pixels having a pixel dimension chosen such that a
spatial sampling frequency for the imaging system is at least twice
an optical resolution of the imaging system. In some embodiments, a
combination of the objective lens and the at least one tube lens is
configured to optimize a modulation transfer function in the
spatial frequency range from 700 cycles per mm to 1100 cycles per
mm in the sample plane. In some embodiments, the at least one tube
lens is designed to correct modulation transfer function (MTF) at
one or more specified spatial frequencies, defocus, spherical
aberration, chromatic aberration, coma, astigmatism, field
curvature, image distortion, image contrast-to-noise ratio (CNR),
or any combination thereof, for a combination of the objective lens
and the at least one tube lens.
[0005] Also disclosed herein are methods of sequencing a nucleic
acid molecule, the methods comprising: a) imaging a first surface
and an axially-displaced second surface using an optical system
which comprises an objective lens and at least one image sensor,
wherein said optical system has a numerical aperture (NA) of less
than 0.6 and a field-of-view (FOV) of greater than 1.0 mm.sup.2,
and wherein images of the first surface and the axially-displaced
second surface having substantially the same optical resolution are
acquired without moving an optical compensator into an optical path
between said objective lens and said at least one image sensor; and
b) detecting a fluorescently-labeled composition comprising the
nucleic acid molecule, or a complement thereof, disposed on the
first surface or the axially-displaced second surface to determine
an identity of a nucleotide in the nucleic acid molecule.
[0006] In some embodiments, a focusing mechanism is utilized to
refocus the optical system between acquiring images of the first
surface and the axially-displaced second surface. In some
embodiments, the method further comprises imaging two or more
fields-of-view on at least one of the first surface or
axially-displaced second surface. In some embodiments, the first
surface and the axially-displaced second surface comprise two
surfaces of a flow cell. In some embodiments, said two surfaces of
the flow cell are coated with a hydrophilic coating layer. In some
embodiments, said hydrophilic coating layer further comprises
labeled nucleic acid colonies disposed thereon at a surface density
of >10,000 nucleic acid colonies/mm.sup.2. In some embodiments,
an image of a surface of said two surfaces acquired using said
optical system shows a contrast to noise ratio (CNR) of at least 5
when the nucleic acid colonies are labeled with cyanine dye 3
(Cy3), the optical system comprises a dichroic mirror and bandpass
filter set optimized for Cy3 emission, and the image is acquired
under non-signal saturating conditions while the surface is
immersed in 25 mM ACES, pH 7.4 buffer. In some embodiments, said
optical system comprises 1, 2, 3, or 4 imaging channels configured
to detect nucleic acid colonies disposed on at least one of the
first surface and the axially-displaced second surface that have
been labeled with 1, 2, 3, or 4 distinct detectable labels. In some
embodiments, the at least one image sensor comprises pixels having
a pixel dimension chosen such that a spatial sampling frequency for
the optical system is at least twice an optical resolution of the
optical system. In some embodiments, the optical system comprises
at least one tube lens positioned between the objective lens and
the at least one image sensor, and wherein the at least one tube
lens is configured to correct an imaging performance metric for
imaging a first interior surface of a flow cell and a second
interior surface of the flow cell. In some embodiments, the flow
cell has a wall thickness of at least 700 .mu.m and a gap between
the first interior surface and the second interior surface of at
least 50 .mu.m. In some embodiments, the at least one tube lens
comprises, in order, an asymmetric convex-convex lens, a
convex-plano lens, an asymmetric concave-concave lens, and an
asymmetric convex-concave lens. In some embodiments, the optical
system comprises two or more tube lenses which are designed to
provide optimal imaging performance at two or more fluorescence
wavelengths. In some embodiments, a combination of objective lens
and tube lens is configured to optimize a modulation transfer
function in the mid to high spatial frequency range. In some
embodiments, the imaging performance metric comprises a measurement
of modulation transfer function (MTF) at one or more specified
spatial frequencies, defocus, spherical aberration, chromatic
aberration, coma, astigmatism, field curvature, image distortion,
image contrast-to-noise ratio (CNR), or any combination thereof. In
some embodiments, the optical resolution of images of the first
surface and axially-displaced second surface are
diffraction-limited across the entire field-of-view (FOV). In some
embodiments, the sequencing of the nucleic acid molecule further
comprises performing a sequencing-by-avidity,
sequencing-by-nucleotide base-pairing, sequencing-by-nucleotide
binding, or sequencing-by-nucleotide incorporation reaction on at
least one of the first surface and axially-displaced second surface
and detecting a bound or incorporated nucleotide base. In some
embodiments, the method further comprises determining a genotype of
a sample, wherein determining the genotype of the sample comprises
preparing said nucleic acid molecule for sequencing, and then
sequencing said nucleic acid molecule.
[0007] Disclosed herein are imaging systems configured to image two
distinct, axially-displaced surfaces, the imaging systems
comprising an objective lens and at least one image sensor, wherein
said imaging system has a numerical aperture (NA) of less than 0.6
and a field-of-view (FOV) of greater than 1.0 mm2, and wherein said
imaging system is capable of acquiring images of the two distinct,
axially-displaced surfaces that have substantially the same optical
resolution without moving an optical compensator into an optical
path between said objective lens and said at least one image
sensor.
[0008] In some embodiments, the imaging system has a numerical
aperture of greater than 0.3. In some embodiments, the imaging
system further comprises a focusing mechanism used to refocus the
optical system between acquiring images of the two distinct,
axially-displaced surfaces. In some embodiments, the imaging system
is configured to image two or more fields-of-view on at least one
of said two distinct, axially-displaced surfaces. In some
embodiments, said two distinct, axially-displaced surfaces comprise
two surfaces of a flow cell. In some embodiments, said two distinct
surfaces of the flow cell are coated with a hydrophilic coating
layer, and wherein said hydrophilic coating layer further comprises
labeled nucleic acid colonies disposed thereon at a surface density
of >10,000 nucleic acid colonies/mm.sup.2. In some embodiments,
said imaging system comprises 1, 2, 3, or 4 imaging channels
configured to detect nucleic acid colonies disposed on at least one
of said two distinct surfaces that have been labeled with 1, 2, 3,
or 4 distinct detectable labels. In some embodiments, the at least
one image sensor comprises pixels having a pixel dimension chosen
such that a spatial sampling frequency for the imaging system is at
least twice an optical resolution of the imaging system. In some
embodiments, the imaging system comprises at least one tube lens
positioned between the objective lens and the at least one image
sensor, and wherein the at least one tube lens is configured to
correct an imaging performance metric for imaging a first interior
surface of a flow cell and a second interior surface of the flow
cell. In some embodiments, the flow cell has a wall thickness of at
least 700 .mu.m and a gap between the first interior surface and
the second interior surface of at least 50 .mu.m. In some
embodiments, the imaging system comprises two or more tube lenses
which are designed to provide optimal imaging performance at two or
more fluorescence wavelengths. In some embodiments, the optical
resolution of images of the two distinct, axially-displaced
surfaces are diffraction-limited across the entire field-of-view
(FOV).
[0009] Disclosed herein are methods of sequencing a nucleic acid
molecule, the method comprising: a) imaging a first surface and an
axially-displaced second surface using a compensation-free optical
system which comprises an objective lens and at least one image
sensor, wherein said optical system has a numerical aperture (NA)
of less than 0.6 and a field-of-view (FOV) of greater than 1.0
mm.sup.2; b) processing the images of the first surface and the
axially-displaced second surface to correct for optical aberration
such that the images of the first surface and the axially-displaced
second surface have substantially the same optical resolution; and
c) detecting a fluorescently-labeled composition comprising the
nucleic acid molecule, or a complement thereof, disposed on the
first surface or the axially-displaced second surface to determine
an identity of a nucleotide in the nucleic acid molecule.
[0010] In some embodiments, the images of the first surface and the
axially-displaced second surface are acquired without moving an
optical compensator into an optical path between said objective
lens and said at least one image sensor. In some embodiments, the
images of the first surface and the axially-displaced second
surface are acquired by just refocusing the optical system. In some
embodiments, the method further comprises imaging two or more
fields-of-view on at least one of the first surface or
axially-displaced second surface. In some embodiments, the first
surface and the axially-displaced second surface comprise two
surfaces of a flow cell. In some embodiments, said two surfaces of
the flow cell are coated with a hydrophilic coating layer. In some
embodiments, said hydrophilic coating layer further comprises
labeled nucleic acid colonies disposed thereon at a surface density
of >10,000 nucleic acid colonies/mm.sup.2. In some embodiments,
an image of a surface of said two surfaces acquired using said
optical system shows a contrast to noise ratio (CNR) of at least 5
when the nucleic acid colonies are labeled with cyanine dye 3
(Cy3), the optical system comprises a dichroic mirror and bandpass
filter set optimized for Cy3 emission, and the image is acquired
under non-signal saturating conditions while the surface is
immersed in 25 mM ACES, pH 7.4 buffer. In some embodiments, said
optical system comprises 1, 2, 3, or 4 imaging channels configured
to detect nucleic acid colonies disposed on at least one of the
first surface and the axially-displaced second surface that have
been labeled with 1, 2, 3, or 4 distinct detectable labels. In some
embodiments, at least one image sensor comprises pixels having a
pixel dimension chosen such that a spatial sampling frequency for
the optical system is at least twice an optical resolution of the
optical system. In some embodiments, the optical system comprises
at least one tube lens positioned between the objective lens and
the at least one image sensor, and wherein the at least one tube
lens is configured to correct an imaging performance metric for
imaging a first interior surface of a flow cell and a second
interior surface of the flow cell. In some embodiments, the flow
cell has a wall thickness of at least 700 .mu.m and a gap between
the first interior surface and the second interior surface of at
least 50 .mu.m. In some embodiments, the at least one tube lens
comprises, in order, an asymmetric convex-convex lens, a
convex-plano lens, an asymmetric concave-concave lens, and an
asymmetric convex-concave lens. In some embodiments, the optical
system comprises two or more tube lenses which are designed to
provide optimal imaging performance at two or more fluorescence
wavelengths. In some embodiments, a combination of objective lens
and tube lens is configured to optimize a modulation transfer
function in the mid to high spatial frequency range. In some
embodiments, the imaging performance metric comprises a measurement
of modulation transfer function (MTF) at one or more specified
spatial frequencies, defocus, spherical aberration, chromatic
aberration, coma, astigmatism, field curvature, image distortion,
image contrast-to-noise ratio (CNR), or any combination thereof. In
some embodiments, the optical resolution of images of the first
surface and axially-displaced second surface are
diffraction-limited across the entire field-of-view (FOV). In some
embodiments, the sequencing of the nucleic acid molecule further
comprises performing a sequencing-by-avidity,
sequencing-by-nucleotide binding, or sequencing-by-nucleotide
incorporation reaction on at least one of the first surface and
axially-displaced second surface and detecting a bound or
incorporated nucleotide base. In some embodiments, the method
further comprises determining a genotype of a sample, wherein
determining the genotype of the sample comprises preparing said
nucleic acid molecule for sequencing, and then sequencing said
nucleic acid molecule.
[0011] Disclosed herein are systems for sequencing a nucleic acid
molecule comprising: a) an optical system comprising an objective
lens and at least one image sensor, wherein said optical system has
a numerical aperture (NA) of less than 0.6 and a field-of-view
(FOV) of greater than 1.0 mm.sup.2, and is configured to acquire
images of a first surface and an axially-displaced second surface;
and b) a processor programmed to: i) process images of the first
surface and the axially-displaced second surface to correct for
optical aberration such that the images of the first surface and
the axially-displaced second surface have substantially the same
optical resolution; and ii) detect a fluorescently-labeled
composition comprising the nucleic acid molecule, or a complement
thereof, disposed on the first surface or the axially-displaced
second surface to determine an identity of a nucleotide in the
nucleic acid molecule.
[0012] In some embodiments, the images of the first surface and the
axially-displaced second surface are acquired without moving an
optical compensator into an optical path between said objective
lens and said at least one image sensor. In some embodiments, the
images of the first surface and the axially-displaced second
surface are acquired by just refocusing the optical system. In some
embodiments, the imaging system has a numerical aperture of greater
than 0.3. In some embodiments, the first surface and
axially-displaced second surface comprise two surfaces of a flow
cell. In some embodiments, said two surfaces of the flow cell are
coated with a hydrophilic coating layer, and wherein said
hydrophilic coating layer further comprises labeled nucleic acid
colonies disposed thereon at a surface density of >10,000
nucleic acid colonies/mm.sup.2. In some embodiments, said optical
system comprises 1, 2, 3, or 4 imaging channels configured to
detect nucleic acid colonies disposed on at least one of the first
surface or axially-displaced second surface that have been labeled
with 1, 2, 3, or 4 distinct detectable labels. In some embodiments,
the at least one image sensor comprises pixels having a pixel
dimension chosen such that a spatial sampling frequency for the
optical system is at least twice an optical resolution of the
optical system. In some embodiments, the system comprises at least
one tube lens positioned between the objective lens and the at
least one image sensor, and wherein the at least one tube lens is
configured to correct an imaging performance metric for imaging a
first interior surface of a flow cell and a second interior surface
of the flow cell. In some embodiments, the flow cell has a wall
thickness of at least 700 .mu.m and a gap between the first
interior surface and the second interior surface of at least 50
.mu.m. In some embodiments, the optical system comprises two or
more tube lenses which are designed to provide optimal imaging
performance at two or more fluorescence wavelengths.
[0013] Disclosed herein are fluorescence imaging systems
comprising: a) at least one light source configured to provide
excitation light within one or more specified wavelength ranges; b)
an objective lens configured to collect fluorescence arising from
within a specified field-of-view of a sample plane upon exposure of
the sample plane to the excitation light, wherein a numerical
aperture of the objective lens is at least 0.3, wherein a working
distance of the objective lens is at least 700 .mu.m, and wherein
the field-of-view has an area of at least 2 mm.sup.2; and c) at
least one image sensor, wherein the fluorescence collected by the
objective lens is imaged onto the image sensor, and wherein a pixel
dimension for the image sensor is chosen such that a spatial
sampling frequency for the fluorescence imaging system is at least
twice an optical resolution of the fluorescence imaging system.
[0014] In some embodiments, the numerical aperture is at least
0.75. In some embodiments, the numerical aperture is at least 1.0.
In some embodiments, the working distance is at least 850 .mu.m. In
some embodiments, the working distance is at least 1,000 .mu.m. In
some embodiments, the field-of-view has an area of at least 2.5
mm.sup.2. In some embodiments, the field-of-view has an area of at
least 3 mm.sup.2. In some embodiments, the spatial sampling
frequency is at least 2.5 times the optical resolution of the
fluorescence imaging system. In some embodiments, the spatial
sampling frequency is at least 3 times the optical resolution of
the fluorescence imaging system. In some embodiments, the system
further comprises an X-Y-Z translation stage such that the system
is configured to acquire a series of two or more fluorescence
images in an automated fashion, wherein each image of the series is
acquired for a different field-of-view. In some embodiments, a
position of the sample plane is simultaneously adjusted in an X
direction, a Y direction, and a Z direction to match the position
of an objective lens focal plane in between acquiring images for
different fields-of-view. In some embodiments, the time required
for the simultaneous adjustments in the X direction, Y direction,
and Z direction is less than 0.4 seconds. In some embodiments, the
system further comprises an autofocus mechanism configured to
adjust the focal plane position prior to acquiring an image of a
different field-of-view if an error signal indicates that a
difference in the position of the focal plane and the sample plane
in the Z direction is greater than a specified error threshold. In
some embodiments, the specified error threshold is 100 nm. In some
embodiments, the specified error threshold is 50 nm. In some
embodiments, the system comprises three or more image sensors, and
wherein the system is configured to image fluorescence in each of
three or more wavelength ranges onto a different image sensor. In
some embodiments, a difference in the position of a focal plane for
each of the three or more image sensors and the sample plane is
less than 100 nm. In some embodiments, a difference in the position
of a focal plane for each of the three or more image sensors and
the sample plane is less than 50 nm. In some embodiments, the total
time required to reposition the sample plane, adjust focus if
necessary, and acquire an image is less than 0.4 seconds per
field-of-view. In some embodiments, the total time required to
reposition the sample plane, adjust focus if necessary, and acquire
an image is less than 0.3 seconds per field-of-view.
[0015] Also discloser herein are fluorescence imaging systems for
dual-side imaging of a flow cell comprising: a) an objective lens
configured to collect fluorescence arising from within a specified
field-of-view of a sample plane within the flow cell; b) at least
one tube lens positioned between the objective lens and at least
one image sensor, wherein the at least one tube lens is configured
to correct an imaging performance metric for a combination of the
objective lens, the at least one tube lens, and the at least one
image sensor when imaging an interior surface of the flow cell, and
wherein the flow cell has a wall thickness of at least 700 .mu.m
and a gap between an upper interior surface and a lower interior
surface of at least 50 .mu.m; wherein the imaging performance
metric is substantially the same for imaging the upper interior
surface or the lower interior surface of the flow cell without
moving an optical compensator into or out of an optical path
between the flow cell and the at least one image sensor, without
moving one or more optical elements of the tube lens along the
optical path, and without moving one or more optical elements of
the tube lens into or out of the optical path.
[0016] In some embodiments, the objective lens is a
commercially-available microscope objective. In some embodiments,
the commercially-available microscope objective has a numerical
aperture of at least 0.3. In some embodiments, the objective lens
has a working distance of at least 700 .mu.m. In some embodiments,
the objective lens is corrected to compensate for a cover slip
thickness (or flow cell wall thickness) of 0.17 mm. In some
embodiments, the fluorescence imaging system further comprising an
electro-optical phase plate positioned adjacent to the objective
lens and between the objective lens and the tube lens, wherein the
electro-optical phase plate provides correction for optical
aberrations caused by a fluid filling the gap between the upper
interior surface and the lower interior surface of the flow cell.
In some embodiments, the at least one tube lens is a compound lens
comprising three or more optical components. In some embodiments,
the at least one tube lens is a compound lens comprising four
optical components. In some embodiments, the four optical
components comprise, in order, a first asymmetric convex-convex
lens, a second convex-plano lens, a third asymmetric
concave-concave lens, and a fourth asymmetric convex-concave lens.
In some embodiments, the at least one tube lens is configured to
correct an imaging performance metric for a combination of the
objective lens, the at least one tube lens, and the at least one
image sensor when imaging an interior surface of a flow cell having
a wall thickness of at least 1 mm. In some embodiments, the at
least one tube lens is configured to correct an imaging performance
metric for a combination of the objective lens, the at least one
tube lens, and the at least one image sensor when imaging an
interior surface of a flow cell having a gap of at least 100 .mu.m.
In some embodiments, the at least one tube lens is configured to
correct an imaging performance metric for a combination of the
objective lens, the at least one tube lens, and the at least one
image sensor when imaging an interior surface of a flow cell having
a gap of at least 200 .mu.m. In some embodiments, the system
comprises a single objective lens, two tube lenses, and two image
sensors, and each of the two tube lenses is designed to provide
optimal imaging performance at a different fluorescence wavelength.
In some embodiments, the system comprises a single objective lens,
three tube lenses, and three image sensors, and each of the three
tube lenses is designed to provide optimal imaging performance at a
different fluorescence wavelength. In some embodiments, the system
comprises a single objective lens, four tube lenses, and four image
sensors, and each of the four tube lenses is designed to provide
optimal imaging performance at a different fluorescence wavelength.
In some embodiments, the design of the objective lens or the at
least one tube lens is configured to optimize the modulation
transfer function in the mid to high spatial frequency range. In
some embodiments, the imaging performance metric comprises a
measurement of modulation transfer function (MTF) at one or more
specified spatial frequencies, defocus, spherical aberration,
chromatic aberration, coma, astigmatism, field curvature, image
distortion, contrast-to-noise ratio (CNR), or any combination
thereof. In some embodiments, the difference in the imaging
performance metric for imaging the upper interior surface and the
lower interior surface of the flow cell is less than 10%. In some
embodiments, the difference in imaging performance metric for
imaging the upper interior surface and the lower interior surface
of the flow cell is less than 5%. In some embodiments, the use of
the at least one tube lens provides for an at least equivalent or
better improvement in the imaging performance metric for dual-side
imaging compared to that for a conventional system comprising an
objective lens, a motion-actuated compensator, and an image sensor.
In some embodiments, the use of the at least one tube lens provides
for an at least 10% improvement in the imaging performance metric
for dual-side imaging compared to that for a conventional system
comprising an objective lens, a motion-actuated compensator, and an
image sensor.
[0017] Disclosed herein are illumination systems for use in
imaging-based solid-phase genotyping and sequencing applications,
the illumination system comprising: a) a light source; and b) a
liquid light-guide configured to collect light emitted by the light
source and deliver it to a specified field-of-illumination on a
support surface comprising tethered biological macromolecules.
[0018] In some embodiments, the illumination system further
comprises a condenser lens. In some embodiments, the specified
field-of-illumination has an area of at least 2 mm.sup.2. In some
embodiments, the light delivered to the specified
field-of-illumination is of uniform intensity across a specified
field-of-view for an imaging system used to acquire images of the
support surface. In some embodiments, the specified field-of-view
has an area of at least 2 mm.sup.2. In some embodiments, the light
delivered to the specified field-of-illumination is of uniform
intensity across the specified field-of-view when a coefficient of
variation (CV) for light intensity is less than 10%. In some
embodiments, the light delivered to the specified
field-of-illumination is of uniform intensity across the specified
field-of-view when a coefficient of variation (CV) for light
intensity is less than 5%. In some embodiments, the light delivered
to the specified field-of-illumination has a speckle contrast value
of less than 0.1. In some embodiments, the light delivered to the
specified field-of-illumination has a speckle contrast value of
less than 0.05.
INCORPORATION BY REFERENCE
[0019] All publications, patents, and patent applications mentioned
in this specification are herein incorporated by reference in their
entirety to the same extent as if each individual publication,
patent, or patent application was specifically and individually
indicated to be incorporated by reference in its entirety. In the
event of a conflict between a term herein and a term in an
incorporated reference, the term herein controls.
BRIEF DESCRIPTION OF THE DRAWINGS
[0020] The novel features of the invention are set forth with
particularity in the appended claims. A better understanding of the
features and advantages of the present invention will be obtained
by reference to the following detailed description that sets forth
illustrative embodiments, in which the principles of the invention
are utilized, and the accompanying drawings of which:
[0021] FIGS. 1A-1B schematically illustrate non-limiting examples
of imaging dual surface support structures for presenting sample
sites for imaging by the imaging systems disclosed herein. FIG. 1A:
illustration of imaging front and rear interior surfaces of a flow
cell. FIG. 1B: illustration of imaging front and rear exterior
surfaces of a substrate.
[0022] FIGS. 2A-2B illustrate a non-limiting example of a
multi-channel fluorescence imaging module comprising a dichroic
beam splitter for transmitting an excitation light beam to a
sample, and for receiving and redirecting by reflection the
resultant fluorescence emission to four detection channels
configured for detection of fluorescence emission at four different
respective wavelengths or wavelength bands. FIG. 2A: top isometric
view. FIG. 2B: bottom isometric view.
[0023] FIGS. 3A-3B illustrate the optical paths within the
multi-channel fluorescence imaging module of FIGS. 2A and 2B
comprising a dichroic beam splitter for transmitting an excitation
light beam to a sample, and for receiving and redirecting by
reflection a resultant fluorescence emission to four detection
channels for detection of fluorescence emission at four different
respective wavelengths or wavelength bands. FIG. 3A: top view. FIG.
3B: side view.
[0024] FIG. 4 is a graph illustrating a relationship between
dichroic filter performance and beam angle of incidence.
[0025] FIG. 5 is a graph illustrating a relationship between beam
footprint size and beam angle of incidence on a dichroic
filter.
[0026] FIGS. 6A-6B schematically illustrate an example
configuration of dichroic filters and detection channels of a
multi-channel fluorescence imaging module wherein the dichroic
filters have reflective surface tilted such that the angle between
the incident beam (e.g., the central angle) and the reflective
surface of the dichroic filter is less than 45. FIG. 6A: schematic
illustration of a multichannel fluorescence imaging module
comprising four detection channels. FIG. 6B: detail view
illustrating the angle of incidence (AOI) of a light beam on a
dichroic reflector.
[0027] FIG. 7 provides a graph illustrating improved dichroic
filter performance corresponding to the imaging module
configuration illustrated in FIGS. 6A and 6B.
[0028] FIG. 8 provides a graph illustrating improved dichroic
filter performance corresponding to the imaging module
configuration illustrated in FIGS. 6A and 6B.
[0029] FIGS. 9A-9B provide graphs illustrating reduced surface
deformation resulting from the imaging module configuration of
FIGS. 6A and 6B. FIG. 9A illustrates the effect of folding angle on
image quality degradation induced by the addition of 1 wave of PV
spherical power to the last mirror. FIG. 9B illustrates the effect
of folding angle on image quality degradation induced by the
addition of 0.1 wave of PV spherical power to the last mirror.
[0030] FIGS. 10A-10B provide graphs illustrating improved
excitation filter performance (e.g. sharper transitions between
pass bands and surrounding stop bands) resulting from use of
s-polarization of the excitation beam. FIG. 10A: transmission
spectra for an example bandpass dichroic filter at angles of
incidence of 40 degrees and 45 degrees, where the incident beam is
linearly polarized and is p-polarized with respect to the plane of
the dichroic filter. FIG. 10B: changing the orientation of the
light source with respect to the dichroic filter, such that the
incident beam is s-polarized with respect to the plane of the
dichroic filter, results in a substantially sharper edge between
the passband and the stopband.
[0031] FIGS. 11A-11B illustrate the modulation transfer function
(MTF) of an example dual surface imaging system disclosed herein
having a numerical aperture (NA) of 0.3. FIG. 11A: first
surface.
[0032] FIG. 11B: second surface.
[0033] FIGS. 12A-12B illustrate the MTF of an example dual surface
imaging system disclosed herein having an NA of 0.4. FIG. 12A:
first surface. FIG. 12B: second surface.
[0034] FIGS. 13A-13B illustrate the MTF of an example dual surface
imaging system disclosed herein having an NA of 0.5. FIG. 13A:
first surface. FIG. 13B: second surface.
[0035] FIGS. 14A-14B illustrate the MTF of an example dual surface
imaging system disclosed herein having an NA of 0.6. FIG. 14A:
first surface. FIG. 14B: second surface.
[0036] FIGS. 15A-15B illustrate the MTF of an example dual surface
imaging system disclosed herein having an NA of 0.7. FIG. 15A:
first surface. FIG. 15B: second surface.
[0037] FIGS. 16A-16B illustrate the MTF of an example dual surface
imaging system disclosed herein having an NA of 0.8. FIG. 16A:
first surface. FIG. 16B: second surface.
[0038] FIGS. 17A-17B provide plots of the calculated Strehl ratio
for imaging a second flow cell surface through a first flow cell
surface. FIG. 17A: plot of the Strehl ratios for imaging a second
flow cell surface through a first flow cell surface as a function
of the thickness of the intervening fluid layer (fluid channel
height) for different objective lens and/or optical system
numerical apertures. FIG. 17B: plot of the Strehl ratio as a
function of numerical aperture for imaging a second flow cell
surface through a first flow cell surface and an intervening layer
of water having a thickness of 0.1 mm.
[0039] FIG. 18 provides a schematic illustration of a
dual-wavelength excitation/four channel emission fluorescence
imaging system of the present disclosure.
[0040] FIG. 19 provides an optical ray tracing diagram for an
objective lens design that has been designed for imaging a surface
on the opposite side of a 0.17 mm thick coverslip.
[0041] FIG. 20 provides a plot of the modulation transfer function
for the objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface on the opposite side
of a 0.17 mm thick coverslip.
[0042] FIG. 21 provides a plot of the modulation transfer function
for the objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface on the opposite side
of a 0.3 mm thick coverslip.
[0043] FIG. 22 provides a plot of the modulation transfer function
for the objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface that is separated
from that on the opposite side of a 0.3 mm thick coverslip by a 0.1
mm thick layer of aqueous fluid.
[0044] FIG. 23 provides a plot of the modulation transfer function
for the objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface on the opposite side
of a 1.0 mm thick coverslip.
[0045] FIG. 24 provides a plot of the modulation transfer function
for the objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface that is separated
from that on the opposite side of a 1.0 mm thick coverslip by a 0.1
mm thick layer of aqueous fluid.
[0046] FIG. 25 provides a ray tracing diagram for a tube lens
design which, if used in conjunction with the objective lens
illustrated in FIG. 19, provides for improved dual-side imaging
through a 1 mm thick coverslip.
[0047] FIG. 26 provides a plot of the modulation transfer function
for the combination of objective lens and tube lens illustrated in
FIG. 25 as a function of spatial frequency when used to image a
surface on the opposite side of a 1.0 mm thick coverslip.
[0048] FIG. 27 provides a plot of the modulation transfer function
for the combination of objective lens and tube lens illustrated in
FIG. 25 as a function of spatial frequency when used to image a
surface that is separated from that on the opposite side of a 1.0
mm thick coverslip by a 0.1 mm thick layer of aqueous fluid.
[0049] FIG. 28 provides ray tracing diagrams for tube lens design
(left) of the present disclosure that has been optimized to provide
high-quality, dual-side imaging performance. Because the tube lens
is no longer infinity-corrected, an appropriately designed null
lens (right) may be used in combination with the tube lens to
compensate for the non-infinity-corrected tube lens for
manufacturing and testing purposes.
[0050] FIG. 29 illustrates one non-limiting example of a single
capillary flow cell having 2 fluidic adaptors.
[0051] FIG. 30 illustrates one non-limiting example of a flow cell
cartridge comprising a chassis, fluidic adapters, and optionally
other components, that is designed to hold two capillaries.
[0052] FIG. 31 illustrates one non-limiting example of a system
comprising a single capillary flow cell connected to various fluid
flow control components, where the single capillary is compatible
with mounting on a microscope stage or in a custom imaging
instrument for use in various imaging applications.
[0053] FIG. 32 illustrates one non-limiting example of a system
that comprises a capillary flow cell cartridge having integrated
diaphragm valves to reduce or minimize dead volume and conserve
certain key reagents.
[0054] FIG. 33 illustrates one non-limiting example of a system
that comprises a capillary flow cell, a microscope setup, and a
temperature control mechanism.
[0055] FIG. 34 illustrates one non-limiting example for temperature
control of the capillary flow cells through the use of a metal
plate that is placed in contact with the flow cell cartridge.
[0056] FIG. 35 illustrates one non-limiting approach for
temperature control of the capillary flow cells that comprises a
non-contact thermal control mechanism.
[0057] FIGS. 36A-36C illustrates non-limiting examples of flow cell
device fabrication. FIG. 36A shows the preparation of one-piece
glass flow cell. FIG. 36B shows the preparation of two-piece glass
flow cell. FIG. 36C shows the preparation of three-piece glass flow
cell.
[0058] FIGS. 37A-37C illustrates non-limiting examples of glass
flow cell designs. FIG. 37A shows a one-piece glass flow cell
design. FIG. 37B shows a two-piece glass flow cell design. FIG. 37C
shows a three-piece glass flow cell design.
[0059] FIG. 38 illustrates visualization of cluster amplification
in a capillary lumen.
DETAILED DESCRIPTION
[0060] There is a need for fluorescence imaging methods and systems
that provide increased optical resolution and improved image
quality for genomics applications that lead to corresponding
improvements in genomic testing accuracy. Disclosed herein are
optical system designs for high-performance fluorescence imaging
methods and systems that may provide any one or more of improved
optical resolution (including high performance optical resolution),
improved image quality, and higher throughput for fluorescence
imaging-based genomics applications. The disclosed optical
illumination and imaging system designs may provide any one or more
of the following advantages: improved dichroic filter performance,
increased uniformity of dichroic filter frequency response,
improved excitation beam filtering, larger fields-of-view,
increased spatial resolution, improved modulation transfer,
contrast-to-noise ratio, and image quality, higher spatial sampling
frequency, faster transitions between image capture when
repositioning the sample plane to capture a series of images (e.g.,
of different fields-of-view), improved imaging system duty cycle,
and higher throughput image acquisition and analysis.
[0061] In some instances, improvements in imaging performance,
e.g., for dual-side (flow cell) imaging applications comprising the
use of thick flow cell walls (e.g., wall (or coverslip)
thickness>700 .mu.m) and fluid channels (e.g., fluid channel
height or thickness of 50-200 .mu.m) may be achieved using novel
objective lens designs that correct for optical aberration
introduced by imaging surfaces on the opposite side of thick
coverslips and/or fluid channels from the objective.
[0062] In some instances, improvements in imaging performance,
e.g., for dual-side (flow cell) imaging applications comprising the
use of thick flow cell walls (e.g., wall (or coverslip)
thickness>700 .mu.m) and fluid channels (e.g., fluid channel
height or thickness of 50-200 .mu.m) may be achieved even when
using commercially-available, off-the-shelf objectives by using a
novel tube lens design that, unlike the tube lens in a conventional
microscope that simply forms an image at the intermediate image
plane, corrects for the optical aberrations induced by the thick
flow cell walls and/or intervening fluid layer in combination with
the objective.
[0063] In some instances, improvements in imaging performance,
e.g., for multichannel (e.g., two-color or four-color) imaging
applications, may be achieved by using multiple tube lenses, one
for each imaging channel, where each tube lens design has been
optimized for the specific wavelength range used in that imaging
channel.
[0064] In some instances, improvements in imaging performance,
e.g., for dual-side (flow cell) imaging applications, may be
achieved by using an electro-optical phase plate in combination
with an objective lens to compensate for the optical aberrations
induced by the layer of fluid separating the upper (near) and lower
(far) interior surfaces of a flow cell. In some instances, this
design approach may also compensate for vibrations introduced by,
e.g., a motion-actuated compensator that is moved in or out of the
optical path depending on which surface of the flow cell is being
imaged.
[0065] Various multichannel fluorescence imaging module designs are
disclosed that may include illumination and imaging optical paths
comprising folded optical paths (e.g., comprising one or more beam
splitters or beam combiners, such as dichroic beam splitters or
combiners) that direct an excitation light beam to an objective
lens, and direct emission light transmitted through the objective
lens to a plurality of detection channels. Some particularly
advantageous features of the fluorescence imaging modules described
herein include specification of dichroic filter incidence angles
that result in sharper and/or more uniform transitions between
passband and stopband wavelength regions of the dichroic filters.
Such filters may be included within the folded optics and may
comprise dichroic beam splitters or combiners. Further advantageous
features of the disclosed imaging optics designs may include the
position and orientation of one or more excitation light sources
and one or more detection optical paths with respect to the
objective lens and to a dichroic filter that receives the
excitation beam. The excitation beam may also be linearly-polarized
and the orientation of the linear polarization may be such that
s-polarized light is incident on the dichroic reflective surface of
the dichroic filter. Such features may potentially improve
excitation beam filtering and/or reduce wavefront error introduced
into the emission light beam due to surface deformation of dichroic
filters. The fluorescence imaging modules described herein may or
may not include any of these features and may or may not include
any of these advantages.
[0066] Also described herein are devices and systems configured to
analyze large numbers of different nucleic acid sequences by
imaging, e.g., arrays of immobilized nucleic acid molecules or
amplified nucleic acid clusters formed on flow cell surfaces. The
devices and systems described herein can also be useful in, e.g.,
performing sequencing for comparative genomics, tracking gene
expression, performing micro RNA sequence analysis, epigenomics,
aptamer and phage display library characterization, and for
performing other sequencing applications. The devices and systems
disclosed herein comprise various combinations of optical,
mechanical, fluidic, thermal, electrical, and computing
devices/aspects. The advantages conferred by the disclosed flow
cell devices, cartridges, and systems include, but are not limited
to: (i) reduced device and system manufacturing complexity and
cost, (ii) significantly lower consumable costs (e.g., as compared
to those for currently available nucleic acid sequencing systems),
(iii) compatibility with typical flow cell surface
functionalization methods, (iv) flexible flow control when combined
with microfluidic components, e.g., syringe pumps and diaphragm
valves, etc., and (v) flexible system throughput.
[0067] Disclosed herein are capillary flow-cell devices and
capillary flow cell cartridges that are constructed from
off-the-shelf, disposable, single lumen (e.g., single fluid flow
channel) or multi-lumen capillaries that may also comprise fluidic
adaptors, cartridge chassis, one or more integrated fluid flow
control components, or any combination thereof. Also disclosed
herein are capillary flow cell-based systems that may comprise one
or more capillary flow cell devices (or microfluidic chips), one or
more capillary flow cell cartridges (or microfluidic cartridges),
fluid flow controller modules, temperature control modules, imaging
modules, or any combination thereof.
[0068] The design features of some disclosed capillary flow cell
devices, cartridges, and systems include, but are not limited to,
(i) unitary flow channel construction, (ii) sealed, reliable, and
repetitive switching between reagent flows that can be implemented
with a simple load/unload mechanism such that fluidic interfaces
between the system and capillaries are reliably sealed, thereby
facilitating capillary replacement and system reuse, and enabling
precise control of reaction conditions such as reagent
concentration, pH, and temperature, (iii) replaceable single fluid
flow channel devices or capillary flow cell cartridges comprising
multiple flow channels that can be used interchangeably to provide
flexible system throughput, and (iv) compatibility with a wide
variety of detection methods such as fluorescence imaging.
[0069] Although the disclosed capillary flow cell devices and
systems, capillary flow cell cartridges, capillary flow cell-based
systems, microfluidic devices and cartridges, and microfluidic
chip-based systems, are described primarily in the context of their
use for nucleic acid sequencing applications, various aspects of
the disclosed devices and systems may be applied not only to
nucleic acid sequencing but also to any other type of chemical
analysis, biochemical analysis, nucleic acid analysis, cell
analysis, or tissue analysis application. It shall be understood
that different aspects of the disclosed methods, devices, and
systems can be appreciated individually, collectively, or in
combination with each other. Although discussed herein primarily in
the context of fluorescence imaging (including, e.g., fluorescence
microscopy imaging, fluorescence confocal imaging, two-photon
fluorescence, and the like), it will be understood by those of
skill in the art that many of the disclosed optical design
approaches and features are applicable to other imaging modes,
e.g., bright-field imaging, dark-field imaging, phase contrast
imaging, and the like.
[0070] Definitions: Unless otherwise defined, all of the technical
terms used herein have the same meaning as commonly understood by
one of ordinary skill in the art in the field to which this
disclosure belongs.
[0071] As used in this specification and the appended claims, the
singular forms "a", "an", and "the" include plural references
unless the context clearly dictates otherwise. Any reference to
"or" herein is intended to encompass "and/or" unless otherwise
stated.
[0072] As used herein, the term `about` a number refers to that
number plus or minus 10% of that number. The term `about` when used
in the context of a range refers to that range minus 10% of its
lowest value and plus 10% of its greatest value.
[0073] As used herein, the phrases "imaging module", "imaging
unit", "imaging system", "optical imaging module", "optical imaging
unit", and "optical imaging system" are used interchangeably, and
may comprise components or sub-systems of a larger system that may
also include, e.g., fluidics modules, temperature control modules,
translation stages, robotic fluid dispensing and/or microplate
handling, processor or computers, instrument control software, data
analysis and display software, etc.
[0074] As used herein, the term "detection channel" refers to an
optical path (and/or the optical components therein) within an
optical system that is configured to deliver an optical signal
arising from a sample to a detector. In some instances, a detection
channel may be configured for performing spectroscopic
measurements, e.g., monitoring a fluorescence signal or other
optical signal using a detector such as a photomultiplier. In some
instances, a "detection channel" may be an "imaging channel", i.e.,
an optical path (and/or the optical components therein) within an
optical system that is configured to capture and deliver an image
to an image sensor.
[0075] As used herein, a "detectable label" may refer to any of a
variety of detectable labels or tags known to those of skill in the
art. Examples include, but are not limited to, chromophores,
fluorophores, quantum dots, upconverting phosphors, luminescent or
chemiluminescent molecules, radioisotopes, magnetic nanoparticles,
mass tags, and the like. In some instances, a preferred label may
comprise a fluorophore.
[0076] As used herein, the term "excitation wavelength" refers to
the wavelength of light used to excite a fluorescent indicator
(e.g., a fluorophore or dye molecule) and generate fluorescence.
Although the excitation wavelength is typically specified as a
single wavelength, e.g., 620 nm, it will be understood by those of
skill in the art that this specification refers to a wavelength
range or excitation filter bandpass that is centered on the
specified wavelength. For example, in some instances, light of the
specified excitation wavelength comprises light of the specified
wavelength.+-.2 nm, .+-.5 nm, .+-.10 nm, .+-.20 nm, .+-.40 nm,
.+-.80 nm, or more. In some instances, the excitation wavelength
used may or may not coincide with the absorption peak maximum of
the fluorescent indicator.
[0077] As used herein, the term "emission wavelength" refers to the
wavelength of light emitted by a fluorescent indicator (e.g., a
fluorophore or dye molecule) upon excitation by light of an
appropriate wavelength. Although the emission wavelength is
typically specified as a single wavelength, e.g., 670 nm, it will
be understood by those of skill in the art that this specification
refers to a wavelength range or emission filter bandpass that is
centered on the specified wavelength. In some instances, light of
the specified emission wavelength comprises light of the specified
wavelength.+-.2 nm, .+-.5 nm, .+-.10 nm, .+-.20 nm, .+-.40 nm,
.+-.80 nm, or more. In some instances, the emission wavelength used
may or may not coincide with the emission peak maximum of the
fluorescent indicator.
[0078] As used herein, fluorescence is `specific` if it arises from
fluorophores that are annealed or otherwise tethered to the
surface, such as fluorescently labeled nucleic acid sequences
having a region of reverse complementarity to a corresponding
segment of an oligonucleotide adapter on the surface and annealed
to said corresponding segment. This fluorescence is contrasted with
fluorescence arising from fluorophores not tethered to the surface
through such an annealing process, or in some cases to background
florescence of the surface.
[0079] As used herein, a "nucleic acid" (also referred to as a
"nucleic acid molecule", a "polynucleotide", "oligonucleotide",
ribonucleic acid (RNA), or deoxyribonucleic acid (DNA)) is a linear
polymer of two or more nucleotides joined by covalent
internucleosidic linkages, or variants or functional fragments
thereof. In naturally occurring examples of nucleic acids, the
internucleoside linkage is typically a phosphodiester bond.
However, other examples optionally comprise other internucleoside
linkages, such as phosphorothiolate linkages and may or may not
comprise a phosphate group. Nucleic acids include double- and
single-stranded DNA, as well as double- and single-stranded RNA,
DNA/RNA hybrids, peptide-nucleic acids (PNAs), hybrids between PNAs
and DNA or RNA, and may also include other types of nucleic acid
modifications.
[0080] As used herein, a "nucleotide" refers to a nucleotide,
nucleoside, or analog thereof. In some cases, the nucleotide is an
N- or C-glycoside of a purine or pyrimidine base (e.g., a
deoxyribonucleoside containing 2-deoxy-D-ribose or ribonucleoside
containing D-ribose). Examples of other nucleotide analogs include,
but are not limited to, phosphorothioates, phosphoramidates, methyl
phosphonates, chiral-methyl phosphonates, 2-O-methyl
ribonucleotides, and the like.
[0081] Fluorescence imaging viewed as an information pipeline: A
useful abstraction of the role that fluorescence imaging systems
plays in typical genomic assay techniques (including nucleic acid
sequencing applications) is as an information pipeline, where the
photon signal enters at one end of the pipeline, e.g., the
objective lens used for imaging, and location specific information
regarding the fluorescence signal emerges at the other end of the
pipeline, e.g., at the position of the image sensor. When more
information is pumped through this pipeline, some content,
inevitably, will be lost during this transfer process and never
recovered. An example of this case is when too many labeled
molecules (or clonally-amplified clusters of molecules) are present
within a small region of a substrate surface to be clearly resolved
in the image; at the position of the image sensor, it becomes
difficult to differentiate photon signals arising from adjacent
clusters of molecules, thus increasing the probability of
attributing the signal to the wrong cluster and leading to
detection errors.
[0082] Design of optical imaging modules: The goal of designing an
optical imaging module is thus to maximize the flow of information
content through this detection pipeline and to minimize detection
errors. Several key design elements need to be addressed in the
design process, including:
[0083] 1) Matching the physical feature density on the substrate
surface to be imaged with the overall image quality of the optical
imaging system and the pixel sampling frequency of the image sensor
used. A mismatch of these parameters may result in loss of
information or sometimes even the generation of false information,
e.g., spatial aliasing may arise when pixel sampling frequency is
lower than twice the optical resolution limit.
[0084] 2) Matching the size of the area to be imaged with the
overall image quality of the optical imaging system and focus
quality across the entire field of view.
[0085] 3) Matching the optical collection efficiency, modulation
transfer function, and image sensor performance characteristics of
the optical system design with the fluorescence photon flux
expected for the input excitation photon flux, dye efficiency
(related to dye extinction coefficient and fluorescence quantum
yield), while accounting for background signal and system noise
characteristics.
[0086] 4) Maximizing the separation of spectral content to reduce
cross talk between fluorescence imaging channels.
[0087] 5) Effective synchronization of image acquisition steps with
repositioning of the sample or optics between image capture of
different fields-of-view to minimize the down time (or maximize the
duty cycle) of the imaging system and thus maximize the overall
throughput of the image capture process.
[0088] This disclosure describes a systematic way to address each
of the design elements outlined above and to create component level
specifications for the imaging system.
[0089] Improved optical resolution and image quality to improve or
maximize information transfer and throughput: One non-limiting
design practice may be to start with the optical resolution
required to distinguish two adjacent features as specified in terms
of a number, X, of line pairs per mm (lp/mm) and translate it to a
corresponding numerical aperture (NA) requirement. The numerical
aperture requirement can then be used to assess the resulting
impact on modulation transfer function and image contrast.
[0090] The standard modulation transfer function (MTF) describes
the spatial frequency response for image contrast (modulation)
transferred through an optical system; image contrast decreases as
a function of spatial frequency and increases with increasing NA.
This function limits the contrast/modulation that can be achieved
for a given NA. Furthermore, wave front error can negatively impact
the MTF, thus making it desirable to improve or optimize the
optical system design using the true system MTF instead of that
predicted by diffraction-limited optics. Note that, as used herein,
MTF will refer to the total system MTF (including the complete
optical path from coverslip to image sensor) although design
practice may primarily consider the MTF of the objective lens.
[0091] In genomic testing applications, where the target to be
imaged is an array of high density "spots" on a surface (either
randomly distributed or patterned), one can determine the minimum
modulation transfer value required by downstream analysis to
resolve two adjacent spots and discriminate between four possible
states (e.g., ON-OFF, ON-ON, OFF-ON and OFF-OFF). For example,
assume that the spots are small enough to be approximated as point
sources of light. Assuming that the detection task is to determine
if the two adjacent spots separated by a distance, d, are ON or OFF
(in other words, bright or dark), and that the contrast-to-noise
ratio (CNR) for the fluorescence signals arising from the spots at
the sample plane (or object plane) is C.sub.sample, then under
ideal conditions the CNR of the readout signal for the two adjacent
spots at the image sensor plane, C.sub.image, can be closely
approximated as C.sub.image=C.sub.sample*MTF(1/d), where MTF(1/d)
is the MTF value at spatial frequency=(1/d).
[0092] In a typical design, the value of C may need to be at least
4 so that a simple threshold method can be used to avoid
misclassification of fluorescence signals. Assuming a Gaussian
distribution of fluorescence signal intensities around a mean
value, at C.sub.image>4, the expected error in correctly
classifying fluorescence signals (e.g., as being ON or OFF) is
<0.035%. The use of proprietary high CNR sequencing and surface
chemistry, such as that described in U.S. patent application Ser.
No. 16/363,842, allows one to achieve sample plane CNR
(C.sub.sample) values for clusters of clonally-amplified, labeled
oligonucleotide molecules tethered to a substrate surface of
greater than 12 (or even much higher) when measured for a sparse
field (i.e., at a low surface density of clusters or spots) where
the MTF has a value of close to 100%. Assuming a sample plane CNR
value of C.sub.sample>12 and targeting a classification error
rate of <0.1% (thus, C.sub.image>4), in some implementations
the minimum value for M(1/d) can be determined as
M(1/d)=4/12.about.33%. Thus, a modulation transfer function
threshold of at least 33% may be used to retain the information
content of the transferred image.
[0093] Design practice can relate the minimum separation distance
of two features or spots, d, to the optical resolution requirement
(specified as noted above in terms of X (lp/mm)) as d=(1 mm)/X,
i.e., d is the minimum separation distance between two features or
spots which can be fully resolved by the optical system. In some
designs disclosed herein, where the objective of the design
analysis is to increase or maximize relevant information transfer,
this design criterion can be relaxed to d=(1 mm)/X/A, where
2>A>1. For the same optical resolution of X lp/mm, the value
of d, the minimum resolvable spot separation distance at the sample
plane, is reduced, thereby enabling the use of higher feature
densities.
[0094] Design practice determines the minimum spatial sampling
frequency at the sample plane using the Nyquist criteria, where
spatial sampling frequency S.gtoreq.2*X (and where X is the optical
resolution of the imaging system specified in terms of X lp/mm as
noted above). When the system spatial sampling frequency is close
to the Nyquist criteria, as is often the case, imaging system
resolution of greater than S results in aliasing as the higher
frequency information resolved by the optical system cannot be
sufficiently sampled by the image sensor.
[0095] In the some of the designs disclosed herein, an oversampling
scheme based on the relationship S=B*Y (where B.gtoreq.2 and Y is
the true optical system MTF limit) may be used to further improve
the information transfer capacity of the imaging system. As
indicated above, X (lp/mm) corresponds to a practical, non-zero
(>33%) minimum modulation transfer value, whereas Y (lp/mm) is
the limit of optical resolution so modulation at Y(lp/mm) is 0.
Thus, in the disclosed designs, Y (lp/mm) may advantageously be
significantly greater than X For values of B.gtoreq.2, the
disclosed designs are oversampling for the sample object frequency
X, i.e., S.gtoreq.B*Y>2*X.
[0096] The above relationship can be used to determine the system
magnification and may provide an upper bound for image sensor pixel
size. The choice of image sensor pixel size is matched to the
system optical quality as well to the spatial sampling frequency
required to reduce aliasing. The lower bound of image sensor pixel
size can be determined based on photon throughput, as relative
noise contributions increase with smaller pixels.
[0097] Other design approaches are, however, also possible. For
example, reducing the NA to less than 0.6 (e.g., 0.5 or less,) may
provide increased depth of field. Such increased depth of field may
enable dual surface imagining wherein two surfaces at different
depths can be imaged at the same time with or without refocusing.
As discussed above, reducing NA may reduce optical resolution. In
some implementations, use of higher excitation beam power, e.g., 1
W or higher, may be employed to produce strong signal. An
inherently high contrast sample (i.e., comprising a sample surface
that exhibits strong foreground signal and dramatically reduced
background signal, may also be used to facilitate acquisition of
high contrast-to-noise ratio (CNR) images, e.g., having CNR values
of >20, that provide for improved signal discrimination for
base-calling in nucleic acid sequencing applications, etc. In some
optical system designs disclosed herein, sample support structures
such as flow cells having hydrophilic surfaces are used to reduce
background noise.
[0098] In various implementations, a large field-of-view (FOV) is
provided by the disclosed optical systems. For example, a FOV of
greater than 2 or 3 mm may be provided with some optical imaging
systems comprising, e.g., an objective lens and a tube lens. In
some cases, the optical imaging system provides a reduced
magnification, for example, a magnification of less than 10.times..
Such reduced magnification may in some implementations facilitate
large FOV designs. Despite a reduced magnification, the optical
resolution of such systems can still be sufficient as detector
arrays having small pixel size or pitch may be used. In some
implementations, image sensors comprising a pixel size that is
smaller than twice the optical resolution provided by the optical
imaging system (e.g., objective and tube lens) may be used to
satisfy the Nyquist theorem.
[0099] Still other designs are also possible. In some optical
designs configured to provide for dual surface imaging where two
surfaces at different depths can be imaged at the same time, the
optical imaging system (e.g., the objective lens and/or tube lens)
is configured to reduce optical aberration for imaging said two
surfaces (e.g., two planes) at those two respective depths more
than at other locations (e.g., other planes) at other depths.
Additionally, the optical imaging system may be configured to
reduce aberration for imaging said two surfaces (e.g., two planes)
at those two respective depths through a transmissive layer on said
sample support structure (such as a layer of glass (e.g., a cover
slip) and through a solution (e.g., an aqueous solution) comprising
the sample or in contact with a sample on at least one of said two
surfaces.
[0100] Multichannel fluorescence imaging modules and systems: In
some instances, the imaging modules or systems disclosed herein may
comprise fluorescence imaging modules or systems. In some
instances, the fluorescence imaging systems disclosed herein may
comprise a single fluorescence excitation light source (for
providing excitation light at a single wavelength or within a
single excitation wavelength range) and an optical path configured
to deliver the excitation light to a sample (e.g.,
fluorescently-tagged nucleic acid molecules or clusters thereof
disposed on a substrate surface). In some instances, the
fluorescence imaging systems disclosed herein may comprise a single
fluorescence emission imaging and detection channel, e.g., an
optical path configured to collect fluorescence emitted by the
sample and deliver an image of the sample (e.g., an image of a
substrate surface on which fluorescently-tagged nucleic acid
molecules or clusters thereof are disposed) to an image sensor or
other photodetection device. In some instances, the fluorescence
imaging systems may comprise two, three, four, or more than four
fluorescence excitation light sources and/or optical paths
configured to deliver excitation light at two, three, four, or more
than four excitation wavelengths (or within two, three, four, or
more than four excitation wavelength ranges). In some instances,
the fluorescence imaging systems disclosed herein may comprise two,
three, four, or more than four fluorescence emission imaging and
detection channels configured to collect fluorescence emitted by
the sample at two, three, four, or more than four emission
wavelengths (or within two, three, four, or more than four emission
wavelength ranges and deliver an image of the sample (e.g., an
image of a substrate surface on which fluorescently-tagged nucleic
acid molecules or clusters thereof are disposed) to two, three,
four, or more than four image sensors or other photodetection
devices.
[0101] Dual surface imaging: In some instances, the imaging systems
disclosed herein, including fluorescence imaging systems, may be
configured to acquire high-resolution images of a single sample
support structure or substrate surface. In some instances, the
imaging systems disclosed herein, including fluorescence imaging
systems, may be configured to acquire high-resolution images of two
or more sample support structures or substrate surfaces, e.g., two
or more surfaces of a flow cell. In some instances, the
high-resolution images provided by the disclosed imaging systems
may be used to monitor reactions occurring on the two or more
surfaces of the flow cell (e.g., nucleic acid hybridization,
amplification, and/or sequencing reactions) as various reagents
flow through the flow cell or around a flow cell substrate. FIG. 1A
and FIG. 1B provide schematic illustrations of such dual surface
support structures. FIG. 1A shows a dual surface support structure
such as a flow cell that includes an internal flow channel through
which an analyte or reagent can be flowed. The flow channel may be
formed between first and second, top and bottom, and/or front and
back layers such as first and second, top and bottom, and/or front
and back plates as shown. One or more of the plates may include a
glass plate, such as a coverslip, or the like. In some
implementations, the layer comprises borosilicate glass, quartz, or
plastic. Interior surfaces of these top and bottom layers provide
walls of the flow channel that assist in confining the flow of
analyte or reagent through the flow channel of the flow cell. In
some designs, these interior surfaces are planar. Similarly, the
top and bottom layers may be planar. In some designs, at least one
additional layer (not shown) is disposed between the top and bottom
layers. This additional layer may have one or more pathways cut
therein that assist in defining one or more flow channels and
controlling the flow of the analyte or reagent within the flow
channel. Additional discussion of sample support structures, e.g.,
flow cells, can be found below.
[0102] FIG. 1A schematically illustrates a plurality of fluorescing
sample sites on the first and second, top and bottom, and/or front
and back interior surfaces of the flow cell. In some
implementations, reactions may occur at these at these sites to
bind sample such that fluorescence is emitted from these sites
(note that FIG. 1A is schematic and not drawn to scale; for
example, the size and spacing of the fluorescing sample sites may
be smaller than shown).
[0103] FIG. 1B shows another dual surface support structure having
two surfaces containing fluorescing sample sites to be imaged. The
sample support structure comprises a substrate having first and
second, top and bottom, and/or front and back exterior surfaces. In
some designs, these exterior surfaces are planar. In various
implementations, the analyte or reagent is flowed across these
first and second exterior surfaces. FIG. 1B schematically
illustrates a plurality of fluorescing sample sites on the first
and second, top and bottom, and/or front and back exterior surfaces
of the sample support structure. In some implementations, reactions
may occur at these at these sites to bind sample such that
fluorescence is emitted from these sites (note that FIG. 1B is
schematic and not drawn to scale; for example, the size and spacing
of the fluorescing sample sites may be smaller than shown).
[0104] In some instances, the fluorescence imaging modules and
systems described herein may be configured to image such
fluorescing sample sites on first and second surfaces at different
distances from the objective lens. In some designs, only one of the
first or second surfaces is in focus at a time. Accordingly, in
such designs, one of the surfaces is imaged at a first time, and
the other surface is imaged at a second time. The focus of the
fluorescence imaging module may be changed after imaging one of the
surfaces in order to image the other surface with comparable
optical resolution, as the images of the two surfaces are not
simultaneously in focus. In some designs, an optical compensation
element may be introduced into the optical path between the sample
support structure and the image sensor in order to image one of the
two surfaces. The depth of field in such fluorescence imaging
configurations may not be sufficiently large to include both the
first and second surfaces. In some implementations of the
fluorescence imaging modules described herein, both the first and
second surfaces may be imaged at the same time, i.e.,
simultaneously. For example, the fluorescence imaging module may
have a depth of field that is sufficiently large to include both
surfaces. In some instances, this increased depth of field may be
provided by, for example, reducing the numerical aperture of the
objective lens (or microscope objective) as will be discussed in
more detail below.
[0105] As shown in FIGS. 1A and 1B, the imaging optics (e.g., an
objective lens) may be positioned at a suitable distance (e.g., a
distance corresponding to the working distance) from the first and
second surfaces to form in-focus images of the first and second
surfaces on an image sensor of a detection channel. As shown in the
example of FIGS. 1A and 1B, the first surface may be between said
objective lens and the second surface. For example, as illustrated,
the objective lens is disposed above both the first and second
surfaces, and the first surface is disposed above the second
surface. The first and second surfaces, for example, are at
different depths. The first and second surfaces are at different
distances from any one or more of the fluorescence imaging module,
the illumination and imaging module, imaging optics, or the
objective lens. The first and second surfaces are separated from
each other with the first surface spaced apart above the second
surface. In the example shown, the first and second surfaces are
planar surfaces and are separated from each other along a direction
normal to said first and second planar surfaces. Also, in the
example shown, said objective lens has an optical axis and said
first and second surfaces are separated from each other along the
direction of said optical axis. Similarly, the separation between
the first and second surfaces may correspond to the longitudinal
distance such as along the optical path of the excitation beam
and/or along an optical axis through the fluorescence imaging
module and/or the objective lens. Accordingly, these two surfaces
may be separated by a distance from each other in the longitudinal
(Z) direction, which may be along the direction of the central axis
of the excitation beam and/or the optical axis of the objective
lens and/or the fluorescence imaging module. This separation may
correspond, for example, to a flow channel within a flow cell in
some implementations.
[0106] In various designs, the objective lens (possibly in
combination with another optical component, e.g., a tube lens) have
a depth of field and/or depth of focus that is at least as large as
the longitudinal separation (in the Z direction) between the first
and second surfaces. The objective lens, alone or in combination
with the additional optical component, may thus simultaneously form
in-focus images of both the first and the second surface on an
image sensor of one or more detection channels where these images
have comparable optical resolution. In some implementations, the
imaging module may or may not need to be re-focused to capture
images of both the first and second surfaces with comparable
optical resolution. In some implementations, compensation optics
need not be moved into or out of an optical path of the imaging
module to form in-focus images of the first and second surfaces.
Similarly, in some implementations, one or more optical elements
(e.g., lens elements) in the imaging module (e.g., the objective
lens and/or a tube lens) need not be moved, for example, in the
longitudinal direction along the first and/or second optical paths
(e.g., along the optical axis of the imaging optics) to form
in-focus images of the first surface in comparison to the location
of said one or more optical element when used to form in-focus
images of the second surface. In some implementations, however, the
imaging module includes an autofocus system configured to provide
both the first and second surface in focus at the same time. In
various implementations, the sample is in focus to sufficiently
resolve the sample sites, which are closely spaced together in
lateral directions (e.g., the X and Y directions). Accordingly, in
various implementations, no optical element enters an optical path
between the sample support structure (e.g., between a translation
stage that supports the sample support structure) and an image
sensor (or photodetector array) in the at least one detection
channel in order to form in-focus images of fluorescing sample
sites on a first surface of the sample support structure and on a
second surface of said sample support structure. Similarly, in
various implementations, no optical compensation is used to form an
in-focus image of fluorescing sample sites on a first surface of
the sample support structure on the image sensor or photodetector
array that is not identical to optical compensation used to form an
in-focus image of fluorescing sample sites on a second surface of
the sample support structure on the image sensor or photodetector
array. Additionally, in certain implementations, no optical element
in an optical path between the sample support structure (e.g.,
between a translation stage that supports the sample support
structure) and an image sensor in the at least one detection
channel is adjusted differently to form an in-focus image of
fluorescing sample sites on a first surface of the sample support
structure than to form an in-focus image of fluorescing sample
sites on a second surface of the sample support structure.
Similarly, in some various implementations, no optical element in
an optical path between the sample support structure (e.g., between
a translation stage that supports the sample support structure) and
an image sensor in the at least one detection channel is moved a
different amount or a different direction to form an in-focus image
of fluorescing sample sites on the a first surface of the sample
support structure on the image sensor than to form an in-focus
image of fluorescing sample sites on a second surface of said
sample support structure on the image sensor. Any combination of
the features is possible. For example, in some implementations,
in-focus images of the upper interior surface and the lower
interior surface of the flow cell can be obtained without moving an
optical compensator into or out of an optical path between the flow
cell and the at least one image sensor and without moving one or
more optical elements of the imaging system (e.g., the objective
and/or tube lens) along the optical path (e.g., optical axis)
therebetween. For example, in-focus images of the upper interior
surface and the lower interior surface of the flow cell can be
obtained without moving one or more optical elements of the tube
lens into or out of the optical path, or without moving one or more
optical elements of the tube lens along the optical path (e.g.,
optical axis) therebetween.
[0107] Any one or more of the fluorescence imaging module, the
illumination optical path, the imaging optical path, the objective
lens, or the tube lens may be designed to reduce or minimize
optical aberration at two locations such as two planes
corresponding to two surfaces on a flow cell or other sample
support structure, for example, where fluorescing sample sites are
located. Any one or more of the fluorescence imaging module, the
illumination optical path, the imaging optical path, the objective
lens, or the tube lens may be designed to reduce or minimize
optical aberration at the selected locations or planes relative to
other locations or planes, such as first and second surfaces
containing fluorescing sample sites on a dual surface flow cell.
For example, any one or more of the fluorescence imaging module,
the illumination optical path, the imaging optical path, the
objective lens, or the tube lens may be designed to reduce or
minimize optical aberration at two depths or planes located at
different distances from the objective lens as compared to the
aberrations associated with other depths or planes at other
distances from the objective lens. For example, optical aberration
may be less for imaging the first and second surfaces than
elsewhere in a region ranging from about 1 to about 10 mm from the
objective lens. Additionally, any one or more of the fluorescence
imaging module, the illumination optical path, the imaging optical
path, the objective lens, or the tube lens may, in some instances,
be configured to compensate for optical aberration induced by
transmission of emission light through one or more portions of the
sample support structure such as a layer that includes one of the
surfaces on which sample adheres as well as possibly a solution
that is in contact with the sample. This layer (e.g., a coverslip
or the wall of a flow cell) may comprise, e.g., glass, quartz,
plastic, or other transparent material having a refractive index
and that introduces optical aberration.
[0108] Accordingly, the imaging performance may be substantially
the same when imaging the first surface and second surface. For
example, the optical transfer functions (OTF) and/or modulation
transfer functions (MTF) may be the substantially the same for
imaging of the first and second surfaces. Either or both of these
transfer functions may, for example, be within 20%, within 15%,
within 10%, within 5%, within 2.5%, or within 1% of each other, or
within any range formed by any of these values at one or more
specified spatial frequencies or when averaged over a range of
spatial frequencies. Accordingly, an imaging performance metric may
be substantially the same for imaging the upper interior surface or
the lower interior surface of the flow cell without moving an
optical compensator into or out of an optical path between the flow
cell and the at least one image sensor, and without moving one or
more optical elements of the imaging system (e.g., the objective
and/or tube lens) along the optical path (e.g., optical axis)
therebetween. For example, an imaging performance metric may be
substantially the same for imaging the upper interior surface or
the lower interior surface of the flow cell without moving one or
more optical elements of the tube lens into or out of the optical
path or without moving one or more optical elements of the tube
lens along the optical path (e.g., optical axis) therebetween.
Additional discussion of MTF is included below and in U.S.
Provisional Application No. 62/962,723 filed Jan. 17, 2020, which
is incorporated herein by reference in its entirety.
[0109] It will be understood by those of skill in the art that the
disclosed imaging modules or systems may, in some instances, be
stand-alone optical systems designed for imaging a sample or
substrate surface. In some instances, they may comprise one or more
processors or computers. In some instances, they may comprise one
or more software packages that provide instrument control
functionality and/or image processing functionality. In some
instances, in addition to optical components such as light sources
(e.g., solid-state lasers, dye lasers, diode lasers, arc lamps,
tungsten-halogen lamps, etc.), lenses, prisms, mirrors, dichroic
reflectors, beam splitters, optical filters, optical bandpass
filters, light guides, optical fibers, apertures, and image sensors
(e.g., complementary metal oxide semiconductor (CMOS) image sensors
and cameras, charge-coupled device (CCD) image sensors and cameras,
etc.), they may also include mechanical and/or optomechanical
components, such as X-Y translation stages, X-Y-Z translation
stages, piezoelectic focusing mechanisms, electro-optical phase
plates, and the like. In some instances, they may function as
modules, components, sub-assemblies, or sub-systems of larger
systems designed for, e.g., genomics applications (e.g., genetic
testing and/or nucleic acid sequencing applications). For example,
in some instances, they may function as modules, components,
sub-assemblies, or sub-systems of larger systems that further
comprise light-tight and/or other environmental control housings,
temperature control modules, flow cells and cartridges, fluidics
control modules, fluid dispensing robotics, cartridge- and/or
microplate-handling (pick-and-place) robotics, one or more
processors or computers, one or more local and/or cloud-based
software packages (e.g., instrument/system control software
packages, image processing software packages, data analysis
software packages), data storage modules, data communication
modules (e.g., Bluetooth, WiFi, intranet, or internet communication
hardware and associated software), display modules, etc., or any
combination thereof. These additional components of larger systems,
e.g., systems designed for genomics applications, will be discussed
in more detail below.
[0110] FIGS. 2A and 2B illustrate a non-limiting example of an
illumination and imaging module 100 for multi-channel fluorescence
imaging. The illumination and imaging module 100 includes an
objective lens 110, an illumination source 115, a plurality of
detection channels 120, and a first dichroic filter 130, which may
comprise a dichroic reflector or beam splitter. An autofocus
system, which may include an autofocus laser 102, for example, that
projects a spot the size of which is monitored to determine when
the imaging system is in-focus may be included in some designs.
Some or all components of the illumination and imaging module 100
may be coupled to a baseplate 105.
[0111] The illumination or light source 115 may include any
suitable light source configured to produce light of at least a
desired excitation wavelength (discussed in more detail below). The
light source may be a broadband source that emits light within one
or more excitation wavelength ranges (or bands). The light source
may be a narrowband source that emits light within one or more
narrower wavelength ranges. In some instances, the light source may
produce a single isolated wavelength (or line) corresponding to the
desired excitation wavelength, or multiple isolated wavelengths (or
lines). In some instances, the lines may have some very narrow
bandwidth. Example light sources that may be suitable for use in
the illumination source 115 include, but are not limited to, an
incandescent filament, xenon arc lamp, mercury-vapor lamp, a
light-emitting diode, a laser source such as a laser diode or a
solid-state laser, or other types of light sources. As discussed
below, in some designs, the light source may comprise a polarized
light source such as a linearly polarized light source. In some
implementations, the orientation of the light source is such that
s-polarized light is incident on one or more surfaces of one or
more optical components such as the dichroic reflective surface of
one or more dichroic filters.
[0112] The illumination source 115 may further include one or more
additional optical components such as lenses, filters, optical
fibers, or any other suitable transmissive or reflective optics as
appropriate to output an excitation light beam having suitable
characteristics toward a first dichroic filter 130. For example,
beam shaping optics may be included, for example, to receive light
from a light emitter in the light source and produce a beam and/or
provide a desired beam characteristic. Such optics may, for
example, comprise a collimating lens configured to reduce the
divergence of light and/or increase collimation and/or to collimate
the light.
[0113] In some implementations, multiple light sources are included
in the illumination and imaging module 100. In some such
implementations, different light sources may produce light having
different spectral characteristics, for example, to excite
different fluorescence dyes. In some implementations, light
produced by the different light sources may directed to coincide
and form an aggregate excitation light beam. This composite
excitation light beam may be composed of excitation light beams
from each of the light sources. The composite excitation light beam
will have more optical power than the individual beams that overlap
to form the composite beam. For example, in some implementations
that include two light sources that produce two excitation light
beams, the composite excitation light beam formed from the two
individual excitation light beams may have optical power that is
the sum of the optical power of the individual beams. Similarly, in
some implementations, three, four, five or more light sources may
be included, and these light sources may each output excitation
light beams that together form a composite beam that that has an
optical power that is the sum of the optical power of the
individual beams.
[0114] In some implementations, the light source 115 outputs a
sufficiently large amount of light to produce sufficiently strong
fluorescence emission. Stronger fluorescence emission can increase
the signal-to-noise ratio (SNR) and the contrast-to-noise ratio
(CNR) of images acquired by the fluorescence imaging module. In
some implementations, the output of the light source and/or an
excitation light beam derived therefrom (including a composite
excitation light beam) may range in power from about 0.5 W to about
5.0 W, or more (as will be discussed in more detail below).
[0115] Referring again to FIGS. 2A and 2B, the first dichroic
filter 130 is disposed with respect to the light source to receive
light therefrom. The first dichroic filter may comprise a dichroic
mirror, dichroic reflector, dichroic beam splitter, or dichroic
beam combiner configured to transmit light in a first spectral
region (or wavelength range) and reflect light having a second
spectral region (or wavelength range). The first spectral region
may include one or more spectral bands, e.g., one or more spectral
bands in the ultraviolet and blue wavelength ranges. Similarly, a
second spectral region may include one or more spectral bands,
e.g., one or more spectral bands extending from the green to red
and infrared wavelengths. Other spectral regions or wavelength
ranges are also possible.
[0116] In some implementations, the first dichroic filter may be
configured to transmit light from the light source to a sample
support structure such as to a microscope slide, a capillary, a
flow cell, a microfluidic chip, or other substrate or support
structure. The sample support structure supports and positions the
sample, e.g., a composition comprising a fluorescently-labeled
nucleic acid molecule or complement thereof, with respect to the
illumination and imaging module 100. Accordingly, a first optical
path extends from the light source to the sample via the first
dichroic filter. In various implementations, the sample support
structure includes at least one surface on which the sample is
disposed or to which the sample binds. In some instances, the
sample may be disposed within or bound to different localized
regions or sites on the at least one surface of the sample support
structure.
[0117] In some instances, the support structure may include two
surfaces located at different distances from objective lens 110
(i.e., at different positions or depths along the optical axis of
objective lens 110) on which the sample is disposed. As discussed
below, for example, a flow cell may comprise a fluid channel formed
at least in part by first and second (e.g., upper and lower)
interior surfaces, and the sample may be disposed at localized
sites on the first interior surface, the second interior surface,
or both interior surfaces. The first and second surface may be
separated by the region corresponding to the fluid channel through
which a solution flows, and thus be at different distances or depth
with respect to objective lens 110 of the illumination and imaging
module 100.
[0118] The objective lens 110 may be included in the first optical
path between the first dichroic filter and the sample. This
objective lens may be configured, for example, to have a focal
length, working distance, and/or be positioned to focus light from
the light source(s) onto the sample, e.g., onto a surface of the
microscope slide, capillary, flow cell, microfluidic chip, or other
substrate or support structure. Similarly, the objective lens 110
may be configured to have suitable focal length, working distance,
and/or be positioned to collect light reflected, scattered, or
emitted from the sample (e.g., fluorescence emission) and to form
an image of the sample (e.g., a fluorescence image).
[0119] In some implementations, objective lens 110 may comprise a
microscope objective such as an off-the-shelf objective. In some
implementations, objective lens 110 may comprise a custom
objective. An example of a custom objective lens and/or custom
objective--tube lens combination is described below and in U.S.
Provisional Application No. 62/962,723 filed on Jan. 17, 2020,
which is incorporated herein by reference in its entirety. The
objective lens 110 may be designed to reduce or minimize optical
aberration at two locations such as two planes corresponding to two
surfaces of a flow cell or other sample support structure. The
objective lens 110 may be designed to reduce the optical aberration
at the selected locations or planes, e.g., the first and second
surfaces of a dual surface flow cell, relative to other locations
or planes in the optical path. For example, the objective lens 110
may be designed to reduce the optical aberration at two depths or
planes located at different distances from the objective lens as
compared to the optical aberrations associated with other depths or
planes at other distances from the objective. For example, in some
instances, optical aberration may be less for imaging the first and
second surfaces of a flow cell than that exhibited elsewhere in a
region spanning from 1 to 10 mm from the front surface of the
objective lens. Additionally, a custom objective lens 110 may in
some instances be configured to compensate for optical aberration
induced by transmission of fluorescence emission light through one
or more portions of the sample support structure, such as a layer
that includes one or more of the flow cell surfaces on which a
sample is disposed, or a layer comprising a solution filling the
fluid channel of a flow cell. These layers may comprise, e.g.,
glass, quartz, plastic, or other transparent material having a
refractive index, and which may introduce optical aberration.
[0120] In some implementations, objective lens 110 may have a
numerical aperture (NA) of 0.6 or more (as discussed in more detail
below). Such a numerical aperture may provide for reduced depth of
focus and/or depth of field, improved background discrimination,
and increased imaging resolution.
[0121] In some implementations, objective lens 110 may have a
numerical aperture (NA) of 0.6 or less (as discussed in more detail
below). Such a numerical aperture may provide for increased depth
of focus and/or depth of field. Such increased depth of focus
and/or depth of field may increase the ability to image planes
separated by a distance such as that that separates the first and
second surfaces of a dual surface flow cell.
[0122] As discussed above, a flow cell may comprise, for example,
first and second layers comprising first and second interior
surfaces respectively that are separated by a fluid channel through
which an analyte or reagent can flow. In some implementations, the
objective lens 110 and/or illumination and imaging module 100 may
be configured to provide a depth of field and/or depth of focus
sufficiently large to image both the first and second interior
surfaces of the flow cell, either sequentially by re-focusing the
imaging module between imaging the first and second surfaces, or
simultaneously by ensuring a sufficiently large depth of field
and/or depth of focus, with comparable optical resolution. In some
instances, the depth of field and/or depth of focus may be at least
as large or larger than the distance separating the first and
second surfaces of the flow cell to be imaged, such as the first
and second interior surfaces of the flow cell. In some instances,
the first and second surfaces, e.g., the first and second interior
surfaces of a dual surface flow cell or other sample support
structure, may be separated, for example, by a distance ranging
from about 10 .mu.m to about 700 .mu.m, or more (as will be
discussed in more detail below). In some instances, the depth of
field and/or depth of focus may thus range from about 10 .mu.m to
about 700 .mu.m, or more (as will be discussed in more detail
below).
[0123] In some designs, compensation optics (e.g., an "optical
compensator" or "compensator") may be moved into or out of an
optical path in the imaging module, for example, an optical path by
which light collected by the objective lens 110 is delivered to an
image sensor, to enable the imaging module to image the first and
second surfaces of the dual surface flow cell. The imaging module
may be configured, for example, to image the first surface when the
compensation optics is included in the optical path between the
objective lens and an image sensor or photodetector array
configured to capture an image of the first surface. In such a
design, the imaging module may be configured to image the second
surface when the compensation optics is removed from or not
included in the optical path between the objective lens 110 and the
image sensor or photodetector array configured to capture an image
of the second surface. The need for an optical compensator may be
more pronounced when using an objective lens 110 with a high
numerical aperture (NA) value, e.g., for numerical aperture values
of at least 0.6, least 0.65, at least 0.7, at least 0.75, at least
0.8, at least 0.85, at least 0.9, at least 0.95, at least 1.0, or
higher. In some implementations, the optical compensation optics
(e.g., an optical compensator or compensator) comprises a
refractive optical element such as a lens, a plate of
optically-transparent material such as glass, a plate of
optically-transparent material such as glass, or in the case of
polarized light beams, a quarter-wave plate or half-wave plate,
etc. Other configurations may be employed to enable the first and
second surfaces to be imaged at different times. For example, one
or more lenses or optical elements may be configured to be
translated in and out of, or along, an optical path between the
objective lens 110 and the image sensor.
[0124] In certain designs, however, the objective lens 110 is
configured to provide sufficiently large depth of focus and/or
depth of field to enable the first and second surfaces to be imaged
with comparable optical resolution without such compensation optics
moving into and out of an optical path in the imaging module, such
as an optical path between the objective lens and the image sensor
or photodetector array. Similarly, in various designs, the
objective lens 110 is configured to provide sufficiently large
depth of focus and/or depth of field to enable the first and second
surfaces to be imaged with comparable optical resolution without
optics being moved, such as one or more lenses or other optical
components being translated along an optical path in the imaging
module, such as an optical path between the objective lens and the
image sensor or photodetector array. Examples of such objective
lenses will be described in more detail below.
[0125] In some implementations, the objective lens (or microscope
objective) 110 may be configured to have reduced magnification. The
objective lens 110 may be configured, for example, such that the
fluorescence imaging module has a magnification of from less than
2.times. to less than 10.times. (as will be discussed in more
detail below). Such reduced magnification may alter design
constraints such that other design parameters can be achieved. For
example, the objective lens 110 may also be configured such that
the fluorescence imaging module has a large field-of-view (FOV)
ranging, for example, from about 1.0 mm to about 5.0 mm (e.g., in
diameter, width, length, or longest dimension) as will be discussed
in more detail below.
[0126] In some implementations, the objective lens 110 may be
configured to provide the fluorescence imaging module with a
field-of-view as indicated above such that the FOV has
diffraction-limited performance, e.g., less than 0.15 waves of
aberration over at least 60%, 70%, 80%, 90%, or 95% of the field,
as will be discussed in more detail below.
[0127] In some implementations, the objective lens 110 may be
configured to provide the fluorescence imaging module with a
field-of-view as indicated above such that the FOV has
diffraction-limited performance, e.g., a Strehl ratio of greater
than 0.8 over at least 60%, 70%, 80%, 90%, or 95% of the field, as
will be discussed in more detail below.
[0128] Referring again to FIGS. 2A and 2B, the first dichroic beam
splitter or beam combiner is disposed in the first optical path
between the light source and the sample so as to illuminate the
sample with one or more excitation beams. This first dichroic beam
splitter or combiner is also in one or more second optical path(s)
from the sample to the different optical channels used to detect
the fluorescence emission. Accordingly, the first dichroic filter
130 couples the first optical path of the excitation beam emitted
by the illumination source 115 and second optical path of the
emission light emitted by a sample specimen to the various optical
channels where the light is directed to respective image sensors or
photodetector arrays for capturing images of the sample.
[0129] In various implementations, the first dichroic filter 130,
e.g., first dichroic reflector or beam splitter or beam combiner,
has a passband selected to transmit light from the illumination
source 115 only within a specified wavelength band or possibly a
plurality of wavelength bands that include the desired excitation
wavelength or wavelengths. For example, the first dichroic beam
splitter 130 includes a reflective surface comprising a dichroic
reflector that has spectral transmissivity response that is, e.g.,
configured to transmit light having at least some of the
wavelengths output by the light source that form part of the
excitation beam. The spectral transmissivity response may be
configured not to transmit (e.g., instead to reflect) light of one
or more other wavelengths, for example, of one or more other
fluorescence emission wavelengths. In some implementations, the
spectral transmissivity response may also be configured not to
transmit (e.g., instead to reflect) light of one or more other
wavelengths output by the light source. Accordingly, the first
dichroic filter 130 may be utilized to select which wavelength or
wavelengths of light output by the light source reach the sample.
Conversely, the dichroic reflector in the first dichroic beam
splitter 130 has a spectral reflectivity response that reflects
light having one or more wavelengths corresponding to the desired
fluorescence emission from the sample and possible reflects light
having one or more wavelengths output from the light source that is
not intended to reach the sample. Accordingly, in some
implementations, the dichroic reflector has a spectral
transmissivity that includes one or more pass bands to transmit the
light to be incident on the sample and one or more stop bands that
reflects light outside the pass bands, for example, light at one or
more emission wavelengths and possibly one or more wavelengths
output by the light source that are not intended to reach the
sample. Likewise, in some implementations the dichroic reflector
has a spectral reflectivity that includes one or more spectral
regions configured to reflect one or more emission wavelengths and
possible one or more wavelengths output by the light source that
are not intended to reach the sample and includes one or more
regions that transmit light outside these reflection regions. The
dichroic reflector included in the first dichroic filter 130 may
comprise a reflective filter such as an interference filter (e.g.,
a quarter-wave stack) configured to provide the appropriate
spectral transmission and reflection distributions. FIGS. 2A and 2B
also show a dichroic filter 105, which may comprise for example a
dichroic beam splitter or beam combiner, that may be used to direct
the autofocus laser 102 though the objective and to the sample
support structure.
[0130] Although the imaging module 100 shown in FIGS. 2A and 2B and
discussed above is configured such that the excitation beam is
transmitted by the first dichroic filter 130 to the objective lens
110, in some designs the illumination source 115 may be disposed
with respect to the first dichroic filter 130 and/or the first
dichroic filter is configured (e.g., oriented) such that the
excitation beam is reflected by the first dichroic filter 130 to
the objective lens 110. Similarly, in some such designs, the first
dichroic filter 130 is configured to transmit fluorescence emission
from the sample and possibly transmit light having one or more
wavelengths output from the light source that is not intended to
reach the sample. As will be discussed below, a design where the
fluorescence emission is transmitted instead of reflected may
potentially reduce wavefront error in the detected emission and/or
possibly have other advantages. In either case, in various
implementations the first dichroic reflector 130 is disposed in the
second optical path so as to receive fluorescence emission from the
sample, at least some of which continues on to the detection
channels 120.
[0131] FIGS. 3A and 3B illustrate the optical paths within the
multi-channel fluorescence imaging module of FIGS. 2A and 2B. In
the example show in FIG. 2A and FIG. 3A, the detection channels 120
are disposed to receive fluorescence emission from a sample
specimen that is transmitted by the objective lens 110 and
reflected by the first dichroic filter 130. As referred to above
and described more below, in some designs the detection channels
120 may be disposed to receive the portion of the emission light
that is transmitted, rather than reflected, by the first dichroic
filter. In either case, the detection channels 120 may include
optics for receiving at least a portion of the emission light. For
example, the detection channels 120 may include one or more lenses,
such as tube lenses, and may include one or more image sensors or
detectors such as photodetector arrays (e.g., CCD or CMOS sensor
arrays) for imaging or otherwise producing a signal based on the
received light. The tube lenses may, for example, comprise one or
more lens elements configured to form an image of the sample onto
the sensor or photodetector array to capture an image thereof.
Additional discussion of detection channels is included below and
in U.S. Provisional Application No. 62/962,723, filed Jan. 17,
2020, which is incorporated herein by reference in its entirety. In
some instances, improved optical resolution may be achieved using
an image sensor having relatively high sensitivity, small pixels,
and high pixel count, in conjunction with a suitable sampling
scheme, which may include oversampling or undersampling.
[0132] FIGS. 3A and 3B are ray tracing diagrams illustrating
optical paths of the illumination and imaging module 100 of FIGS.
2A and 2B. FIG. 3A corresponds to a top view of the illumination
and imaging module 100. FIG. 3B corresponds to a side view of the
illumination and imaging module 100. The illumination and imaging
module 100 illustrated in these figures includes four detection
channels 120. However, it will be understood that the disclosed
illumination and imaging modules may equally be implemented in
systems including more or fewer than four detection channels 120.
For example, the multi-channel systems disclosed herein may be
implemented with as few as one detection channel 120, or as many as
two detection channels 120, three detection channels 120, four
detection channels 120, five detection channels 120, six detection
channels 120, seven detection channels 120, eight detection
channels 120, or more than eight detection channels 120, without
departing from the spirit or scope of the present disclosure.
[0133] The non-limiting example of imaging module 100 illustrated
in FIGS. 3A and 3B includes four detection channels 120, a first
dichroic filter 130 that reflects a beam 150 of emission light, a
second dichroic filter (e.g., a dichroic beam splitter) 135 that
splits the beam 150 into a transmitted portion and a reflected
portion, and two channel-specific dichroic filters (e.g., dichroic
beam splitters) 140 that further split the transmitted and
reflected portions of the beam 150 among individual detection
channels 120. The dichroic reflecting surface in the dichroic beam
splitters 135 and 140 for splitting the beam 150 among detection
channels are shown disposed at 45 degrees relative to a central
beam axis of the beam 150 or an optical axis of the imaging module.
However, as discussed below, an angle smaller than 45 degrees may
be employed and may offer advantages such as sharper transitions
from pass band to stop band.
[0134] The different detection channels 120 includes imaging
devices 124, which may include an image sensor or photodetector
array (e.g., a CCD or CMOS detector array). The different detection
channels 120 further include optics 126 such as lenses (e.g., one
or more tube lenses each comprising one or more lens elements)
disposed to focus the portion of the emission light entering the
detection channel 120 at a focal plane coincident with a plane of
the photodetector array 124. The optics 126 (e.g., a tube lens)
combined with the objective lens 110 are configured to form an
image of the sample onto the photodetector array 124 to capture an
image of the sample, for example, an image of a surface on the flow
cell or other sample support structure after the sample has bound
to that surface. Accordingly, such an image of the sample may
comprise a plurality of fluorescent emitting spots or regions
across a spatial extent of the sample support structure where the
sample is emitting fluorescence light. The objective lens 110
together with the optics 126 (e.g., tube lens) may provide a field
of view (FOV) that includes a portion of the sample or the entire
sample. Similarly, the photodetector array 124 of the different
detection channels 120 may be configured to capture images of a
full field of view (FOV) provided by the objective lens and the
tube lens, or a portion thereof. In some implementations, the
photodetector array 124 of some or all detection channels 120 can
detect the emission light emitted by a sample disposed on the
sample support structure, e.g., a surface of the flow cell, or a
portion thereof and record electronic data representing an image
thereof. In some implementations, the photodetector array 124 of
some or all detection channels 120 can detect features in the
emission light emitted by a specimen without capturing and/or
storing an image of the sample disposed on the flow cell surface
and/or of the full field of view (FOV) provided by the objective
lens and optics 126 and/or 122 (e.g., elements of a tube lens). In
some implementations, the FOV of the disclosed imaging modules
(e.g., that provided by the combination of objective lens 110 and
optics 126 and/or 122) may range, for example, between about 1 mm
and 5 mm (e.g., in diameter, width, length, or longest dimension)
as will be discussed below. The FOV may be selected, for example,
to provide a balance between magnification and resolution of the
imaging module and/or based on one or more characteristics of the
image sensors and/or objective lenses. For example, a relatively
smaller FOV may be provided in conjunction with a smaller and
faster imaging sensor to achieve high throughput.
[0135] Referring again to FIGS. 3A and 3B, in some implementations,
the optics 126 in the detection channel (e.g., the tube lens) may
be configured to reduce optical aberration in images acquired using
optics 126 in combination with objective lens 110. In some
implementations comprising multiple detection channels for imaging
at different emission wavelengths, the optics 126 (e.g., the tube
lens) for different detection channels have different designs to
reduce aberration for the respective emission wavelengths at which
that particular channel is configured to image. In some
implementations, the optics 126 (e.g., the tube lens) may be
configured to reduce aberrations when imaging a specific surface
(e.g., a plane, object plane, etc.) on the sample support structure
comprising fluorescing sample sites disposed thereon as compared to
other locations (e.g., other planes in object space). Similarly, in
some implementations, the optics 126 (e.g., the tube lens) may be
configured to reduce aberrations when imaging first and second
surfaces (e.g., first and second planes, first and second object
planes, etc.) on a dual surface sample support structure (e.g., a
dual surface flow cell) having fluorescing sample sites disposed
thereon as compared to other locations (e.g., other planes in
object space). For example, the optics 126 in the detection channel
(e.g., tube lens) may be designed to reduce the aberration at two
depths or planes located at different distances from the objective
lens as compared to the aberrations associated with other depths or
planes at other distances from the objective. For example, optical
aberration may be less for imaging the first and second surfaces
than elsewhere in a region from about 1 to about 10 mm from the
objective lens. Additionally, custom optic 126 in the detection
channel (e.g., a tube lens) may in some embodiments be configured
to compensate for aberration induced by transmission of emission
light through one or more portions of the sample support structure
such as a layer that includes one of the surfaces on which the
sample is disposed as well as possibly a solution adjacent to and
in contact with the surface on which the sample is disposed. The
layer comprising one of the surfaces on which the sample is
disposed may comprise, e.g., glass, quartz, plastic, or other
transparent material having a refractive index, and which
introduces optical aberration. Custom optic 126 in the detection
channel (e.g., the tube lens), for example, may in some
implementations be configured to compensate for optical aberration
induced by a sample support structure, e.g., a coverslip or flow
cell wall, or other sample support structure components, as well as
possibly a solution adjacent to and in contact with the surface on
which the sample is disposed.
[0136] In some implementations, the optics 126 in the detection
channel (e.g., a tube lens) are configured to have reduced
magnification. The optics 126 in the detection channel (e.g., a
tube lens) may be configured, for example, such that the
fluorescence imaging module has a magnification of less than, for
example, 10.times., as will be discussed further below. Such
reduced magnification may alter design constraints such that other
design parameters can be achieved. For example, the optics 126
(e.g., a tube lens) may also be configured such that the
fluorescence imaging module has a large field-of-view (FOV), for
example, of at least 1.0 mm or larger (e.g., in diameter, width,
length, or longest dimension), as will be discussed further
below.
[0137] In some implementations, the optics 126 (e.g., a tube lens)
may be configured to provide the fluorescence imaging module with a
field-of-view as indicated above such that the FOV has less than
0.15 waves of aberration over at least 60%, 70%, 80%, 90%, or 95%
of the field, as will be discussed further below.
[0138] Referring again to FIGS. 3A and 3B, in various
implementations, a sample is located at or near a focal position
112 of the objective lens 110. As described above with reference to
FIGS. 2A and 2B, a light source such as a laser source provides an
excitation beam to the sample to induce fluorescence. At least a
portion of fluorescence emission is collected by the objective lens
110 as emission light. The objective lens 110 transmits the
emission light toward the first dichroic filter 130, which reflects
some or all of the emission light as the beam 150 incident upon the
second dichroic filter 135 and to the different detection channels,
each comprising optics 126 that form an image of the sample (e.g.,
a plurality of fluorescing sample sites on a surface of a sample
support structure) onto a photodetector array 124.
[0139] As discussed above, in some implementations, the sample
support structure comprises a flow cell such as a dual surface flow
cell having two surfaces (e.g., two interior surfaces, a first
surface and a second surface, etc.) containing sample sites that
emit fluorescent emission. These two surfaces may be separated by a
distance from each other in the longitudinal (Z) direction along
the direction of the central axis of the excitation beam and/or the
optical axis of the objective lens. This separation may correspond,
for example, to a flow channel within the flow cell. Analytes or
reagents may be flowed through the flow channel and contact the
first and second interior surfaces of the flow cell, which may
thereby be contacted with a binding composition such that
fluorescence emission is radiated from a plurality of sites on the
first and second interior surfaces. The imaging optics (e.g.,
objective lens 110) may be positioned at a suitable distance (e.g.,
a distance corresponding to the working distance) from the sample
to form in-focus images of the sample on one or more detector
arrays 124. As discussed above, in various designs, the objective
lens 110 (possibly in combination with the optics 126) may have a
depth of field and/or depth of focus that is at least as large as
the longitudinal separation between the first and second surfaces.
The objective lens 110 and the optics 126 (of each detection
channel) can thus simultaneously form images of both the first and
the second flow cell surfaces on the photodetector array 124, and
these images of the first and second surfaces are both in focus and
have comparable optical resolution (or may be brought into focus
with only minor refocusing of the objects to acquire images of the
first and second surfaces that have comparable optical resolution).
In various implementations, compensation optics need not be moved
into or out of an optical path of the imaging module (e.g., into or
out of the first and/or second optical paths) to form in-focus
images of the first and second surfaces that are of comparable
optical resolution. Similarly, in various implementations, one or
more optical elements (e.g., lens elements) in the imaging module
(e.g., the objective lens 110 or optics 126) need not be moved, for
example, in the longitudinal direction along the first and/or
second optical paths to form in-focus images of the first surface
in comparison to the location of said one or more optical elements
when used to form in-focus images of the second surface. In some
implementations, the imaging module includes an autofocus system
configured to quickly and sequentially refocus the imaging module
on the first and/or second surface such that the images have
comparable optical resolution. In some implementations, objective
lens 110 and/or optics 126 are configured such that both the first
and second flow cell surfaces are in focus simultaneously with
comparable optical resolution without moving an optical compensator
into or out of the first and/or second optical path, and without
moving one or more lens elements (e.g., objective lens 110 and/or
optics 126 (such as a tube lens) longitudinally along the first
and/or second optics path. In some implementations, images of the
first and/or second surfaces, acquired either sequentially (e.g.,
with refocusing between surfaces) or simultaneously (e.g., without
refocusing between surfaces) using the novel objective lens and/or
tube lens designs disclosed herein, may be further processed using
a suitable image processing algorithm to enhance the effective
optical resolution of the images such that the images of the first
and second surfaces have comparable optical resolution. In various
implementations, the sample plane is sufficiently in focus to
resolve sample sites on the first and/or second flow cell surfaces,
the sample sites being closely spaced in lateral directions (e.g.,
in the X and Y directions).
[0140] As discussed above, the dichroic filters may comprise
interference filters that selectively transmit and reflect light of
different wavelengths based on the principle of thin-film
interference, using layers of optical coatings having different
refractive indices and particular thickness. Accordingly, the
spectral response (e.g., transmission and/or reflection spectra) of
the dichroic filters implemented within multi-channel fluorescence
imaging modules may be at least partially dependent upon the angle
of incidence, or range of angles of incidence, at which the light
of the excitation and/or emission beams are incident upon the
dichroic filters. Such effects may be especially significant with
respect to the dichroic filters of the detection optical path
(e.g., the dichroic filters 135 and 140 of FIGS. 3A and 3B).
[0141] FIG. 4 is a graph illustrating a relationship between
dichroic filter performance and beam angle of incidence (AOI).
Specifically, the graph of FIG. 4 illustrates the effect of angle
of incidence on the transition width or spectral span of a dichroic
filter, which corresponds to the range of wavelengths where the
spectral response (e.g., transmission spectrum and/or reflection
spectrum) transitions between the passband and stopband regions of
a dichroic filter. Thus, a transmission edge (or reflection edge)
having a relatively small spectral span (e.g., a small delta
.lamda. value in the graph of FIG. 4) corresponds to a sharper
transition between passband and stopband regions or the
transmission and reflection regions (or conversely between
reflection and transmission regions), while a transmission edge (or
reflection edge) having a relatively large spectral span (e.g., a
large delta .lamda. value in the graph of FIG. 4) corresponds to a
less sharp transition between passband and stopband regions. In
various implementations, sharper transitions between passband and
stopband regions are generally desirable. Moreover, it may also be
desirable to have increased consistency or a relatively consistent
transition width across all or most of the field of view and/or
beam area.
[0142] Fluorescence imaging modules, in which the dichroic mirrors
are disposed at 45 degrees relative to a central beam axis of the
emission light or the optical axis of the optical paths (e.g., of
the objective lens and/or tube lens), accordingly can have a
transition width of roughly 50 nm for an example dichroic filter,
as shown in FIG. 4. Because the emission light beam is not
collimated and has some degree of divergence, fluorescence imaging
modules may have a range of angles of incidence of approximately 5
degrees between opposing sides of the beam. Thus, as shown in FIG.
4, different portions of the beam of emission light may be incident
upon a channel splitting dichroic filter at various angles of
incidence between 40 degrees and 50 degrees. This range of
relatively large angles of incidence corresponds to a range of
transition widths between about 40 nm and about 62 nm. This range
of relatively large angles of incidence thereby leads to an
increase in transition width of the dichroic filter in the imaging
module. Performance of multi-channel fluorescence imaging modules
may thus be improved by providing smaller angles of incidence
across the full beam, thereby making the transmission edge sharper
and allowing better discrimination between different fluorescence
emission bands.
[0143] FIG. 5 is a graph illustrating a relationship between beam
footprint size (DBS) and beam angle of incidence (DBS angle) on a
dichroic filter. In some instances, a smaller beam footprint may be
desirable. For example, a small beam footprint allows smaller
dichroic filters to be used to split a beam into different
wavelength ranges. The use of smaller dichroic filters in turn
reduces manufacturing costs and improves the ease of manufacturing
suitably flat dichroic filters. As shown in FIG. 5, any angle of
incidence greater than 0 degrees (i.e., perpendicular to the
surface of the dichroic filter) results in an elliptical beam
footprint having an area larger than the cross-sectional area of
the beam. An angle of incidence of 45 degrees results in a large
beam footprint on the dichroic reflector that is greater than 1.4
times the cross-sectional area of the beam when incident at zero
degrees.
[0144] FIGS. 6A and 6B schematically illustrate a non-limiting
example configuration of dichroic filters and detection channels in
a multi-channel fluorescence imaging module where the dichroic
mirrors are disposed at an angle of less than 45 degrees relative
to a central beam axis of the emission light or the optical axis of
the optical paths (e.g., of the objective lens and/or tube lens).
FIG. 6A depicts an imaging module 500 including a plurality of
detection channels 520a, 520b, 520c, 520d. FIG. 6B is a detailed
view of the portion of the imaging module 500 within the circle 5B
as shown in FIG. 6A. As will be described in greater detail, the
configuration illustrated in FIGS. 6A and 6B includes a number of
aspects that may result in significant improvements over
conventional multi-channel fluorescence imaging module designs. In
some instances, fluorescence imaging modules and systems of the
present disclosure may, however, may be implemented with one or a
subset of the features described with respect to FIGS. 6A and 6B
without departing from the spirit or scope of the present
disclosure.
[0145] The imaging module 500 depicted in FIG. 6A includes an
objective lens 510 and four detection channels 520a, 520b, 520c,
and 520d disposed to receive and/or image emission light
transmitted by the objective lens 510. A first dichroic filter 530
is provided to couple the excitation and detection optical paths.
In contrast to the design shown in FIGS. 2A and 2B, as well as in
FIGS. 3A and 3B, the first dichroic filter 530 (e.g., a dichroic
beam splitter or combiner) is configured to reflect light from the
light source to the objective lens 510 and sample, and transmit
fluorescence emission from the sample to the detection channels
520a, 520b, 520c, and 520d. A second dichroic filter 535 splits a
beam of emission light among at least two detection channels 520a,
520b by transmitting a first portion 550a and reflecting a second
portion 550b. Additional dichroic filters 540a, 540b are provided
to further split the emission light. Dichroic filter 540a transmits
at least a portion of the first portion 550a of the emission light
and reflects a portion 550c to a third detection channel 520c.
Dichroic filter 540b transmits at least a portion of the second
portion 550b of the emission light and reflects a portion 550d to a
fourth detection channel 520d. Although the imaging module 500 is
depicted with four detection channels, in various embodiments the
imaging module 500 may include more or fewer detection channels,
with a correspondingly larger or smaller number of dichroic filters
as appropriate to provide a portion of the emission light to each
detection channel. For example, in some embodiments, the features
of the imaging module 500 may be implemented with similar
advantageous effects in a simplified imaging module including only
two detection channels 520a, 520b, and omitting additional dichroic
filters 540a, 540b. In some implementations, only one detection
channel may be included. Alternatively, three or more detection
channels may be employed.
[0146] The detection channels 520a, 520b, 520c, 520d illustrated in
FIG. 6A may include some or all of the same or similar components
to those of the detection channels 120 illustrated in FIGS. 2A-3B.
For example, different detection channel 520a, 520b, 520c, 520d may
include one or more image sensors or photodetectors arrays, and may
include transmissive and/or reflective optics such as one or more
lenses (e.g., tube lenses) that focus the light received by the
detection channel onto its respective image sensor or photodetector
array.
[0147] The objective lens 510 is disposed to receive emission light
emitted by fluorescence from a specimen. In particular, the first
dichroic filter 530 is disposed to receive the emission light
collected and transmitted by the objective lens 510. As discussed
above and shown in FIG. 6A, in some designs, an illumination source
(e.g., the illumination source 115 of FIGS. 2A and 2B) such as a
laser source or the like is disposed to provide an excitation beam
which is incident on the first dichroic filter 530 such that the
first dichroic filter 530 reflects the excitation beam into the
same objective lens 510 that transmits the emission light, for
example, in an epifluorescence configuration. In some other
designs, the illumination source may be directed to the specimen by
other optical components along a different optical path that does
not include the same objective lens 510. In such configurations,
the first dichroic filter 530 may be omitted.
[0148] Similarly, as discussed above and shown in FIG. 6A, the
detection optics (e.g., including the detection channels 520a,
520b, 520c, 520d and any optical components such as dichroic
filters 535, 540a, 540b along the optical path between the
objective lens 510 and the detection channels 520a, 520b, 520c,
520d) may be disposed on the transmission path of the first
dichroic filter 530, rather than on the reflected path of the first
dichroic filter 530. In one example implementation, the objective
lens 510 and detection optics are disposed such that the objective
lens 510 transmits the beam 550 of emission light directly toward
the second dichroic filter 535. The wavefront quality of the
emission light may be degraded somewhat by the presence of the
first dichroic filter 530 along the path of the beam 550 of
emission light (e.g., by imparting some wavefront error to the beam
550). However, the wavefront error introduced by a beam transmitted
through a dichroic reflector of a dichroic beam splitter is
generally significantly smaller than the wavefront error of a beam
reflected from the dichroic reflecting surface of a dichroic beam
splitter (e.g., an order of magnitude smaller). Thus, the wavefront
quality and subsequent imaging quality of the emission light in a
multi-channel fluorescence imaging module may be substantially
improved by placing the detection optics along the transmitted beam
path of the first dichroic filter 530 rather than along the
reflected beam path.
[0149] Still referring to FIG. 6A, within the detection optics of
the imaging module 500, dichroic filters 535, 540a, and 540b are
provided to split the beam 550 of emission light among the
detection channels 520a, 520b, 520c, 520d. For example, the
dichroic filters 535, 540a, and 540b split the beam 550 on the
basis of wavelength, such that a first wavelength or wavelength
band of the emission light can be received by the first detection
channel 520a, a second wavelength or wavelength band of the
emission light can be received by the second detection channel
520b, a third wavelength or wavelength band of the emission light
can be received by the third detection channel 520c, and a fourth
wavelength or wavelength band of the emission light can be received
by the fourth detection channel 520d. In some implementations,
multiple separated wavelengths or wavelength bands can be received
by the detection channel.
[0150] In contrast to the multi-channel fluorescence imaging module
design shown in FIGS. 2A and 2B, as well as FIGS. 3A and 3B, the
imaging module 500 has dichroic filters 535, 540a, and 540b
disposed at angles of incidence of less than 45 degrees with
respect to the central beam axis of the incident beams. As shown in
FIG. 6B, the different beams 550, 550a, 550b have respective
central beam axes 552, 552a, 552b. In various implementations, the
central beam axes 552, 552a, 552b is at the center of a
cross-section of the beam orthogonal to the propagation direction
of the beam. These central beam axes 552, 552a, 552b may correspond
to the optical axis of the objective lens and/or the optics within
the separate channels, for example, the optical axes of the
respective tube lenses. Additional rays 554, 554a, 554b of each
beam 550, 550a, 550b are illustrated in FIG. 6B to indicate the
diameter of each beam 550, 550a, 550b. Beam diameter may be
defined, for example, as a full width at half maximum diameter, a
D4.sigma. (i.e., 4 times G, where G is the standard deviation of
the horizontal or vertical marginal distribution of the beam
respectively) or second-moment width, or any other suitable
definition of beam diameter.
[0151] The central beam axis 552 of the beam 550 of emission light
may serve as a reference point for defining the angle of incidence
of the beam 550 on the second dichroic filter 535. Accordingly, the
"angle of incidence" (AOI) of a beam 550 may be the angle between
the central beam axis 552 of the incident beam 550 and a line N
normal to the surface the beam is incident on, for example, the
dichroic reflective surface. When the beam 550 of emission light is
incident upon the dichroic reflective surface of the second
dichroic filter 535 at an angle of incidence AOI, the second
dichroic filter 535 transmits a first portion 550a of the emission
light (e.g., the portion having wavelengths within the passband
region of the second dichroic filter 535) and reflects a second
portion 550b of the emission light (e.g., the portion having
wavelengths within the stopband region of the second dichroic
filter 535). The first portion 550a and the second portion 550b may
each be similarly described in terms of a central beam axis 552a,
552b. As referred to above, the optical axis may alternatively or
additionally be used.
[0152] In the example configuration of FIGS. 6A and 6B, the second
dichroic filter 535 is disposed such that the central beam axis 552
of the beam 550 is incident at an angle of incidence of 30 degrees.
Similarly, the additional dichroic filters 540a, 540b are disposed
such that the central beam axes 552a, 552b of the first and second
portions 550a, 550b of the beam 550 are also incident at angles of
incidence of 30 degrees. However, in various implementations these
angles of incidence may be other angles smaller than 45 degrees. In
some instances, for example, the angles of incidence may range
between about 20 degrees and about 45 degrees, as will be discussed
further below. Moreover, the angles of incidence on each of the
dichroic filters 535, 540a, 540b need not necessarily be the same.
In some embodiments, some or all of the dichroic filters 535, 540a,
540b may be disposed such that their incident beams 550, 550a, 550b
have different angles of incidence. As described above, the angle
of incidence may be with respect to the optical axis of the optics
within the imaging module, for example, the objective lens and/or
the optics in the detection channels (e.g., the tube lenses) and
the dichroic reflective surface in the respective dichroic beam
splitter. The same ranges and values for the angle of incidence
apply to the case when the optical axis is used to specify the
AOI.
[0153] The beams 550, 550a, 550b of emission light in a
fluorescence imaging module system are typically diverging beams.
As noted above, the beams of emission light can have a beam
divergence large enough that regions of the beam within the beam
diameter are incident upon the dichroic filters at angles of
incidence that differ by up to 5 degrees or more relative to the
angle of incidence of the central beam axis and/or optical axis of
the optics. In some designs, the objective lens 510 may be
configured, for example, to have an f-number or numerical aperture
selected to produce a smaller beam diameter for a given field of
view of the microscope. In one example, the f-number or numerical
aperture of the objective lens 510 may be selected such that the
full diameter of the beams 550, 550a, 550b are incident upon
dichroic filters 535, 540a, 540b at angles of incidence within, for
example, 1 degree, 1.5 degrees, 2 degrees, 2.5 degrees, 3 degrees,
3.5 degrees, 4 degrees, 4.5 degrees, or 5 degrees of the angle of
incidence of the central beam axes 552, 552a, 552b.
[0154] In some implementations, the focal length of the objective
lens that is suitable for producing such a narrow beam diameter may
be longer than those typically employed in fluorescence microscopes
or imaging systems. For example, in some implementations, the focal
length of the objective lens may range between 20 mm and 40 mm, as
will be discussed further below. In one example, an objective lens
510 having a focal length of 36 mm may produce a beam 550
characterized by a divergence small enough that light across the
full diameter of the beam 550 is incident upon the second dichroic
filter 535 at angles within 2.5 degrees of the angle of incidence
of the central beam axis.
[0155] FIG. 7 and FIG. 8 provide graphs illustrating improved
dichroic filter performance due to aspects of the imaging module
configuration of FIGS. 6A and 6B (or any of the imaging module
configurations disclosed herein). The graph in FIG. 7 is similar to
that of FIG. 4 and illustrates the effect of angle of incidence on
the transition width (e.g., the spectral span of the transmission
edge) of a dichroic filter. FIG. 7 shows an example where the
orientation of a dichroic filter (e.g., dichroic filters 535, 540a,
and 540b) and the dichroic reflective surface therein is such that
its incident beam has an angle of incidence of 30 degrees, rather
than 45 degrees. FIG. 7 shows how this reduced angle of incidence
significantly improves the sharpness and the uniformity of the
transition width across the full beam diameter. For example, while
an angle of incidence of 45 degrees at the central beam axis
results in a range of transition widths between about 40 nm and
about 62 nm, an angle of incidence of 30 degrees at the central
beam axis results in a range of transition widths between about 16
nm and about 30 nm. In this example, the average transition width
is reduced from about 51 nm to about 23 nm, indicating a sharper
transition between passband and stopband. Moreover, the variation
in transition widths across the beam diameter is reduced by nearly
40% from a 22 nm range to a 14 nm range, indicating a more uniform
sharpness of the transition over the area of the beam.
[0156] FIG. 8 illustrates additional advantages that may be
realized by selecting the appropriate f-number or numerical
aperture for the objective lens to reduce beam divergence in any of
the imaging module configurations disclosed herein. In some
implementations, a longer focal length is used. In the example of
FIG. 8, the objective lens 510 has a focal length of 36 mm, which
with the appropriate numerical aperture (e.g., less than 5),
reduces the range of angles of incidence within the beam 550 from
30 degrees.+-.5 degrees to 30 degrees.+-.2.5 degrees. With this
design, the range of transition widths may be reduced to between
about 19 nm and about 26 nm. When compared to the improved system
of FIG. 7, although the average transition width is substantially
the same (e.g., a spectral span of roughly 23 nm), the variation in
transition widths across the beam diameter is further reduced to a
7 nm range, representing a reduction of nearly 70% relative to the
range of transition widths illustrated in FIG. 4.
[0157] Referring back to FIG. 5, the reduction in angle of
incidence from 45 degrees to 30 degrees at the central beam axis is
further advantageous because it reduces the beam spot size on the
dichroic filter. As shown in FIG. 5, an angle of incidence of 45
degrees results in a beam footprint on the dichroic filter having
an area greater than 1.4 times the cross-sectional area of the
beam. However, an angle of incidence of 30 degrees results in a
beam footprint on the dichroic filter having an area only about
1.15 times the cross-sectional area of the beam. Thus, reducing the
angle of incidence at the dichroic filters 535, 540a, 540b from 45
degrees to 30 degrees results in a reduction of about 18% in the
area of the beam footprint on the dichroic filters 535, 540a, 540b.
This reduction in beam footprint area allows smaller dichroic
filters to be used.
[0158] Referring now jointly to FIGS. 9A-B, the reduction in angle
of incidence from 45 degrees to 30 degrees may also provide
improved performance with regard to surface deformation caused by
the dichroic filters in any of the imaging module configurations
disclosed herein, as indicated by improvements in the modulation
transfer function. In general, the amount of surface deformation
increases with larger area optical elements. If a larger area on
the dichroic filter is employed, a larger amount of surface
deformation is encountered, thereby introducing more wavefront
error into the beam. FIG. 9A illustrates the effect of folding
angle on image quality degradation induced by the addition of 1
wave of peak-to-valley (PV) spherical power to the last mirror.
FIG. 9B illustrates the effect of folding angle on image quality
degradation induced by the addition of 0.1 wave of PV spherical
power to the last mirror. As shown in FIGS. 9A and 9B, the
reduction in angle of incidence to 30 degrees significantly reduces
the effect of surface deformation to achieve close to
diffraction-limited performance of the detection optics.
[0159] In some implementations of the disclosed imaging modules,
the polarization state of the excitation beam may be utilized to
further improve the performance of the multi-channel fluorescence
imaging modules disclosed herein. Referring back to FIGS. 2A, 2B,
and 6A, for example, some implementations of the multi-channel
fluorescence imaging modules disclosed herein have an
epifluorescence configuration in which a first dichroic filter 130
or 530 merges the optical paths of the excitation beam and the beam
of emission light such that both the excitation and emission light
are transmitted through the objective lens 110, 510. As discussed
above, the illumination source 115 may include a light source such
as a laser or other source which provides the light that forms the
excitation beam. In some designs, the light source comprises a
linearly polarized light source and the excitation beam may be
linearly polarized. In some designs, polarization optics are
included to polarize the light and/or rotate the polarization of
the light. For example, a polarizer such as a linear polarizer may
be included in an optical path of the excitation beam to polarize
the excitation beam. Retarders such as half wave retarders or a
plurality of quarter wave retarders or retarders having other
amounts of retardance may be included to rotate the linear
polarization in some designs.
[0160] The linearly polarized excitation beam, when it is incident
upon any dichroic filter or other planar interface, may be
p-polarized (e.g., having an electric field component parallel to
the plane of incidence), s-polarized (e.g., having an electric
field component normal to the plane of incidence), or may have a
combination of p-polarization and s-polarization states within the
beam. The p- or s-polarization state of the excitation beam may be
selected and/or changed by selecting the orientation of the
illumination source 115 and/or one or more components thereof with
respect to the first dichroic filter 130, 530 and/or with respect
to any other surfaces with which the excitation beam will interact.
In some implementations where the light source output linearly
polarized light, the light source can be configured to provide
s-polarized light. For example, the light source may comprise an
emitter such as a solid-state laser or a laser diode that may be
rotated about its optical axis or the central axis of the beam to
orient the linearly polarized light output therefrom.
Alternatively, or in addition, retarders may be employed to rotate
the linear polarization about the optical axis or the central axis
of the beam. As discussed above, in some implementations, for
example when the light source does not output polarized light, a
polarizer disposed in the optical path of the excitation beam can
polarize the excitation beam. In some designs, for example, a
linear polarizer is disposed in the optical path of the excitation
beam. This polarizer may be rotated to provide the proper
orientation of the linear polarization to provide s-polarized
light.
[0161] In some designs, the linear polarization is rotated about
the optical axis or the central axis of the beam such that
s-polarization is incident on the dichroic reflector of the
dichroic beam splitter. When s-polarized light is incident on the
dichroic reflector of the dichroic beam splitter the transition
between the pass band and the stop band is sharper as opposed to
when p-polarized light is incident on the dichroic reflector of the
dichroic beam splitter.
[0162] As shown in FIGS. 10A and 10B, use of the p- or
s-polarization state of the excitation beam may significantly
affect the narrowband performance of any excitation filters such as
the first dichroic filter 130, 530. FIG. 10A illustrates a
transmission spectrum between 610 nm and 670 nm for an example
bandpass dichroic filter at angles of incidence of 40 degrees and
45 degrees, where the incident beam is linearly polarized and is
p-polarized with respect to the plane of the dichroic filter. As
shown in FIG. 10B, changing the orientation of the light source
with respect to the dichroic filter, such that the incident beam is
s-polarized with respect to the plane of the dichroic filter,
results in a substantially sharper edge between the passband and
the stopband of the dichroic filter. Thus, the illumination and
imaging modules 100, 500 disclosed herein may advantageously have
an illumination source 115 oriented relative to the first dichroic
filter 130, 530 such that the excitation beam is s-polarized with
respect to the plane of the first dichroic filter 130, 530. As
discussed above, in some implementation, a polarizer such as a
linear polarizer may be used to polarize the excitation beam. This
polarizer may be rotated to provide an orientation of the linearly
polarized light corresponding to s-polarized light. Also as
discussed above, in some implementations, other approaches to
rotating the linearly polarized light may be used. For example,
optical retarders such as half wave retarders or multiple quarter
wave retarders may be used to rotate the polarization direction.
Other arrangements are also possible.
[0163] As discussed elsewhere herein, reducing the numerical
aperture (NA) of the fluorescence imaging module and/or of the
objective lens may increase the depth of field to enable the
comparable imaging of the two surfaces. FIGS. 11A-16B, show how the
MTF is more similar at first and second surfaces separated by 1 mm
of glass for lower numerical apertures than for larger numerical
apertures.
[0164] FIGS. 11A and 11B show the MTF at first (FIG. 11A) and
second (FIG. 11B) surfaces for an NA of 0.3.
[0165] FIGS. 12A and 12B show the MTF at first (FIG. 12A) and
second (FIG. 12B) surfaces for an NA of 0.4.
[0166] FIGS. 13A and 13B show the MTF at first (FIG. 13A) and
second (FIG. 13B) surfaces for an NA of 0.5.
[0167] FIGS. 14A and 14B show the MTF at first (FIG. 14A) and
second (FIG. 14B) surfaces for an NA of 0.6.
[0168] FIGS. 15A and 15B show the MTF at first (FIG. 15A) and
second (FIG. 15B) surfaces for an NA of 0.7.
[0169] FIGS. 16A and 16B show the MTF at first (FIG. 16A) and
second (FIG. 16B) surfaces for an NA of 0.8. The first and second
surfaces in each of these figures correspond to, e.g., the top and
bottom surfaces of a flow cell.
[0170] FIGS. 17A-B provide plots of the calculated Strehl ratio
(i.e., the ratio of peak light intensity focused or collected by
the optical system versus that focused or collected by an ideal
optical system and point light source) for imaging a second flow
cell surface through a first flow cell surface. FIG. 17A shows a
plot of the Strehl ratios for imaging a second flow cell surface
through a first flow cell surface as a function of the thickness of
the intervening fluid layer (fluid channel height) for different
objective lens and/or optical system numerical apertures. As shown,
the Strehl ratio decreases with increasing separation between the
first and second surfaces. One of the surfaces would thus have
deteriorated image quality with increasing separation between the
two surfaces. The decrease in second surface imaging performance
with increased separation distance between the two surfaces is
reduced for imaging systems having smaller numeral apertures as
compared to those having larger numerical apertures. FIG. 17B shows
a plot of the Strehl ratio as a function of numerical aperture for
imaging a second flow cell surface through a first flow cell
surface and an intervening layer of water having a thickness of 0.1
mm. The loss of imaging performance at higher numerical apertures
may be attributed to the increased optical aberration induced by
the fluid for the second surface imaging. With increasing NA, the
increased optical aberration introduced by the fluid for the second
surface imaging degrades the image quality significantly. In
general, however, reducing the numeral aperture of the optical
system reduces the achievable resolution. This loss of image
quality can be at least partially offset by providing an increased
sample plane (or object plane) contrast-to-noise ratio, for
example, by using chemistries for nucleic acid sequencing
applications that enhance the fluorescence emission for labeled
nucleic acid clusters and/or that reduce background fluorescence
emission. In some instances, for example, sample support structures
comprising hydrophilic substrate materials and/or hydrophilic
coatings may be employed. In some cases, such hydrophilic
substrates and/or hydrophilic coatings may reduce background noise.
Additional discussion of sample support structures, hydrophilic
surfaces and coatings, and methods for enhancing contrast-to-noise
ratios, e.g., for nucleic acid sequencing applications, can be
found below.
[0171] In some implementations, any one or more of the fluorescence
imaging system, the illumination and imaging module 100, the
imaging optics (e.g., optics 126), the objective lens, and/or the
tube lens is configured to have reduced magnification, such as a
magnification of less than 10.times., as will be discussed further
below. Such reduced magnification may adjust design constraints
such that other design parameters can be achieved. For example, any
one or more of the fluorescence microscope, illumination and
imaging module 100, the imaging optics (e.g., optics 126), the
objective lens or the tube lens may also be configured such that
the fluorescence imaging module has a large field-of-view (FOV),
for example, a field-of-view of at least 3.0 mm or larger (e.g., in
diameter, width, height, or longest dimension), as will be
discussed further below. Any one or more of the fluorescence
imaging system, the illumination and imaging module 100, the
imaging optics (e.g., optics 126), the objective lens and/or the
tube lens may be configured to provide the fluorescence microscope
with such a field-of-view such that the FOV has less than, e.g.,
0.1 waves of aberration over at least 80% of field. Similarly, any
one or more of the fluorescence imaging system, illumination and
imaging module 100, the imaging optics (e.g., optics 126), the
objective lens and/or the tube lens may be configured such that the
fluorescence imaging module has such a FOV and is diffraction
limited or is diffraction limited over such an FOV.
[0172] As discussed above, in various implementations, a large
field-of-view (FOV) is provided by the disclosed optical systems.
In some implementations, obtaining an increased FOV is facilitated
in part by the use of larger image sensors or photodetector arrays.
The photodetector array, for example, may have an active area with
a diagonal of at least 15 mm or larger, as will be discussed
further below. As discussed above, in some implementations the
disclosed optical imaging systems provide a reduced magnification,
for example, of less than 10.times. which may facilitate large FOV
designs. Despite the reduced magnification, the optical resolution
of the imaging module may still be sufficient as detector arrays
having small pixel size or pitch may be used. The pixel size and/or
pitch may, for example, be about 5 .mu.m or less, as will be
discussed in more detail below. In some implementations, the pixel
size is smaller than twice the optical resolution provided by the
optical imaging system (e.g., objective and tube lens) to satisfy
the Nyquist theorem. Accordingly, the pixel dimension and/or pitch
for the image sensor(s) may be such that a spatial sampling
frequency for the imaging module is at least twice an optical
resolution of the imaging module. For example, the spatial sampling
frequency for the photodetector array may be is at least 2 times,
at least 2.5 times, at least 3 times, at least 4 times, or at least
5 times the optical resolution of the fluorescence imaging module
(e.g., the illumination and imaging module, the objective and tube
lens, the object lens and optics 126 in the detection channel, the
imaging optics between the sample support structure or stage
configured to support the sample support stage and the
photodetector array) or any spatial sampling frequency in a range
between any of these values.
[0173] Although a wide range of features are discussed herein with
respect to fluorescence imaging modules, any of the features and
designs describe herein may be applied to other types of optical
imaging systems including without limitation bright-field and
dark-field imaging, and may apply to luminescence or
phosphorescence imaging.
[0174] Dual wavelength excitation/four channel imaging system: FIG.
18 illustrates a dual excitation wavelength/four channel imaging
system for dual-side imaging applications that includes an
objective and tube lens combination that is scanned in a direction
perpendicular to the optical axis to provide for large area
imaging, e.g., by tiling several images to create a composite image
having a total field-of-view (FOV) that is much larger than that
for each individual image. The system comprises two excitation
light sources, e.g., lasers or laser diodes, operating at different
wavelengths and an autofocus laser. The two excitation light beams
and autofocus laser beam are combined using a series of mirrors
and/or dichroic reflectors and delivered to an upper or lower
interior surface of the flow cell through the objective.
Fluorescence that is emitted by labeled oligonucleotides (or other
biomolecules) tethered to one of the flow cell surfaces is
collected by the objective, transmitted through the tube lens, and
directed to one of four imaging sensors according to the wavelength
of the emitted light by a series of intermediate dichroic
reflectors. Autofocus laser light that has been reflected from the
flow cell surface is collected by the objective, transmitted
through the tube lens, and directed to an autofocus sensor by a
series of intermediate dichroic reflectors. The system allows
accurate focus to be maintained (e.g., by adjusting the relative
distance between the flow cell surface and the objective using a
precision linear actuator, translation stage, or microscope
turret-mounted focus adjustment mechanism, to reduce or minimize
the reflected light spot size on the autofocus image sensor) while
the objective/tube lens combination is scanned in a direction
perpendicular to the optical axis of the objective. Dual wavelength
excitation used in combination with four channel (i.e. four
wavelength) imaging capability provides for high-throughput imaging
of the upper (near) and lower (far) interior surfaces of the flow
cell.
[0175] Improved or optimized objective and/or tube lens for use
with thicker coverslips: Existing design practice includes the
design of objective lenses and/or use of commonly available
off-the-shelf microscope objectives to optimize image quality when
images are acquired through thin (e.g., <200 .mu.m thick)
microscope coverslips. When used to image on both sides of a
fluidic channel or flow cell, the extra height of the gap between
the two surfaces (i.e., the height of the fluid channel; typically,
about 50 .mu.m to 200 .mu.m) introduces optical aberration in
images captured for the non-optimal side of the fluidic channel,
thereby causing lower optical resolution. This is primarily because
the additional gap height is significant compared to the optimal
coverslip thickness (typical fluid channel or gap heights of 50-200
.mu.m vs. coverslip thicknesses of <200 .mu.m). Another common
design practice is to utilize an additional "compensator" lens in
the optical path when imaging is to be performed on the non-optimal
side of the fluid channel or flow cell. This "compensator" lens and
the mechanism required to move it in or out of the optical path so
that either side of the flow cell may be imaged further increases
system complexity and imaging system down time, and potentially
degrades image quality due to vibration, etc.
[0176] In the present disclosure, the imaging system is designed
for compatibility with flow cell consumables that comprise a
thicker coverslip or flow cell wall (thickness .gtoreq.700 .mu.m).
The objective lens design may be improved or optimized for a
coverslip that is equal to the true cover slip thickness plus half
of the effective gap thickness (e.g., 700 .mu.m+1/2*fluid channel
(gap) height). This design significantly reduces the effect of gap
height on image quality for the two surfaces of the fluid channel
and balances the optical quality for images of the two surfaces, as
the gap height is small relative to the total coverslip thickness
and thus its impact on optical quality is reduced.
[0177] Additional advantages of using a thicker coverslip include
improved control of thickness tolerance error during manufacturing,
and a reduced likelihood that the coverslip undergoes deformation
due to thermal and mounting-induced stress. Coverslip thickness
error and deformation adversely impact imaging quality for both the
top surface and the bottom surface of a flow cell.
[0178] To further improve the dual surface imaging quality for
sequencing applications, our optical system design places a strong
emphasis on improving or optimizing MTF (e.g., through improving or
optimizing the objective lens and/or tube lens design) in the mid-
to high-spatial frequency range that is most suitable for imaging
and resolving small spots or clusters.
[0179] Improved or optimized tube lens design for use in
combination with commercially-available, off-the-shelf objectives:
For low-cost sequencer design, the use of a commercially-available,
off-the-shelf objective lens may be preferred due to its relatively
low price. However, as noted above, low-cost, off-the-shelf
objectives are mostly optimized for use with thin coverslips of
about 170 .mu.m in thickness. In some instances, the disclosed
optical systems may utilize a tube lens design that compensates for
a thicker flow cell coverslip while enabling high image quality for
both interior surfaces of a flow cell in dual-surface imaging
applications. In some instances, the tube lens designs disclosed
herein enable high quality imaging for both interior surfaces of a
flow cell without moving an optical compensator into or out of the
optical path between the flow cell and an image sensor, without
moving one or more optical elements or components of the tube lens
along the optical path, and without moving one or more optical
elements or components of the tube lens into or out of the optical
path.
[0180] FIG. 19 provides an optical ray tracing diagram for a low
light objective lens design that has been improved or optimized for
imaging a surface on the opposite side of a 0.17 mm thick
coverslip. The plot of modulation transfer function for this
objective, shown in FIG. 20, indicates near-diffraction limited
imaging performance when used with the designed-for 0.17 mm thick
coverslip.
[0181] FIG. 21 provides a plot of the modulation transfer function
for the same objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface on the opposite side
of a 0.3 mm thick coverslip. The relatively minor deviations of MTF
value over the spatial frequency range of about 100 to about 800
lines/mm (or cycles/mm) indicates that the image quality obtained
even when using a 0.3 mm thick coverslip is still reasonable.
[0182] FIG. 22 provides a plot of the modulation transfer function
for the same objective lens illustrated in FIG. 19 as a function of
spatial frequency when used to image a surface that is separated
from that on the opposite side of a 0.3 mm thick coverslip by a 0.1
mm thick layer of aqueous fluid (i.e., under the kind of conditions
encountered for dual-side imaging of a flow cell when imaging the
far surface). As can be seen in the plot of FIG. 22, imaging
performance is degraded, as indicated by the deviations of the MTF
curves from those for the an ideal, diffraction-limited case over
the spatial frequency range of about 50 lp/mm to about 900
lp/mm.
[0183] FIG. 23 and FIG. 24 provide plots of the modulation transfer
function as a function of spatial frequency for the upper (or near)
interior surface (FIG. 23) and lower (or far) interior surface
(FIG. 24) of a flow cell when imaged using the objective lens
illustrated in FIG. 19 through a 1.0 mm thick coverslip, and when
the upper and lower interior surfaces are separated by a 0.1 mm
thick layer of aqueous fluid. As can be seen, imaging performance
is significantly degraded for both surfaces.
[0184] FIG. 25 provides a ray tracing diagram for a tube lens
design which, if used in conjunction with the objective lens
illustrated in FIG. 19, provides for improved dual-side imaging
through a 1 mm thick coverslip. The optical design 700 comprising a
compound objective (lens elements 702, 703, 704, 705, 706, 707,
708, 709, and 710) and a tube lens (lens elements 711, 712, 713,
and 714) is improved or optimized for use with flow cells
comprising a thick coverslip (or wall), e.g., greater than 700
.mu.m thick, and a fluid channel thickness of at least 50 .mu.m,
and transfers the image of an interior surface from the flow cell
701 to the image sensor 715 with dramatically improved optical
image quality and higher CNR.
[0185] In some instances, the tube lens (or tube lens assembly) may
comprise at least two optical lens elements, at least three optical
lens elements, at least four optical lens elements, at least five
optical lens elements, at least six optical lens elements, at least
seven optical lens elements, at least eight optical lens elements,
at least nine optical lens elements, at least ten optical lens
elements, or more, where the number of optical lens elements, the
surface geometry of each element, and the order in which they are
placed in the assembly is improved or optimized to correct for
optical aberrations induced by the thick wall of the flow cell, and
in some instances, allows one to use a commercially-available,
off-the-shelf objective while still maintaining high-quality,
dual-side imaging capability.
[0186] In some instances, as illustrated in FIG. 25, the tube lens
assembly may comprise, in order, a first asymmetric convex-convex
lens 711, a second convex-plano lens 712, a third asymmetric
concave-concave lens 713, and a fourth asymmetric convex-concave
lens 714.
[0187] FIG. 26 and FIG. 27 provide plots of the modulation transfer
function as a function of spatial frequency for the upper (or near)
interior surface (FIG. 26) and lower (or far) interior surface
(FIG. 27) of a flow cell when imaged using the objective lens
(corrected for a 0.17 mm coverslip) and tube lens combination
illustrated in FIG. 25 through a 1.0 mm thick coverslip, and when
the upper and lower interior surfaces are separated by a 0.1 mm
thick layer of aqueous fluid. As can be seen, the imaging
performance achieved is nearly that expected for a
diffraction-limited optical design.
[0188] FIG. 28 provides ray tracing diagrams for tube lens design
(left) of the present disclosure that has been improved or
optimized to provide high-quality, dual-side imaging performance.
Because the tube lens is no longer infinity-corrected, an
appropriately designed null lens (right) may be used in combination
with the tube lens to compensate for the non-infinity-corrected
tube lens for manufacturing and testing purposes.
[0189] Imaging channel-specific tube lens adaptation or
optimization: In imaging system design, it is possible to improve
or optimize both the objective lens and the tube lens in the same
wavelength region for all imaging channels. Typically, the same
objective lens is shared by all imaging channels (see, for example,
FIG. 18), and each imaging channel either uses the same tube lens
or has a tube lens that shares the same design.
[0190] In some instances, the imaging systems disclosed herein may
further comprise a tube lens for each imaging channel where the
tube lens has been independently improved or optimized for the
specific imaging channel to improve image quality, e.g., to reduce
or minimize distortion and field curvature, and improve
depth-of-field (DOF) performance for each channel. Because the
wavelength range (or bandpass) for each specific imaging channel is
much narrower than the combined wavelength range for all channels,
the wavelength- or channel-specific adaptation or optimization of
the tube lens used in the disclosed systems results in significant
improvements in imaging quality and performance. This
channel-specific adaptation or optimization results in improved
image quality for both the top and bottom surfaces of the flow cell
in dual-side imaging applications.
[0191] Dual-side imaging w/o fluid present in flow cell: For
optimal imaging performance of both top and bottom interior
surfaces of a flow cell, a motion-actuated compensator is typically
required to correct for optical aberrations induced by the fluid in
the flow cell (typically comprising a fluid layer thickness of
about 50-200 .mu.m). In some instances of the disclosed optical
system designs, the top interior surface of the flow cell may be
imaged with fluid present in the flow cell. Once the sequencing
chemistry cycle has been completed, the fluid may be extracted from
the flow cell for imaging of the bottom interior surface. Thus, in
some instances, even without the use of a compensator, the image
quality for the bottom surface is maintained.
[0192] Compensation for optical aberration and/or vibration using
electro-optical phase plates: In some instances, dual-surface image
quality may be improved without requiring the removal of the fluid
from the flow cell by using an electro-optical phase plate (or
other corrective lens) in combination with the objective to cancel
the optical aberrations induced by the presence of the fluid. In
some instances, the use of an electro-optical phase plate (or lens)
may be used to remove the effects of vibration arising from the
mechanical motion of a motion-actuated compensator and may provide
faster image acquisition times and sequencing cycle times for
genomic sequencing applications.
[0193] Improved contrast-to-noise ratio (CNR), field-of-view (FOV),
spectral separation, and timing design to increase or maximize
information transfer and throughput: Another way to increase or
maximize information transfer in imaging systems designed for
genomics applications is to increase the size of the field-of-view
(FOV) and reduce the time required to image a specific FOV. With
typical large NA optical imaging systems, it may be common to
acquire images for fields-of-view that are on the order of 1
mm.sup.2 in area, where in the presently disclosed imaging system
designs large FOV objectives with long working distances are
specified to enable imaging of areas of 2 mm.sup.2 or larger.
[0194] In some cases, the disclosed imaging systems are designed
for use in combination with proprietary low-binding substrate
surfaces and DNA amplification processes that reduce fluorescence
background arising from a variety of confounding signals including,
but are not limited to, nonspecific adsorption of fluorescent dyes
to substrate surfaces, nonspecific nucleic acid amplification
products (e.g., nucleic acid amplification products that arise the
substrate surface in areas between the spots or features
corresponding to clonally-amplified clusters of nucleic acid
molecules (i.e., specifically amplified colonies), nonspecific
nucleic acid amplification products that may arise within the
amplified colonies, phased and pre-phased nucleic acid strands,
etc. The use of low-binding substrate surfaces and DNA
amplification processes that reduce fluorescence background in
combination with the disclosed optical imaging systems may
significantly cut down on the time required to image each FOV.
[0195] The presently disclosed system designs may further reduce
the required imaging time through imaging sequence improvement or
optimization where multiple channels of fluorescence images are
acquired simultaneously or with overlapping timing, and where
spectral separation of the fluorescence signals is designed to
reduce cross-talks between fluorescence detection channels and
between the excitation light and the fluorescence signal(s).
[0196] The presently disclosed system designs may further reduce
the required imaging time through improvement or optimization of
scanning motion sequence. In the typical approach, an X-Y
translation stage is used to move the target FOV into position
underneath the objective, an autofocus step is performed where
optimal focal position is determined and the objective is moved in
the Z direction to the determined focal position, and an image is
acquired. A sequence of fluorescence images is acquired by cycling
through a series of target FOV positions. From an information
transfer duty cycle perspective, information is only transferred
during the fluorescence image acquisition portion of the cycle. In
the presently disclosed imaging system designs, a single-step
motion in which all axes (X-Y-Z) are repositioned simultaneously is
performed, and the autofocus step is used to check focal position
error. The additional Z motion is only commanded if the focal
position error (i.e., the difference between the focal plane
position and the sample plane position) exceeds a certain limit
(e.g., a specified error threshold). Coupled with high speed X-Y
motion, this approach increases the duty cycle of the system, and
thus increases the imaging throughput per unit time.
[0197] Furthermore, by matching the optical collection efficiency,
modulation transfer function, and image sensor performance
characteristics of the design with the fluorescence photon flux
expected for the input excitation photon flux, dye efficiency
(related to dye extinction coefficient and fluorescence quantum
yield), while accounting for background signal and system noise
characteristics, the time required to acquire high quality (high
contrast-to-noise ratio (CNR) images) may be reduced or
minimized.
[0198] The combination of efficient image acquisition and improved
or optimized translation stage step and settle times leads to fast
imaging times (i.e., the overall time required per field-of-view)
and higher throughput imaging system performance.
[0199] Along with the large FOV and fast image acquisition duty
cycle, the disclosed designs may comprise also specifying image
plane flatness, chromatic focus performance between fluorescence
detection channels, sensor flatness, image distortion, and focus
quality specifications.
[0200] Chromatic focus performance is further improved by
individually aligning the image sensors for different fluorescence
detection channels such that the best focal plane for each
detection channel overlaps. The design goal is to ensure that
images across more than 90 percent of the field-of-view are
acquired within .+-.100 nm (or less) relative to the best focal
plane for each channel, thus increasing or maximizing the transfer
of individual spot intensity signals. In some instances, the
disclosed designs further ensure that images across 99 percent of
the field-of-view are acquired within .+-.150 nm (or less) relative
to the best focal plane for each channel, and that images across
more the entire field-of-view are acquired within .+-.200 nm (or
less) relative to the best focal plane for each imaging
channel.
[0201] Illumination optical path design: Another factor for
improving signal-to-noise ratio (SNR), contrast-to-noise ratio
(CNR), and/or increasing throughput is to increase illumination
power density to the sample. In some instances, the disclosed
imaging systems may comprise an illumination path design that
utilizes a high-power laser or laser diode coupled with a liquid
light guide. The liquid light guide removes optical speckle that is
intrinsic to coherent light sources such as lasers and laser
diodes. Furthermore, the coupling optics are designed in such a way
as to underfill the entrance aperture of the liquid light guide.
The underfilling of the liquid light guide entrance aperture
reduces the effective numerical aperture of the illumination beam
entering the objective lens, and thus improves light delivery
efficiency through the objective onto the sample plane. With this
design innovation, one can achieve illumination power densities up
to 3.times. that for conventional designs over a large
field-of-view (FOV).
[0202] By utilizing the angle-dependent discrimination of s- and
p-polarization, in some instances, the illumination beam
polarization may be orientated to reduce the amount of
back-scattered and back-reflected illumination light that reaches
the imaging sensors.
[0203] Assessing image quality: For any of the embodiments of the
optical imaging designs disclosed herein, imaging performance or
imaging quality may be assessed using any of a variety of
performance metrics known to those of skill in the art. Examples
include, but are not limited to, measurements of modulation
transfer function (MTF) at one or more specified spatial
frequencies, defocus, spherical aberration, chromatic aberration,
coma, astigmatism, field curvature, image distortion,
contrast-to-noise ratio (CNR), or any combination thereof.
[0204] In some instances, the disclosed optical designs for
dual-side imaging (e.g., the disclosed objective lens designs, tube
lens designs, the use of an electro-optical phase plate in
combination with an objective, etc., alone or in combination) may
yield significant improvements for image quality for both the upper
(near) and lower (far) interior surfaces of a flow cell, such that
the difference in an imaging performance metric for imaging the
upper interior surface and the lower interior surface of the flow
cell is less than 20%, less than 15%, less than 10%, less than 5%,
less than 4%, less than 3%, less than 2%, or less than 1% for any
of the imaging performance metrics listed above, either
individually or in combination.
[0205] In some instances, the disclosed optical designs for
dual-side imaging (e.g., comprising the disclosed tube lens
designs, the use of an electro-optical phase plate in combination
with an objective, etc.) may yield significant improvements for
image quality such that an image quality performance metric for
dual-side imaging provides for an at least 1%, at least 2%, at
least 3%, at least 4%, at least 5%, at least 10%, at least 15%, at
least 20%, at least 25%, or at least 30% improvement in the imaging
performance metric for dual-side imaging compared to that for a
conventional system comprising, e.g., an objective lens, a
motion-actuated compensator (that is moved out of or into the
optical path when imaging the near or far interior surfaces of a
flow cell), and an image sensor for any of the imaging performance
metrics listed above, either individually or in combination. In
some instances, fluorescence imaging systems comprising one or more
of the disclosed tube lens designs provides for an at least
equivalent or better improvement in an imaging performance metric
for dual-side imaging compared to that for a conventional system
comprising an objective lens, a motion-actuated compensator, and an
image sensor. In some instances, fluorescence imaging systems
comprising one or more of the disclosed tube lens designs provides
for an at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50%
improvement in an imaging performance metric for dual-side imaging
compared to that for a conventional system comprising an objective
lens, a motion-actuated compensator, and an image sensor.
Imaging Module Specifications:
[0206] Excitation light wavelength(s): In any of the disclosed
optical imaging module designs, the light source(s) of the
disclosed imaging modules may produce visible light, such as green
light and/or red light. In some instances, the light source(s),
alone or in combination with one or more optical components, e.g.,
excitation optical filters and/or dichroic beam splitters, may
produce excitation light at about 350 nm, 375 nm, 400 nm, 425 nm,
450 nm, 475 nm, 500 nm, 525 nm, 550 m, 575 nm, 600 nm, 625 nm, 650
nm, 675 nm, 700 nm, 725 nm, 750 nm, 775 nm, 800 nm, 825 nm, 850 nm,
875 nm, or 900 nm. Those of skill in the art will recognize that
the excitation wavelength may have any value within this range,
e.g., about 620 nm.
[0207] Excitation light bandwidths: In any of the disclosed optical
imaging module designs, the light source(s), alone or in
combination with one or more optical components, e.g., excitation
optical filters and/or dichroic beam splitters, may produce light
at the specified excitation wavelength within a bandwidth of .+-.2
nm, .+-.5 nm, .+-.10 nm, .+-.20 nm, .+-.40 nm, .+-.80 nm, or
greater. Those of skill in the art will recognize that the
excitation bandwidths may have any value within this range, e.g.,
about .+-.18 nm.
[0208] Light source power output: In any of the disclosed optical
imaging module designs, the output of the light source(s) and/or an
excitation light beam derived therefrom (including a composite
excitation light beam) may range in power from about 0.5 W to about
5.0 W, or more (as will be discussed in more detail below). In some
instances, the output of the light source and/or the power of an
excitation light beam derived therefrom may be at least 0.5 W, at
least 0.6 W, at least 0.7 W, at least 0.8 W, at least 1 W, at least
1.1 W, at least 1.2 W, at least 1.3 W, at least 1.4 W, at least 1.5
W, at least 1.6 W, at least 1.8 W, at least 2.0 W, at least 2.2 W,
at least 2.4 W, at least 2.6 W, at least 2.8 W, at least 3.0 W, at
least 3.5 W, at least 4.0 W, at least 4.5 W, or at least 5.0 W. In
some implementations, the output of the light source and/or the
power of an excitation light beam derived therefrom (including a
composite excitation light beam) may be at most 5.0 W, at most 4.5
W, at most 4.0 W, at most 3.5 W, at most 3.0 W, at most 2.8 W, at
most 2.6 W, at most 2.4 W, at most 2.2 W, at most 2.0 W, at most
1.8 W, at most 1.6 W, at most 1.5 W, at most 1.4 W, at most 1.3 W,
at most 1.2 W, at most 1.1 W, at most 1 W, at most 0.8 W, at most
0.7 W, at most 0.6 W, or at most 0.5 W. Any of the lower and upper
values described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the output of the light source and/or the power of an
excitation light beam derived therefrom (including a composite
excitation light beam) may range from about 0.8 W to about 2.4 W.
Those of skill in the art will recognize that the output of the
light source and/or the power of an excitation light beam derived
therefrom (including a composite excitation light beam) may have
any value within this range, e.g., about 1.28 W.
[0209] Light source output power and CNR: In some implementations
of the disclosed optical imaging module designs, the output power
of the light source(s) and/or the power of excitation light beam(s)
derived therefrom (including a composite excitation light beam) is
sufficient, in combination with an appropriate sample, to provide
for a contrast-to-noise ratio (CNR) in images acquired by the
illumination and imaging module of at least 5, at least 10, at
least 15, at least 20, at least 21, at least 22, at least 23, at
least 24, at least 25, at least 30, at least 35, at least 40, or at
least 50 or more, or any CNR within any range formed by any of
these values.
[0210] Fluorescence emission bands: In some instances, the
disclosed fluorescence optical imaging modules may be configured to
detect fluorescence emission produced by any of a variety of
fluorophores known to those of skill in the art. Examples of
suitable fluorescence dyes for use in, e.g., genotyping and nucleic
acid sequencing applications (e.g., by conjugation to nucleotides,
oligonucleotides, or proteins) include, but are not limited to,
fluorescein, rhodamine, coumarin, cyanine, and derivatives thereof,
including the cyanine derivatives cyanine dye-3 (Cy3), cyanine
dye-5 (Cy5), cyanine dye-7 (Cy7), etc.
[0211] Fluorescence emission wavelengths: In any of the disclosed
optical imaging module designs, the detection channel or imaging
channel of the disclosed optical systems may include one or more
optical components, e.g., emission optical filters and/or dichroic
beam splitters, configured to collect emission light at about 350
nm, 375 nm, 400 nm, 425 nm, 450 nm, 475 nm, 500 nm, 525 nm, 550 m,
575 nm, 600 nm, 625 nm, 650 nm, 675 nm, 700 nm, 725 nm, 750 nm, 775
nm, 800 nm, 825 nm, 850 nm, 875 nm, or 900 nm. Those of skill in
the art will recognize that the emission wavelength may have any
value within this range, e.g., about 825 nm.
[0212] Fluorescence emission light bandwidths: In any of the
disclosed optical imaging module designs, the detection channel or
imaging channel may comprise one or more optical components, e.g.,
emission optical filters and/or dichroic beam splitters, configured
to collect light at the specified emission wavelength within a
bandwidth of .+-.2 nm, .+-.5 nm, .+-.10 nm, .+-.20 nm, .+-.40 nm,
.+-.80 nm, or greater. Those of skill in the art will recognize
that the excitation bandwidths may have any value within this
range, e.g., about .+-.18 nm.
[0213] Numerical aperture: In some instances, the numerical
aperture of the objective lens and/or optical imaging module (e.g.,
comprising an objective lens and/or tube lens) in any of the
disclosed optical system designs may range from about 0.1 to about
1.4. In some instances, the numerical aperture may be at least 0.1,
at least 0.2, at least 0.3, at least 0.4, at least 0.5, at least
0.6, at least 0.7, at least 0.8, at least 0.9, at least 1.0, at
least 1.1, at least 1.2, at least 1.3, or at least 1.4. In some
instances, the numerical aperture may be at most 1.4, at most 1.3,
at most 1.2, at most 1.1, at most 1.0, at most 0.9, at most 0.8, at
most 0.7, at most 0.6, at most 0.5, at most 0.4, at most 0.3, at
most 0.2, or at most 0.1. Any of the lower and upper values
described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the numerical aperture may range from about 0.1 to about
0.6. Those of skill in the art will recognize that the numerical
aperture may have any value within this range, e.g., about
0.55.
[0214] Optical resolution: In some instances, depending on the
numerical aperture of the objective lens and/or optical system
(e.g., comprising an objective lens and/or tube lens), the minimum
resolvable spot (or feature) separation distance at the sample
plane achieved by any of the disclosed optical system designs may
range from about 0.5 .mu.m to about 2 .mu.m. In some instances, the
minimum resolvable spot separation distance at the sample plane may
be at least 0.5 .mu.m, at least 0.6 .mu.m, at least 0.7 .mu.m, at
least 0.8 .mu.m, at least 0.9 .mu.m, at least 1.0 .mu.m, at least
1.2 .mu.m, at least 1.4 .mu.m, at least 1.6 .mu.m, at least 1.8
.mu.m, or at least 1.0 .mu.m, In some instances, the minimum
resolvable spot separation distance may be at most 2.0 .mu.m, at
most 1.8 .mu.m, at most 1.6 .mu.m, at most 1.4 .mu.m, at most 1.2
.mu.m, at most 1.0 .mu.m, at most 0.9 .mu.m, at most 0.8 .mu.m, at
most 0.7 .mu.m, at most 0.6 .mu.m, or at most 0.5 .mu.m. Any of the
lower and upper values described in this paragraph may be combined
to form a range included within the present disclosure, for
example, in some instances the minimum resolvable spot separation
distance may range from about 0.8 .mu.m to about 1.6 Those of skill
in the art will recognize that the minimum resolvable spot
separation distance may have any value within this range, e.g.,
about 0.95 .mu.m.
[0215] Optical resolution of first and second surfaces at different
depths: In some instances, the use of the novel objective lens
and/or tube lens designs disclosed herein, in any of the optical
modules or systems disclosed herein, may confer comparable optical
resolution for first and second surfaces (e.g. the upper and lower
interior surfaces of a flow cell) with or without the need to
refocus between acquiring the images of the first and second
surfaces. In some instances, the optical resolution of the images
thus obtained of the first and second surfaces may be with 20%,
18%, 16%, 14%, 12%, 10%, 8%, 6%, 4%, 2%, or 1% of each other, or
within any value within this range.
[0216] Magnification: In some instances, the magnification of the
objective lens and/or tube lens, and/or optical system (e.g.,
comprising an objective lens and/or tube lens) in any of the
disclosed optical configurations may range from about 2.times. to
about 20.times.. In some instances, the optical system
magnification may be at least 2.times., at least 3.times., at least
4.times., at least 5.times., at least 6.times., at least 7.times.,
at least 8.times., at least 9.times., at least 10.times., at least
15.times., or at least 20.times.. In some instances, the optical
system magnification may be at most 20.times., at most 15.times.,
at most 10.times., at most 9.times., at most 8.times., at most
7.times., at most 6.times., at most 5.times., at most 4.times., at
most 3.times., or at most 2.times.. Any of the lower and upper
values described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the optical system magnification may range from about
3.times. to about 10.times.. Those of skill in the art will
recognize that the optical system magnification may have any value
within this range, e.g., about 7.5.times..
[0217] Objective lens focal length: In some implementations of the
disclosed optical designs, the focal length of the objective lens
may range between 20 mm and 40 mm. In some instances, the focal
length of the objective lens may be at least 20 mm, at least 25 mm,
at least 30 mm, at least 35 mm, or at least 40 mm. In some
instances, the focal length of the objective lens may be at most 40
mm, at most 35 mm, at most 30 mm, at most 25 mm, or at most 20 mm.
Any of the lower and upper values described in this paragraph may
be combined to form a range included within the present disclosure,
for example, in some instances the focal length of the objective
lens may range from 25 mm to 35 mm. Those of skill in the art will
recognize that the focal length of the objective lens may have any
value within the range of values specified above, e.g., about 37
mm.
[0218] Objective lens working distance: In some implementations of
the disclosed optical designs, the working distance of the
objective lens may range between about 100 .mu.m and 30 mm. In some
instances, the working distance may be at least 100 .mu.m, at least
200 .mu.m, at least 300 .mu.m, at least 400 .mu.m, at least 500
.mu.m, at least 600 .mu.m, at least 700 .mu.m, at least 800 .mu.m,
at least 900 .mu.m, at least 1 mm, at least 2 mm, at least 4 mm, at
least 6 mm, at least 8 mm, at least 10 mm, at least 15 mm, at least
20 mm, at least 25 mm, or at least 30 mm. In some instances, the
working distance may be at most 30 mm, at most 25 mm, at most 20
mm, at most 15 mm, at most 10 mm, at most 8 mm, at most 6 mm, at
most 4 mm, at most 2 mm, at most 1 mm, at most 900 .mu.m, at most
800 .mu.m, at most 700 .mu.m, at most 600 .mu.m, at most 500 .mu.m,
at most 400 .mu.m, at most 300 .mu.m, at most 200 .mu.m, at most
100 .mu.m. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the working
distance of the objective lens may range from 500 .mu.m to 2 mm.
Those of skill in the art will recognize that the working distance
of the objective lens may have any value within the range of values
specified above, e.g., about 1.25 mm.
[0219] Objectives optimized for imaging through thick coverslips:
In some instances of the disclosed optical designs, the design of
the objective lens may be improved or optimized for a different
coverslip of flow cell thickness. For example, in some instances
the objective lens may be designed for optimal optical performance
for a coverslip that is from about 200 .mu.m to about 1,000 .mu.m
thick. In some instances, the objective lens may be designed for
optimal performance with a coverslip that is at least 200 .mu.m, at
least 300 .mu.m, at least 400 .mu.m, at least 500 .mu.m, at least
600 .mu.m, at least 700 .mu.m, at least 800 .mu.m, at least 900
.mu.m, or at least 1,000 .mu.m thick. In some instances, the
objective lens may be designed for optimal performance with a
coverslip that is at most 1,000 .mu.m, at most 900 .mu.m, at most
800 .mu.m, at most 700 .mu.m, at most 600 .mu.m, at most 500 .mu.m,
at most 400 .mu.m, at most 300 .mu.m, or at most 200 .mu.m thick.
Any of the lower and upper values described in this paragraph may
be combined to form a range included within the present disclosure,
for example, in some instances the objective lens may be designed
for optimal optical performance for a coverslip that may range from
about 300 .mu.m to about 900 .mu.m. Those of skill in the art will
recognize that the objective lens may be designed for optimal
optical performance for a coverslip that may have any value within
this range, e.g., about 725 .mu.m.
[0220] Depth of field and depth of focus: In some instances, the
depth of field and/or depth of focus for any of the disclosed
imaging module (e.g., comprising an objective lens and/or tube
lens) designs may range from about 10 .mu.m to about 800 .mu.m, or
more. In some instances, the depth of field and/or depth of focus
may be at least 10 .mu.m, at least 20 .mu.m, at least 30 .mu.m, at
least 40 .mu.m, at least 50 .mu.m, at least 75 .mu.m, at least 100
.mu.m, at least 125 .mu.m, at least 150 .mu.m, at least 175 .mu.m,
at least 200 .mu.m, at least 250 .mu.m, at least 300 .mu.m, at
least 300 .mu.m, at least 400 .mu.m, at least 500 .mu.m, at least
600 .mu.m, at least 700 .mu.m, or at least 800 .mu.m, or more. In
some instances, the depth of field and/or depth of focus be at most
800 .mu.m, at most 700 .mu.m, at most 600 .mu.m, at most 500 .mu.m,
at most 400 .mu.m, at most 300 .mu.m, at most 250 .mu.m, at most
200 .mu.m, at most 175 .mu.m, at most 150 .mu.m, at most 125 .mu.m,
at most 100 .mu.m, at most 75 .mu.m, at most 50 .mu.m, at most 40
.mu.m, at most 30 .mu.m, at most 20 .mu.m, at most 10 .mu.m, or
less. Any of the lower and upper values described in this paragraph
may be combined to form a range included within the present
disclosure, for example, in some instances the depth of field
and/or depth of focus may range from about 100 .mu.m to about 175
.mu.m. Those of skill in the art will recognize that the depth of
field and/or depth of focus may have any value within the range of
values specified above, e.g., about 132 .mu.m.
[0221] Field of view (FOV): In some implementations, the FOV of any
of the disclosed imaging module designs (e.g., that provided by a
combination of objective lens and detection channel optics (such as
a tube lens)) may range, for example, between about 1 mm and 5 mm
(e.g., in diameter, width, length, or longest dimension). In some
instances, the FOV may be at least 1.0 mm, at least 1.5 mm, at
least 2.0 mm, at least 2.5 mm, at least 3.0 mm, at least 3.5 mm, at
least 4.0 mm, at least 4.5 mm, or at least 5.0 mm (e.g., in
diameter, width, length, or longest dimension). In some instances,
the FOV may be at most 5.0 mm, at most 4.5 mm, at most 4.0 mm, at
most 3.5 mm, at most 3.0 mm, at most 2.5 mm, at most 2.0 mm, at
most 1.5 mm, or at most 1.0 mm (e.g., in diameter, width, length,
or longest dimension). Any of the lower and upper values described
in this paragraph may be combined to form a range included within
the present disclosure, for example, in some instances the FOV may
range from about 1.5 mm to about 3.5 mm (e.g., in diameter, width,
length, or longest dimension). Those of skill in the art will
recognize that the FOV may have any value within the range of
values specified above, e.g., about 3.2 mm (e.g., in diameter,
width, length, or longest dimension).
[0222] Field-of-view (FOV) area: In some instances of the disclosed
optical system designs, the area of the field-of-view may range
from about 2 mm.sup.2 to about 5 mm.sup.2. In some instances, the
field-of-view may be at least 2 mm.sup.2, at least 3 mm.sup.2, at
least 4 mm.sup.2, or at least 5 mm.sup.2 in area. In some
instances, the field-of-view may be at most 5 mm.sup.2, at most 4
mm.sup.2, at most 3 mm.sup.2, or at most 2 mm.sup.2 in area. Any of
the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the field-of-view may range from
about 3 mm.sup.2 to about 4 mm.sup.2 in area. Those of skill in the
art will recognize that the area of the field-of-view may have any
value within this range, e.g., 2.75 mm.sup.2.
[0223] Optimization of objective lens and/or tube lens MTF: In some
instances, the design of the objective lens and/or at least one
tube lens in the disclosed imaging modules and systems is
configured to optimize the modulation transfer function in the mid
to high spatial frequency range. For example, in some instances,
the design of the objective lens and/or at least one tube lens in
the disclosed imaging modules and systems is configured to optimize
the modulation transfer function in the spatial frequency range
from 500 cycles per mm to 900 cycles per mm, from 700 cycles per mm
to 1100 cycles per mm, from 800 cycles per mm to 1200 cycles per
mm, or from 600 cycles per mm to 1000 cycles per mm in the sample
plane.
[0224] Optical aberration and diffraction-limited imaging
performance: In some implementations of any of the optical imaging
module designs disclosed herein, the objective lens and/or tube
lens may be configured to provide the imaging module with a
field-of-view as indicated above such that the FOV has less than
0.15 waves of aberration over at least 60%, 70%, 80%, 90%, or 95%
of the field. In some implementations, the objective lens and/or
tube lens may be configured to provide the imaging module with a
field-of-view as indicated above such that the FOV has less than
0.1 waves of aberration over at least 60%, 70%, 80%, 90%, or 95% of
the field. In some implementations, the objective lens and/or tube
lens may be configured to provide the imaging module with a
field-of-view as indicated above such that the FOV has less than
0.075 waves of aberration over at least 60%, 70%, 80%, 90%, or 95%
of the field. In some implementations, the objective lens and/or
tube lens may be configured to provide the imaging module with a
field-of-view as indicated above such that the FOV is
diffraction-limited over at least 60%, 70%, 80%, 90%, or 95% of the
field.
[0225] Angle of incidence of light beams on dichroic reflectors,
beam splitter, and beam combiners: In some instances of the
disclosed optical designs, the angles of incidence for a light beam
incident on a dichroic reflector, beam splitter, or beam combiner
may range between about 20 degrees and about 45 degrees. In some
instances, the angles of incidence may be at least 20 degrees, at
least 25 degrees, at least 30 degrees, at least 35 degrees, at
least 40 degrees, or at least 45 degrees. In some instances, the
angles of incidence may be at most 45 degrees, at most 40 degrees,
at most 35 degrees, at most 30 degrees, at most 25 degrees, or at
most 20 degrees. Any of the lower and upper values described in
this paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the angles of
incidence may range from about 25 degrees to about 40 degrees.
Those of skill in the art will recognize that the angles of
incidence may have any value within the range of values specified
above, e.g., about 43 degrees.
[0226] Image sensor (photodetector array) size: In some instances,
the disclosed optical systems may comprise image sensor(s) having
an active area with a diagonal ranging from about 10 mm to about 30
mm, or larger. In some instances, the image sensors may have an
active area with a diagonal of at least 10 mm, at least 12 mm, at
least 14 mm, at least 16 mm, at least 18 mm, at least 20 mm, at
least 22 mm, at least 24 mm, at least 26 mm, at least 28 mm, or at
least 30 mm. In some instances, the image sensors may have an
active area with a diagonal of at most 30 mm, at most 28 mm, at
most 26 mm, at most 24 mm, at most 22 mm, at most 20 mm, at most 18
mm, at most 16 mm, at most 14 mm, at most 12 mm, or at most 10 mm.
Any of the lower and upper values described in this paragraph may
be combined to form a range included within the present disclosure,
for example, in some instances the image sensor(s) may have an
active area with a diagonal ranging from about 12 mm to about 24
mm. Those of skill in the art will recognize that the image
sensor(s) may have an active area with a diagonal having any value
within the range of values specified above, e.g., about 28.5
mm.
[0227] Image sensor pixel size and pitch: In some instances, the
pixel size and/or pitch selected for the image sensor(s) used in
the disclosed optical system designs may range in at least one
dimension from about 1 .mu.m to about 10 .mu.m. In some instances,
the pixel size and/or pitch may be at least 1 .mu.m, at least 2
.mu.m, at least 3 .mu.m, at least 4 .mu.m, at least 5 .mu.m, at
least 6 .mu.m, at least 7 .mu.m, at least 8 .mu.m, at least 9
.mu.m, or at least 10 .mu.m. In some instances, the pixel size
and/or pitch may be at most 10 .mu.m, at most 9 .mu.m, at most 8
.mu.m, at most 7 .mu.m, at most 6 .mu.m, at most 5 .mu.m, at most 4
.mu.m, at most 3 .mu.m, at most 2 .mu.m, or at most 1 .mu.m. Any of
the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the pixel size and/or pitch may
range from about 3 .mu.m to about 9 .mu.m. Those of skill in the
art will recognize that the pixel size and/or pitch may have any
value within this range, e.g., about 1.4 .mu.m.
[0228] Oversampling: In some instances of the disclosed optical
designs, a spatial oversampling scheme is utilized wherein the
spatial sampling frequency is at least 2.times., 2.5.times.,
3.times., 3.5.times., 4.times., 4.5.times., 5.times., 6.times.,
7.times., 8.times., 9.times., or 10.times. the optical resolution X
(lp/mm).
[0229] Maximum translation stage velocity: In some instances of the
disclosed optical imaging modules, the maximum translation stage
velocity on any one axis may range from about 1 mm/sec to about 5
mm/sec. In some instances, the maximum translation stage velocity
may be at least 1 mm/sec, at least 2 mm/sec, at least 3 mm/sec, at
least 4 mm/sec, or at least 5 mm/sec. In some instances, the
maximum translation stage velocity may be at most 5 mm/sec, at most
4 mm/sec, at most 3 mm/sec, at most 2 mm/sec, or at most 1 mm/sec.
Any of the lower and upper values described in this paragraph may
be combined to form a range included within the present disclosure,
for example, in some instances the maximum translation stage
velocity may range from about 2 mm/sec to about 4 mm/sec. Those of
skill in the art will recognize that the maximum translation stage
velocity may have any value within this range, e.g., about 2.6
mm/sec.
[0230] Maximum translation stage acceleration: In some instances of
the disclosed optical imaging modules, the maximum acceleration on
any one axis of motion may range from about 2 mm/sec.sup.2 to about
10 mm/sec.sup.2. In some instances, the maximum acceleration may be
at least 2 mm/sec.sup.2, at least 3 mm/sec.sup.2, at least 4
mm/sec.sup.2, at least 5 mm/sec.sup.2, at least 6 mm/sec.sup.2, at
least 7 mm/sec.sup.2, at least 8 mm/sec.sup.2, at least 9
mm/sec.sup.2, or at least 10 mm/sec.sup.2. In some instances, the
maximum acceleration may be at most 10 mm/sec.sup.2, at most 9
mm/sec.sup.2, at most 8 mm/sec.sup.2, at most 7 mm/sec.sup.2, at
most 6 mm/sec.sup.2, at most 5 mm/sec.sup.2, at most 4
mm/sec.sup.2, at most 3 mm/sec.sup.2, or at most 2 mm/sec.sup.2.
Any of the lower and upper values described in this paragraph may
be combined to form a range included within the present disclosure,
for example, in some instances the maximum acceleration may range
from about 2 mm/sec.sup.2 to about 8 mm/sec.sup.2. Those of skill
in the art will recognize that the maximum acceleration may have
any value within this range, e.g., about 3.7 mm/sec.sup.2.
[0231] Translation stage positioning repeatability: In some
instances of the disclosed optical imaging modules, the
repeatability of positioning for any one axis may range from about
0.1 .mu.m to about 2 .mu.m. In some instances, the repeatability of
positioning may be at least 0.1 .mu.m, at least 0.2 .mu.m, at least
0.3 .mu.m, at least 0.4 .mu.m, at least 0.5 .mu.m, at least 0.6
.mu.m, at least 0.7 .mu.m, at least 0.8 .mu.m, at least 0.9 .mu.m,
at least 1.0 .mu.m, at least 1.2 .mu.m, at least 1.4 .mu.m, at
least 1.6 .mu.m, at least 1.8 .mu.m, or at least 2.0 .mu.m. In some
instances, the repeatability of positioning may be at most 2.0
.mu.m, at most 1.8 .mu.m, at most 1.6 .mu.m, at most 1.4 .mu.m, at
most 1.2 .mu.m, at most 1.0 .mu.m, at most 0.9 .mu.m, at most 0.8
.mu.m, at most 0.7 .mu.m, at most 0.6 .mu.m, at most 0.5 .mu.m, at
most 0.4 .mu.m, at most 0.3 .mu.m, at most 0.2 .mu.m, or at most
0.1 .mu.m. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the
repeatability of positioning may range from about 0.3 .mu.m to
about 1.2 Those of skill in the art will recognize that the
repeatability of positioning may have any value within this range,
e.g., about 0.47 .mu.m.
[0232] FOV repositioning time: In some instances of the disclosed
optical imaging modules, the maximum time required to reposition
the sample plane (field-of-view) relative to the optics, or vice
versa, may range from about 0.1 sec to about 0.5 sec. In some
instances, the maximum repositioning time (i.e., the scan stage
step and settle time) may be at least 0.1 sec, at least 0.2 sec, at
least 0.3 sec, at least 0.4 sec, or at least 0.5 sec. In some
instances, the maximum repositioning time may be at most 0.5 sec,
at most 0.4 sec, at most 0.3 sec, at most 0.2 sec, or at most 0.1
sec. Any of the lower and upper values described in this paragraph
may be combined to form a range included within the present
disclosure, for example, in some instances the maximum
repositioning time may range from about 0.2 sec to about 0.4 sec.
Those of skill in the art will recognize that the maximum
repositioning time may have any value within this range, e.g.,
about 0.45 sec.
[0233] Error threshold for autofocus correction: In some instances
of the disclosed optical imaging modules, the specified error
threshold for triggering an autofocus correction may range from
about 50 nm to about 200 nm. In some instances, the error threshold
may be at least 50 nm, at least 75 nm, at least 100 nm, at least
125 nm, at least 150 nm, at least 175 nm, or at least 200 nm. In
some instances, the error threshold may be at most 200 nm, at most
175 nm, at most 150 nm, at most 125 nm, at most 100 nm, at most 75
nm, or at most 50 nm. Any of the lower and upper values described
in this paragraph may be combined to form a range included within
the present disclosure, for example, in some instances the error
threshold may range from about 75 nm to about 150 nm. Those of
skill in the art will recognize that the error threshold may have
any value within this range, e.g., about 105 nm.
[0234] Image acquisition time: In some instances of the disclosed
optical imaging modules, the image acquisition time may range from
about 0.001 sec to about 1 sec. In some instances, the image
acquisition time may be at least 0.001 sec, at least 0.01 sec, at
least 0.1 sec, or at least 1 sec. in some instances, the image
acquisition time may be at most 1 sec, at most 0.1 sec, at most
0.01 sec, or at most 0.001 sec. Any of the lower and upper values
described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the image acquisition time may range from about 0.01 sec
to about 0.1 sec. Those of skill in the art will recognize that the
image acquisition time may have any value within this range, e.g.,
about 0.250 seconds.
[0235] Imaging time per FOV: In some instances, the imaging times
may range from about 0.5 seconds to about 3 seconds per
field-of-view. In some instances, the imaging time may be at least
0.5 seconds, at least 1 second, at least 1.5 seconds, at least 2
seconds, at least 2.5 seconds, or at least 3 seconds per FOV. In
some instances, the imaging time may be at most 3 seconds, at most
2.5 seconds, at most 2 seconds, at most 1.5 seconds, at most 1
second, or at most 0.5 seconds per FOV. Any of the lower and upper
values described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the imaging time may range from about 1 second to about
2.5 seconds. Those of skill in the art will recognize that the
imaging time may have any value within this range, e.g., about 1.85
seconds.
[0236] Flatness of field: In some instances, images across 80%,
90%, 95%, 98%, 99%, or 100% percent of the field-of-view are
acquired within .+-.200 nm, .+-.175 nm, .+-.150 nm, .+-.125 nm,
.+-.100 nm, .+-.75 nm, or .+-.50 nm relative to the best focal
plane for each fluorescence (or other imaging mode) detection
channel.
[0237] Systems and system components for genomics and other
applications: As noted above, in some implementations, the
disclosed optical imaging modules may function as modules,
components, sub-assemblies, or sub-systems of larger systems
configured for performing, e.g., genomics applications (e.g.,
genetic testing and/or nucleic acid sequencing applications) or
other chemical analysis, biochemical analysis, nucleic acid
analysis, cell analysis or tissue analysis applications. In
addition to one, two, three, four, or more than four imaging
modules as disclosed herein (each of which may comprise one or more
illumination optical paths and/or one or more detection optical
paths (e.g., one or more detection channels configured for imaging
fluorescence emission within a specified wavelength range onto an
image sensor)), such systems may comprise one or more X-Y
translation stages, one or more X-Y-Z translation stages, flow
cells or cartridges, fluidics systems and fluid flow control
modules, temperature control modules, fluid dispensing robotics,
cartridge- and/or microplate-handling (pick-and-place) robotics,
light-tight housings and/or environmental control chambers, one or
more processors or computers, data storage modules, data
communication modules (e.g., Bluetooth, WiFi, intranet, or internet
communication hardware and associated software), display modules,
one or more local and/or cloud-based software packages (e.g.,
instrument/system control software packages, image processing
software packages, data analysis software packages), etc., or any
combination thereof.
[0238] Translation stages: In some implementations of the imaging
and analysis systems (e.g., nucleic acid sequencing systems)
disclosed herein, the system may comprise one or more (e.g., one,
two, three, four, or more than four) high precision X-Y (or in some
cases, X-Y-Z) translation stage(s) for re-positioning one or more
sample support structure(s) (e.g., flow cell(s)) in relation to the
one or more imaging modules, for example, in order to tile one or
more images, each corresponding to a field-of-view of the imaging
module, to reconstruct composite image(s) of an entire flow cell
surface. In some implementations of the imaging systems and
genomics analysis systems (e.g., nucleic acid sequencing systems)
disclosed herein, the system may comprise one or more (e.g., one,
two, three, four, or more than four) high precision X-Y (or in some
cases, X-Y-Z) translation stage(s) for re-positioning the one or
more imaging modules in relation to one or more sample support
structure(s) (e.g., flow cell(s)), for example, in order to tile
one or more images, each corresponding to a field-of-view of the
imaging module, to reconstruct composite image(s) of an entire flow
cell surface.
[0239] Suitable translation stages are commercially available from
a variety of vendors, for example, Parker Hannifin. Precision
translation stage systems typically comprise a combination of
several components including, but not limited to, linear actuators,
optical encoders, servo and/or stepper motors, and motor
controllers or drive units. High precision and repeatability of
stage movement is required for the systems and methods disclosed
herein in order to ensure accurate and reproducible positioning and
imaging of, e.g., fluorescence signals when interspersing repeated
steps of reagent delivery and optical detection.
[0240] Consequently, the systems disclosed herein may comprise
specifying the precision with which the translation stage is
configured to position a sample support structure in relation to
the illumination and/or imaging optics (or vice versa). In one
aspect of the present disclosure, the precision of the one or more
translation stages is between about 0.1 .mu.m and about 10 .mu.m.
In other aspects, the precision of the translation stage is about
10 .mu.m or less, about 9 .mu.m or less, about 8 .mu.m or less,
about 7 .mu.m or less, about 6 .mu.m or less, about 5 .mu.m or
less, about 4 .mu.m or less, about 3 .mu.m or less, about 2 .mu.m
or less, about 1 .mu.m or less, about 0.9 .mu.m or less, about 0.8
.mu.m or less, about 0.7 .mu.m or less, about 0.6 .mu.m or less,
about 0.5 .mu.m or less, about 0.4 .mu.m or less, about 0.3 .mu.m
or less, about 0.2 .mu.m or less, or about 0.1 .mu.m or less. Those
of skill in the art will appreciate that, in some instances, the
positioning precision of the translation stage may fall within any
range bounded by any of two of these values (e.g. from about 0.5
.mu.m to about 1.5 .mu.m). In some instances, the positioning
precision of the translation stage may have any value within the
range of values included in this paragraph, e.g., about 0.12
.mu.m.
[0241] Flow cells, microfluidic devices, and cartridges: The flow
cell devices and flow cell cartridges disclosed herein may be used
as components of systems designed for a variety of chemical
analysis, biochemical analysis, nucleic acid analysis, cell
analysis, or tissue analysis application. In general, such systems
may comprise one or more one or more of the disclosed single
capillary flow cell devices, multiple capillary flow cell devices,
capillary flow cell cartridges, and/or microfluidic devices and
cartridges described herein. Additional description of the
disclosed flow cell devices and cartridges may be found in PCT
Patent Application Publication WO 2020/118255, which is
incorporated herein by reference in its entirety.
[0242] In some instances, the systems disclosed herein may comprise
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 single capillary
flow cell devices, multiple capillary flow cell devices, capillary
flow cell cartridges, and/or microfluidic devices and cartridges.
In some instances, the single capillary flow cell devices, multiple
capillary flow cell devices, and/or microfluidic devices and
cartridges may be fixed components of the disclosed systems. In
some instances, the single capillary flow cell devices, multiple
capillary flow cell devices, and/or microfluidic devices and
cartridges may be removable, exchangeable components of the
disclosed systems. In some instances, the single capillary flow
cell devices, multiple capillary flow cell devices, and/or
microfluidic devices and cartridges may be disposable or consumable
components of the disclosed systems.
[0243] In some implementations, the disclosed single capillary flow
cell devices (or single capillary flow cell cartridges) comprise a
single capillary, e.g., a glass or fused-silica capillary, the
lumen of which forms a fluid flow path through which reagents or
solutions may flow, and the interior surface of which may form a
sample support structure to which samples of interest are bound or
tethered. In some implementations, the multi-capillary capillary
flow cell devices (or multi-capillary flow cell cartridges)
disclosed herein may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, or more than 20 capillaries
configured for performing an analysis technique that further
comprises imaging as a detection method.
[0244] In some instances, one or more capillaries may be packaged
within a chassis to form a cartridge that facilitates
ease-of-handling, incorporates adapters or connectors for making
external fluid connections, and may optionally include additional
integrated functionality such as reagent reservoirs, waste
reservoirs, valves (e.g., microvalves), pumps (e.g., micropumps),
etc., or any combination thereof.
[0245] FIG. 29 illustrates one non-limiting example of a single
glass capillary flow cell device that comprises two fluidic
adaptors--one affixed to each end of the piece of glass
capillary--that are designed to mate with standard OD fluidic
tubing to provide for convenient, interchangeable fluid connections
with an external fluid flow control system. The fluidic adaptors
can be attached to the capillary using any of a variety of
techniques known to those of skill in the art including, but not
limited to, press fit, adhesive bonding, solvent bonding, laser
welding, etc., or any combination thereof.
[0246] In general, the capillaries used in the disclosed capillary
flow cell devices and capillary flow cell cartridges will have at
least one internal, axially-aligned fluid flow channel (or "lumen")
that runs the full length of the capillary. In some instances, the
capillary may have two, three, four, five, or more than five
internal, axially-aligned fluid flow channels (or "lumen").
[0247] A number specified cross-sectional geometries for suitable
capillaries (or the lumen thereof) are consistent with the
disclosure herein including, but not limited to, circular,
elliptical, square, rectangular, triangular, rounded square,
rounded rectangular, or rounded triangular cross-sectional
geometries. In some instances, the capillary (or lumen thereof) may
have any specified cross-sectional dimension or set of dimensions.
For example, in some instances the largest cross-sectional
dimension of the capillary lumen (e.g. the diameter if the lumen is
circular in shape, or the diagonal if the lumen is square or
rectangular in shape) may range from about 10 .mu.m to about 10 mm.
In some aspects, the largest cross-sectional dimension of the
capillary lumen may be at least 10 .mu.m, at least 25 .mu.m, at
least 50 .mu.m, at least 75 .mu.m, at least 100 .mu.m, at least 200
.mu.m, at least 300 .mu.m, at least 400 .mu.m, at least 500 .mu.m,
at least 600 .mu.m, at least 700 .mu.m, at least 800 .mu.m, at
least 900 .mu.m, at least 1 mm, at least 2 mm, at least 3 mm, at
least 4 mm, at least 5 mm, at least 6 mm, at least 7 mm, at least 8
mm, at least 9 mm, or at least 10 mm. In some aspects, the largest
cross-sectional dimension of the capillary lumen may be at most 10
mm, at most 9 mm, at most 8 mm, at most 7 mm, at most 6 mm, at most
5 mm, at most 4 mm, at most 3 mm, at most 2 mm, at most 1 mm, at
most 900 .mu.m, at most 800 .mu.m, at most 700 .mu.m, at most 600
.mu.m, at most 500 .mu.m, at most 400 .mu.m, at most 300 .mu.m, at
most 200 .mu.m, at most 100 .mu.m, at most 75 .mu.m, at most 50
.mu.m, at most 25 .mu.m, or at most 10 .mu.m. Any of the lower and
upper values described in this paragraph may be combined to form a
range included within the present disclosure, for example, in some
instances the largest cross-sectional dimension of the capillary
lumen may range from about 100 .mu.m to about 500 .mu.m. Those of
skill in the art will recognize that the largest cross-sectional
dimension of the capillary lumen may have any value within this
range, e.g., about 124 .mu.m.
[0248] In some instances, e.g., wherein the lumen of the one or
more capillaries in a flow cell device or cartridge has a square or
rectangular cross-section, the distance between a first interior
surface (e.g., a top or upper surface) and a second interior
surface (e.g., a bottom or lower surface) that defines the gap
height or thickness of a fluid flow channel may range from about 10
.mu.m to about 500 .mu.m. In some instances, the gap height may be
at least 10 .mu.m, at least 20 .mu.m, at least 30 .mu.m, at least
40 .mu.m, at least 50 .mu.m, at least 60 .mu.m, at least 70 .mu.m,
at least 80 .mu.m, at least 90 .mu.m, at least 100 .mu.m, at least
125 .mu.m, at least 150 .mu.m, at least 175 .mu.m, at least 200
.mu.m, at least 225 .mu.m, at least 250 .mu.m, at least 275 .mu.m,
at least 300 .mu.m, at least 325 .mu.m, at least 350 .mu.m, at
least 375 .mu.m, at least 400 .mu.m, at least 425 .mu.m, at least
450 .mu.m, at least 475 .mu.m, or at least 500 .mu.m. In some
instances, the gap height may be at most 500 .mu.m, at most 475
.mu.m, at most 450 .mu.m, at most 425 .mu.m, at most 400 .mu.m, at
most 375 .mu.m, at most 350 .mu.m, at most 325 .mu.m, at most 300
.mu.m, at most 275 .mu.m, at most 250 .mu.m, at most 225 .mu.m, at
most 200 .mu.m, at most 175 .mu.m, at most 150 .mu.m, at most 125
.mu.m, at most 100 .mu.m, at most 90 .mu.m, at most 80 .mu.m, at
most 70 .mu.m, at most 60 .mu.m, at most 50 .mu.m, at most 40
.mu.m, at most 30 .mu.m, at most 20 .mu.m, or most 10 .mu.m. Any of
the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the gap height may range from about
40 .mu.m to about 125 .mu.m. Those of skill in the art will
recognize that the gap height may have any value within the range
of values in this paragraph, e.g., about 122 .mu.m.
[0249] In some instances, the length of the one or more capillaries
used to fabricate the disclosed capillary flow cell devices or flow
cell cartridges may range from about 5 mm to about 5 cm or greater.
In some instances, the length of the one or more capillaries may be
less than 5 mm, at least 5 mm, at least 1 cm, at least 1.5 cm, at
least 2 cm, at least 2.5 cm, at least 3 cm, at least 3.5 cm, at
least 4 cm, at least 4.5 cm, or at least 5 cm. In some instances,
the length of the one or more capillaries may be at most 5 cm, at
most 4.5 cm, at most 4 cm, at most 3.5 cm, at most 3 cm, at most
2.5 cm, at most 2 cm, at most 1.5 cm, at most 1 cm, or at most 5
mm. Any of the lower and upper values described in this paragraph
may be combined to form a range included within the present
disclosure, for example, in some instances the length of the one or
more capillaries may range from about 1.5 cm to about 2.5 cm. Those
of skill in the art will recognize that the length of the one or
more capillaries may have any value within this range, e.g., about
1.85 cm. In some instances, devices or cartridges may comprise a
plurality of two or more capillaries that are the same length. In
some instances, devices or cartridges may comprise a plurality of
two or more capillaries that are of different lengths.
[0250] The capillaries used for constructing the disclosed
capillary flow cell devices or capillary flow cell cartridges may
be fabricated from any of a variety of materials known to those of
skill in the art including, but not limited to, glass (e.g.,
borosilicate glass, soda lime glass, etc.), fused silica (quartz),
polymer (e.g., polystyrene (PS), macroporous polystyrene (MPPS),
polymethylmethacrylate (PMMA), polycarbonate (PC), polypropylene
(PP), polyethylene (PE), high density polyethylene (HDPE), cyclic
olefin polymers (COP), cyclic olefin copolymers (COC), polyethylene
terephthalate (PET), polydimethylsiloxane (PDMS), etc.),
polyetherimide (PEI) and perfluoroelastomer (FFKM) as more
chemically inert alternatives, or any combination thereof. PEI is
somewhere between polycarbonate and PEEK in terms of both cost and
chemical compatibility. FFKM is also known as Kalrez.
[0251] The one or more materials used to fabricate the capillaries
are often optically transparent to facilitate use with
spectroscopic or imaging-based detection techniques. In some
instances, the entire capillary will be optically transparent.
Alternately, in some instances, only a portion of the capillary
(e.g., an optically transparent "window") will be optically
transparent.
[0252] The capillaries used for constructing the disclosed
capillary flow cell devices and capillary flow cell cartridges may
be fabricated using any of a variety of techniques known to those
of skill in the art, where the choice of fabrication technique is
often dependent on the choice of material used, and vice versa.
Examples of suitable capillary fabrication techniques include, but
are not limited to, extrusion, drawing, precision computer
numerical control (CNC) machining and boring, laser photoablation,
and the like.
[0253] In some implementations, the capillaries used in the
disclosed capillary flow cell devices and cartridges may be
off-the-shelf commercial products. Examples of commercial vendors
that provide precision capillary tubing include Accu-Glass (St.
Louis, Mo.; precision glass capillary tubing), Polymicro
Technologies (Phoenix, Ariz.; precision glass and fused-silica
capillary tubing), Friedrich & Dimmock, Inc. (Millville, N.J.;
custom precision glass capillary tubing), and Drummond Scientific
(Broomall, Pa.; OEM glass and plastic capillary tubing).
[0254] The fluidic adapters that are attached to the capillaries of
the capillary flow cell devices and cartridges disclosed herein,
and other components of the capillary flow cell devices or
cartridges, may be fabricated using any of a variety of suitable
techniques (e.g., extrusion molding, injection molding, compression
molding, precision CNC machining, etc.) and materials (e.g., glass,
fused-silica, ceramic, metal, polydimethylsiloxane, polystyrene
(PS), macroporous polystyrene (MPPS), polymethylmethacrylate
(PMMA), polycarbonate (PC), polypropylene (PP), polyethylene (PE),
high density polyethylene (HDPE), cyclic olefin polymers (COP),
cyclic olefin copolymers (COC), polyethylene terephthalate (PET),
etc.), where again the choice of fabrication technique is often
dependent on the choice of material used, and vice versa.
[0255] FIG. 30 provides a non-limiting example of capillary flow
cell cartridge that comprises two glass capillaries, fluidic
adaptors (two per capillary in this example), and a cartridge
chassis that mates with the capillaries and/or fluidic adapters
such that the capillaries are held in a fixed orientation relative
to the cartridge. In some instances, the fluidic adaptors may be
integrated with the cartridge chassis. In some instances, the
cartridge may comprise additional adapters that mate with the
capillaries and/or capillary fluidic adapters. As noted elsewhere
herein, in some instances, the cartridge may comprise additional
functional components. In some instances, the capillaries are
permanently mounted in the cartridge. In some instances, the
cartridge chassis is designed to allow one or more capillaries of
the flow cell cartridge to be interchangeable removed and replaced.
For example, in some instances, the cartridge chassis may comprise
a hinged "clamshell" configuration which allows it to be opened so
that one or more capillaries may be removed and replaces. In some
instances, the cartridge chassis is configured to mount on, for
example, the stage of a fluorescence microscope or within a
cartridge holder of a fluorescence imaging module or instrument
system of the present disclosure.
[0256] In some instances, the disclosed flow cell devices may
comprise microfluidic devices (or "microfluidic chips") and
cartridges, where the microfluidic devices are fabricated by
forming fluid channels in one or more layers of a suitable material
and comprise one or more fluid channels (e.g., "analysis" channels)
configured for performing an analysis technique that further
comprises imaging as a detection method. In some implementations,
the microfluidic devices or cartridges disclosed herein may
comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, or more than 20 fluid channels (e.g., "analysis" fluid
channels) configured for performing an analysis technique that
further comprises imaging as a detection method. In some instances,
the disclosed microfluidic devices may further comprise additional
fluid channels (e.g., for dilution or mixing of reagents), reagent
reservoirs, waste reservoirs, adapters for making external fluid
connections, and the like, to provide integrated "lab-on-a-chip"
functionality within the device.
[0257] A non-limiting example of microfluidic flow cell cartridge
comprises a chip having two or more parallel glass channels formed
on the chip, fluidic adaptors coupled to the chip, and a cartridge
chassis that mates with the chip and/or fluidic adapters such that
the chip is posited in a fixed orientation relative to the
cartridge. In some instances, the fluidic adaptors may be
integrated with the cartridge chassis. In some instances, the
cartridge may comprise additional adapters that mate with the chip
and/or fluidic adapters. In some instances, the chip is permanently
mounted in the cartridge. In some instances, the cartridge chassis
is designed to allow one or more chips of the flow cell cartridge
to be interchangeably removed and replaced. For example, in some
instances, the cartridge chassis may comprise a hinged "clamshell"
configuration which allows it to be opened so that one or more
chips may be removed and replaces. In some instances, the cartridge
chassis is configured to mount on, for example, the stage of a
microscope system or within a cartridge holder of an imaging
system. Even through only one chip is described in the non-limiting
example, it is understood that more than one chip can be used in
the microfluidic flow cell cartridge. The flow cell cartridges of
the present disclosure may comprise a single microfluidic chip or a
plurality of microfluidic chips. In some instances, the flow cell
cartridges of the present disclosure may comprise 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than 20
microfluidic chips. The packaging of one or more microfluidic
devices within a cartridge may facilitate ease-of-handling and
correct positioning of the device within the optical imaging
system.
[0258] The fluid channels within the disclosed microfluidic devices
and cartridges may have an of a variety of cross-sectional
geometries including, but not limited to, circular, elliptical,
square, rectangular, triangular, rounded square, rounded
rectangular, or rounded triangular cross-sectional geometries. In
some instances, the fluid channels may have any specified
cross-sectional dimension or set of dimensions. For example, in
some instances, the height (e.g., gap height), width, or largest
cross-sectional dimension of the fluid channels (e.g., the diagonal
if the fluid channel has a square, rounded square, rectangular, or
rounded rectangular cross-section) may range from about 10 .mu.m to
about 10 mm. In some aspects, the height (e.g., gap height), width,
or largest cross-sectional dimension of the fluid channels may be
at least 10 .mu.m, at least 25 .mu.m, at least 50 .mu.m, at least
75 .mu.m, at least 100 .mu.m, at least 200 .mu.m, at least 300
.mu.m, at least 400 .mu.m, at least 500 .mu.m, at least 600 .mu.m,
at least 700 .mu.m, at least 800 .mu.m, at least 900 .mu.m, at
least 1 mm, at least 2 mm, at least 3 mm, at least 4 mm, at least 5
mm, at least 6 mm, at least 7 mm, at least 8 mm, at least 9 mm, or
at least 10 mm. In some aspects, the height (e.g., gap height),
width, or largest cross-sectional dimension of the fluid channels
may be at most 10 mm, at most 9 mm, at most 8 mm, at most 7 mm, at
most 6 mm, at most 5 mm, at most 4 mm, at most 3 mm, at most 2 mm,
at most 1 mm, at most 900 .mu.m, at most 800 .mu.m, at most 700
.mu.m, at most 600 .mu.m, at most 500 .mu.m, at most 400 .mu.m, at
most 300 .mu.m, at most 200 .mu.m, at most 100 .mu.m, at most 75
.mu.m, at most 50 .mu.m, at most 25 .mu.m, or at most 10 .mu.m. Any
of the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the height (e.g., gap height),
width, or largest cross-sectional dimension of the fluid channels
may range from about 20 .mu.m to about 200 .mu.m. Those of skill in
the art will recognize that the height (e.g., gap height), width,
or largest cross-sectional dimension of the fluid channels may have
any value within this range, e.g., about 122 .mu.m.
[0259] In some instances, the length of the fluid channels in the
disclosed microfluidic devices and cartridges may range from about
5 mm to about 10 cm or greater. In some instances, the length of
the fluid channels may be less than 5 mm, at least 5 mm, at least 1
cm, at least 1.5 cm, at least 2 cm, at least 2.5 cm, at least 3 cm,
at least 3.5 cm, at least 4 cm, at least 4.5 cm, at least 5 cm, at
least 6 cm, at least 7 cm, at least 8 cm, at least 9 cm, or at
least 10 cm. In some instances, the length of the fluid channels
may be at most 10 cm, at most 9 cm, at most 8 cm, at most 7 cm, at
most 6 cm, at most 5 cm, at most 4.5 cm, at most 4 cm, at most 3.5
cm, at most 3 cm, at most 2.5 cm, at most 2 cm, at most 1.5 cm, at
most 1 cm, or at most 5 mm. Any of the lower and upper values
described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the length of the fluid channels may range from about 1.5
cm to about 2.5 cm. Those of skill in the art will recognize that
the length of the fluid channels may have any value within this
range, e.g., about 1.35 cm. In some instances, the microfluidic
devices or cartridges may comprise a plurality of fluid channels
that are the same length. In some instances, the microfluidic
devices or cartridges may comprise a plurality of fluid channels
that are of different lengths.
[0260] The disclosed microfluidic devices will comprise at least
one layer of material having one or more fluid channels formed
therein. In some instances, the microfluidic chip may include two
layers bonded together to form one or more fluid channels. In some
instances, the microfluidic chip may include three or more layers
bonded together to form one or more fluid channels. In some
instances, the microfluidic fluid channels may have an open top. In
some instances, the microfluidic fluid channels may be fabricated
within one layer, e.g., the top surface of a bottom layer, and
sealed by bonding the top surface of the bottom layer to the bottom
surface of a top layer of material. In some instances, the
microfluidic channels may be fabricated within one layer, e.g., as
patterned channels the depth of which extends through the full
thickness of the layer, which is then sandwiched between and bonded
to two non-patterned layers to seal the fluid channels. In some
instances, the microfluidic channels are fabricated by the removal
of a sacrificial layer on the surface of a substrate. This method
does not require the bulk substrate (e.g., a glass or silicon
wafer) to be etched away. Instead, the fluid channels are located
on the surface of the substrate. In some instances, the
microfluidic channels may be fabricated in or on the surface of a
substrate and then sealed by deposition of a conformal film or
layer on the surface of the substrate to create sub-surface or
buried fluid channels in the chip.
[0261] The microfluidic chips can be manufactured using a
combination of microfabrication processes. Because the devices are
microfabricated, substrate materials will typically be selected
based upon their compatibility with known microfabrication
techniques, e.g., photolithography, wet chemical etching, laser
ablation, laser irradiation, air abrasion techniques, injection
molding, embossing, and other techniques. The substrate materials
are also generally selected for their compatibility with the full
range of conditions to which the microfluidic devices may be
exposed, including extremes of pH, temperature, salt concentration,
and application of electromagnetic (e.g. light) or electric
fields.
[0262] The disclosed microfluidic chips may be fabricated from any
of a variety of materials known to those of skill in the art
including, but not limited to, glass (e.g., borosilicate glass,
soda lime glass, etc.), fused-silica (quartz), silicon, a polymer
(e.g., polystyrene (PS), macroporous polystyrene (MPPS),
polymethylmethacrylate (PMMA), polycarbonate (PC), polypropylene
(PP), polyethylene (PE), high density polyethylene (HDPE), cyclic
olefin polymers (COP), cyclic olefin copolymers (COC), polyethylene
terephthalate (PET), polydimethylsiloxane (PDMS), etc.),
polyetherimide (PEI) and perfluoroelastomer (FFKM) (as more
chemically inert alternatives), or any combination thereof. In some
preferred instances, the substrate material(s) may include
silica-based substrates, such as borosilicate glass, and quartz, as
well as other substrate materials.
[0263] The disclosed microfluidic devices may be fabricated using
any of a variety of techniques known to those of skill in the art,
where the choice of fabrication technique is often dependent on the
choice of material used, and vice versa. The microfluidic channels
on the chip can be constructed using techniques suitable for
forming micro-structures or micro-patterns on the surface of a
substrate. In some instances, the fluid channels are formed by
laser irradiation. In some instances, the microfluidic channels are
formed by focused femtosecond laser radiation. In some instances,
the microfluidic channels are formed by photolithography and
etching including, but not limited to, chemical etching, plasma
etching, or deep reactive ion etching. In some instances, the
microfluidic channels are formed using laser etching. In some
instances, the microfluidic channels are formed using a
direct-write lithography technique. Examples of direct-write
lithography include electron beam direct-write and focused ion beam
milling.
[0264] In additional preferred instances, the substrate material(s)
may comprise polymeric materials, e.g., plastics, such as
polymethylmethacrylate (PMMA), polycarbonate,
polytetrafluoroethylene (TEFLON.TM.), polyvinylchloride (PVC),
polydimethylsiloxane (PDMS), polysulfone, and the like. Such
polymeric substrates may be readily patterned or micromachined
using available microfabrication techniques, such as those
described above. In some instances, microfluidic chips may be
fabricated from polymeric materials, e.g., from microfabricated
masters, using well known molding techniques, such as injection
molding, embossing, stamping, or by polymerizing the polymeric
precursor material within a mold (see, e.g., U.S. Pat. No.
5,512,131). In some instances, such polymeric substrate materials
are preferred for their ease of manufacture, low cost, and
disposability, as well as their general inertness to most extreme
reaction conditions. As with flow cell devices fabricated from
other materials, e.g., glass, flow cell devices fabricated from
these polymeric materials may include treated surfaces, e.g.,
derivatized or coated surfaces, to enhance their utility in the
microfluidic system, as will be discussed in more detail below.
[0265] The fluid channels and/or fluid chambers of the microfluidic
devices are typically fabricated into the upper surface of a first
substrate as microscale channels (e.g., grooves, indentations,
etc.) using the above described microfabrication techniques. The
first substrate comprises a top side having a first planar surface
and a bottom side. In the microfluidic devices prepared in
accordance with the methods described herein, the plurality of
fluid channels (e.g., grooves and/or indentations) are formed on
the first planar surface. In some instances, the fluid channels
(e.g., grooves and/or indentations) formed in the first planar
surface (prior to bonding to a second substrate) have a bottom and
side walls, with the top remaining open. In some instances, the
fluid channels (e.g., grooves and/or indentations) formed in the
first planar surface (prior to bonding to a second substrate) have
a bottom and side walls and the top remaining closed. In some
instances, the fluid channels (e.g., grooves and/or indentations)
formed in the first planar surfaces (prior to bonding to a second
substrate) have only side walls and no top or bottom surface (i.e.,
the fluid channels span the full thickness of the first
substrate.
[0266] Fluid channels and chambers may be sealed by placing the
first planar surface of the first substrate in contact with, and
bonding to, the planar surface of a second substrate to form the
channels and/or chambers (e.g., the interior portion) of the device
at the interface of these two components. In some instances, after
the first substrate is bonded to a second substrate, the structure
may further be placed in contact with and bonded to a third
substrate. In some instances, the third substrate may be placed in
contact with the side of the first substrate that is not in contact
with the second substrate. In some instances, the first substrate
is placed between the second substrate and the third substrate. In
some instances, the second substrate and the third substrate can
cover and/or seal the grooves, indentations, or apertures formed on
the first substrate to form the channels and/or chambers (e.g., the
interior portion) of the device at the interface of these
components.
[0267] The device can have openings that are oriented such that
they are in fluid communication with at least one of the fluid
channels and/or fluid chambers formed in the interior portion of
the device, thereby forming fluid inlets and/or fluid outlets. In
some instances, the openings are formed on the first substrate. In
some instances, the openings are formed on the first and the second
substrate. In some instances, the openings are formed on the first,
the second, and the third substrate. In some instances, the
openings are positioned at the top side of the device. In some
instances, the openings are positioned at the bottom side of the
device. In some instances, the openings are positioned at the first
and/or the second ends of the device, and the channels run along
the direction from the first end to the second end.
[0268] Conditions under which substrates may be bonded together are
generally widely understood by those of skill in the art, and such
bonding of substrates is generally carried out by any of a variety
of methods, the choice of which may vary depending upon the nature
of the substrate materials used. For example, thermal bonding of
substrates may be applied to a number of substrate materials
including, e.g., glass or silica-based substrates, as well as some
polymer based-substrates. Such thermal bonding techniques typically
comprise mating the substrate surfaces that are to be bonded under
conditions of elevated temperature and, in some cases, application
of external pressure. The precise temperatures and pressures
utilized will generally vary depending upon the nature of the
substrate materials used.
[0269] For example, for silica-based substrate materials, i.e.,
glass (borosilicate glass, Pyrex.TM., soda lime glass, etc.),
fused-silica (quartz), and the like, thermal bonding of substrates
is typically carried out at temperatures ranging from about
500.degree. C. to about 1400.degree. C., and preferably, from about
500.degree. C. to about 1200.degree. C. For example, soda lime
glass is typically bonded at temperatures of around 550.degree. C.,
whereas borosilicate glass is typically thermally bonded at or near
800.degree. C. Quartz substrates, on the other hand, are typically
thermally bonded at temperatures at or near 1200.degree. C. These
bonding temperatures are typically achieved by placing the
substrates to be bonded into high temperature annealing ovens.
[0270] Polymeric substrates that are thermally bonded, on the other
hand, will typically utilize lower temperatures and/or pressures
than silica-based substrates, in order to prevent excessive melting
of the substrates and/or distortion, e.g., flattening of the
interior portion of the device (i.e., the fluid channels or
chambers). Generally, such elevated temperatures for bonding
polymeric substrates will vary from about 80.degree. C. to about
200.degree. C., depending upon the polymeric material used, and
will preferably be between about 90.degree. C. and about
150.degree. C. Because of the significantly reduced temperatures
required for bonding polymeric substrates, such bonding may
typically be carried out without the need for the high temperature
ovens used in the bonding of silica-based substrates. This allows
incorporation of a heat source within a single integrated bonding
system, as described in greater detail below.
[0271] Adhesives may also be used to bond substrates together
according to well-known methods, which typically comprise applying
a layer of adhesive between the substrates that are to be bonded
and pressing them together until the adhesive sets. A variety of
adhesives may be used in accordance with these methods, including,
e.g., UV curable adhesives, that are commercially available.
Alternative methods may also be used to bond substrates together in
accordance with the present invention, including e.g., acoustic or
ultrasonic welding and/or solvent welding of polymeric parts.
[0272] Typically, a number of the described microfluidic chips or
devices will be manufactured at the same time, e.g., using
"wafer-scale" fabrication. For example, polymeric substrates may be
stamped or molded in large separable sheets which can then be mated
and bonded together. Individual devices or bonded substrates may
then be separated from the larger sheet by cutting or dicing.
Similarly, for silica-based substrates, individual devices can be
fabricated from larger substrate wafers or plates, allowing higher
throughput of the manufacturing process. Specifically, a plurality
of fluid channel structures can be fabricated on a first substrate
wafer or plate, which is then overlaid with and bonded to a second
substrate wafer or plate, and optionally further overlaid with and
bonded to a third substrate wafer or plate. The individual devices
are then segmented from the larger substrates using known methods,
such as sawing, scribing and breaking, and the like.
[0273] As noted above, the top or second substrate is overlaid upon
the bottom or first substrate to seal the various channels and
chambers. In carrying out the bonding process according to the
methods of the present disclosure, the bonding of the first and
second substrates may be carried out using vacuum and/or pressure
to maintain the two substrate surfaces in optimal contact. In
particular, the bottom substrate may be maintained in optimal
contact with the top substrate by, e.g., mating the planar surface
of the bottom substrate with the planar surface of the top
substrate and applying a vacuum through holes that are disposed
through the top substrate. Typically, application of a vacuum to
holes in the top substrate is carried out by placing the top
substrate on a vacuum chuck, which typically comprises a mounting
table or surface, having an integrated vacuum source. In the case
of silica-based substrates, the bonded substrates are subjected to
elevated temperatures in order to create an initial bond, so that
the bonded substrates may then be transferred to the annealing
oven, without any shifting relative to each other.
[0274] Alternate bonding systems for incorporation with the
apparatus described herein include, e.g., adhesive dispensing
systems, for applying adhesive layers between the two planar
surfaces of the substrates. This may be done by applying the
adhesive layer prior to mating the substrates, or by placing an
amount of the adhesive at one edge of the adjoining substrates and
allowing the wicking action of the two mated substrates to draw the
adhesive across the space between the two substrates.
[0275] In certain instances, the overall bonding system can include
automatable systems for placing the top and bottom substrates on
the mounting surface and aligning them for subsequent bonding.
Typically, such systems include translation systems for moving
either the mounting surface or one or more of the top and bottom
substrates relative to each other. For example, robotic systems may
be used to lift, translate and place each of the top and bottom
substrates upon the mounting table, and within the alignment
structures, in turn. Following the bonding process, such systems
also can remove the finished product from the mounting surface and
transfer these mated substrates to a subsequent operation, e.g., a
separation or dicing operation, an annealing oven for silica-based
substrates, etc., prior to placing additional substrates thereon
for bonding.
[0276] In some instances, the manufacturing of the microfluidic
chip includes the layering or laminating of two or more layers of
substrate, e.g., patterned and non-patterned polymeric sheets, in
order to produce the chip. For example, in microfluidic devices,
the microfluidic features of the device are typically produced by
laser irradiation, etching, or otherwise fabricating features into
the surface of a first layer. A second layer is then laminated or
bonded to the surface of the first to seal these features and
provide the fluidic elements of the device, e.g., the fluid
channels.
[0277] As noted above, in some instances one or more capillary flow
cell devices or microfluidic chips may be mounted in a cartridge
chassis to form a capillary flow cell cartridge or microfluidic
cartridge. In some instances, the capillary flow cell cartridge or
microfluidic cartridge may further comprise additional components
that are integrated with the cartridge to provide enhanced
performance for specific applications. Examples of additional
components that may be integrated into the cartridge include, but
are not limited to, adapters or connectors for making fluidic
connections to other components of the system, fluid flow control
components (e.g., miniature valves, miniature pumps, mixing
manifolds, etc.), temperature control components (e.g., resistive
heating elements, metal plates that serve as heat sources or sinks,
piezoelectric (Peltier) devices for heating or cooling, temperature
sensors), or optical components (e.g., optical lenses, windows,
filters, mirrors, prisms, fiber optics, and/or light-emitting
diodes (LEDs) or other miniature light sources that may
collectively be used to facilitate spectroscopic measurements
and/or imaging of one or more capillary or fluid flow channels.
[0278] The fluidic adaptors, cartridge chassis, and other cartridge
components may be attached to the capillaries, capillary flow cell
device(s), microfluidic chip(s) (or fluid channels within the chip)
using any of a variety of techniques known to those of skill in the
art including, but not limited to, press fit, adhesive bonding,
solvent bonding, laser welding, etc., or any combination thereof.
In some instances, the inlet(s) and/or outlet(s) of the
microfluidic channels in the microfluidic chip are apertures on the
top surface of the chip, and the fluidic adaptors can be attached
or coupled to the inlet(s) and/or outlet(s) of the microfluidic
channels within the chip. In some instances, the cartridge may
comprise additional adapters (i.e., in addition to the fluidic
adapters) that mate with the chip and/or fluidic adapters and help
to position the chip within the cartridge. These adapters may be
constructed using the same fabrication techniques and materials as
those outlined above for the fluidic adapters.
[0279] The cartridge chassis (or "housing") may be fabricated from
metal and/or polymer materials such as aluminum, anodized aluminum,
polycarbonate (PC), acrylic (PMMA), or Ultem (PEI), while other
materials are also consistent with the present disclosure. A
housing may be fabricated using CNC machining and/or molding
techniques, and designed so that one, two, or more than two
capillaries or microfluidic chips are constrained by the chassis in
a fixed orientation to create one or more independent flow
channels. The capillaries or chips may be mounted in the chassis
using, e.g., a compression fit design, or by mating with
compressible adapters made of silicone or a fluoroelastomer. In
some instances, two or more components of the cartridge chassis
(e.g., an upper half and a lower half) are assembled using, e.g.,
screws, clips, clamps, or other fasteners so that the two halves
are separable. In some instances, two or more components of the
cartridge chassis are assembled using, e.g., adhesives, solvent
bonding, or laser welding so that the two or more components are
permanently attached.
[0280] Flow cell surface coatings: In some instances, one or more
interior surfaces of the capillary lumens or microfluidic channels
in the disclosed flow cell devices may be coated using any of a
variety of surface modification techniques or polymer coatings
known to those of skill in the art. In some instances, the coatings
may be formulated to increase or maximize the number of available
binding sites (e.g., tethered oligonucleotide adapter/primer
sequences) on the one or more interior surfaces to increase or
maximize a foreground signal, e.g., a fluorescence signal arising
from labeled nucleic acid molecules hybridized to tethered
oligonucleotide adapter/primer sequences. In some instances, the
coatings may be formulated to decrease or minimize nonspecific
binding of fluorophores and other small molecules, or labeled or
unlabeled nucleotides, proteins, enzymes, antibodies,
oligonucleotides, or nucleic acid molecules (e.g., DNA, RNA, etc.),
in order to decrease or minimize a background signal, e.g.,
background fluorescence arising from the nonspecific binding of
labeled biomolecules or from autofluorescence of a sample support
structure. The combination of increased foreground signal and
reduced background signal that may be achieved in some instances
through the use of the disclosed coatings may thus provide improved
signal-to-noise ratio (SNR) in spectroscopic measurements or
improved contrast-to-noise ratio (CNR) in imaging methods.
[0281] As will be discussed in more detail below, the disclosed
hydrophilic, polymer-coated flow cell devices, optionally used in
combination with the improved hybridization and/or amplification
protocols, yield solid-phase bioassay reactions that exhibit: (i)
negligible non-specific binding of protein and other reaction
components (thus reducing or minimizing substrate background), (ii)
negligible non-specific nucleic acid amplification product, and
(iii) provide tunable nucleic acid amplification reactions.
Although described herein primarily in the context of nucleic acid
hybridization, amplification, and sequencing assays, it will be
understood by those of skill in the art that the disclosed
low-binding supports may be used in any of a variety of other
bioassay formats including, but not limited to, sandwich
immunoassays, enzyme-linked immunosorbent assays (ELISAs), etc.
[0282] In a preferred aspect, one or more layers of a coating
material may be applied to the interior flow cell device surfaces,
where the number of layers and/or the material composition of each
layer is chosen to adjust one or more surface properties of the
interior flow cell device surfaces, as noted in U.S. patent
application Ser. No. 16/363,842. Examples of surface properties
that may be adjusted include, but are not limited to, surface
hydrophilicity/hydrophobicity, overall coating thickness, the
surface density of chemically-reactive functional groups, the
surface density of grafted linker molecules or oligonucleotide
adapters/primers, etc. In some preferred applications, one or more
surface properties of the capillary or channel lumen are adjusted
to, for example, (i) provide for very low non-specific binding of
proteins, oligonucleotides, fluorophores, and other molecular
components of chemical or biological analysis applications,
including solid-phase nucleic acid amplification and/or sequencing
applications, (ii) provide for improved solid-phase nucleic acid
hybridization specificity and efficiency, and (iii) provide for
improved solid-phase nucleic acid amplification rate, specificity,
and efficiency.
[0283] Any of a variety of molecules known to those of skill in the
art including, but not limited to, silanes, amino acids, peptides,
nucleotides, oligonucleotides, other monomers or polymers, or
combinations thereof may be used in creating the one or more
chemically-modified layers on the interior flow cell device
surfaces, where the choice of components used may be varied to
alter one or more properties of the support surface, e.g., the
surface density of functional groups and/or tethered
oligonucleotide primers, the hydrophilicity/hydrophobicity of the
support surface, or the three three-dimensional nature (i.e.,
"thickness") of the support surface.
[0284] The attachment chemistry used to graft a first
chemically-modified layer to an interior surface of the flow cell
(capillary or channel) will generally be dependent on both the
material from which the flow cell device is fabricated and the
chemical nature of the layer. In some instances, the first layer
may be covalently attached to the interior flow cell device
surfaces. In some instances, the first layer may be non-covalently
attached, e.g., adsorbed to the surface through non-covalent
interactions such as electrostatic interactions, hydrogen bonding,
or van der Waals interactions between the surface and the molecular
components of the first layer. In either case, the substrate
surface may be treated prior to attachment or deposition of the
first layer. Any of a variety of surface preparation techniques
known to those of skill in the art may be used to clean or treat
the support surface. For example, glass or silicon surfaces may be
acid-washed using a Piranha solution (a mixture of sulfuric acid
(H.sub.2SO.sub.4) and hydrogen peroxide (H.sub.2O.sub.2)) and/or
cleaned using an oxygen plasma treatment method.
[0285] Silane chemistries constitute one non-limiting approach for
covalently modifying the silanol groups on glass or silicon
surfaces to attach more reactive functional groups (e.g., amines or
carboxyl groups), which may then be used in coupling linker
molecules (e.g., linear hydrocarbon molecules of various lengths,
such as C6, C12, C18 hydrocarbons, or linear polyethylene glycol
(PEG) molecules) or layer molecules (e.g., branched PEG molecules
or other polymers) to the surface. Examples of suitable silanes
that may be used in creating any of the disclosed low binding
support surfaces include, but are not limited to, (3-Aminopropyl)
trimethoxysilane (APTMS), (3-Aminopropyl) triethoxysilane (APTES),
any of a variety of PEG-silanes (e.g., comprising molecular weights
of 1K, 2K, 5K, 10K, 20K, etc.), amino-PEG silane (i.e., comprising
a free amino functional group), maleimide-PEG silane, biotin-PEG
silane, and the like.
[0286] Examples of preferred polymers that may be used to create
one or more layers of low non-specific binding material in any of
the disclosed support surfaces include, but are not limited to,
polyethylene glycol (PEG) of various molecular weights and
branching structures, streptavidin, polyacrylamide, polyester,
dextran, poly-lysine, and poly-lysine copolymers, or any
combination thereof. Examples of conjugation chemistries that may
be used to graft one or more layers of material (e.g. polymer
layers) to the support surface and/or to cross-link the layers to
each other include, but are not limited to, biotin-streptavidin
interactions (or variations thereof), His tag--Ni/NTA conjugation
chemistries, methoxy ether conjugation chemistries, carboxylate
conjugation chemistries, amine conjugation chemistries, NHS esters,
maleimides, thiol, epoxy, azide, hydrazide, alkyne, isocyanate, and
silane.
[0287] In some instances, the number of layers of polymer or other
chemical layers on the interior flow cell device surfaces may range
from 1 to about 10, or greater than 10. In some instances, the
number of layers is at least 1, at least 2, at least 3, at least 4,
at least 5, at least 6, at least 7, at least 8, at least 9, or at
least 10. In some instances, the number of layers may be at most
10, at most 9, at most 8, at most 7, at most 6, at most 5, at most
4, at most 3, at most 2, or at most 1. Any of the lower and upper
values described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the number of layers may range from about 2 to about 4.
In some instances, the one or more layers may all comprise the same
material. In some instances, each layer may comprise a different
material. In some instances, a plurality of layers may comprise a
plurality of materials.
[0288] One or more layers of a multi-layered surface may comprise a
branched polymer or may be linear. Examples of suitable branched
polymers include, but are not limited to, branched PEG, branched
poly(vinyl alcohol) (branched PVA), branched poly(vinyl pyridine),
branched poly(vinyl pyrrolidone) (branched PVP), branched),
poly(acrylic acid) (branched PAA), branched polyacrylamide,
branched poly(N-isopropylacrylamide) (branched PNIPAM), branched
poly(methyl methacrylate) (branched PMA), branched
poly(2-hydroxylethyl methacrylate) (branched PHEMA), branched
poly(oligo(ethylene glycol) methyl ether methacrylate) (branched
POEGMA), branched polyglutamic acid (branched PGA), branched
poly-lysine, branched poly-glucoside, and dextran.
[0289] In some instances, the branched polymers used to create one
or more layers of any of the multi-layered surfaces disclosed
herein may comprise at least 4 branches, at least 5 branches, at
least 6 branches, at least 7 branches, at least 8 branches, at
least 9 branches, at least 10 branches, at least 12 branches, at
least 14 branches, at least 16 branches, at least 18 branches, at
least 20 branches, at least 22 branches, at least 24 branches, at
least 26 branches, at least 28 branches, at least 30 branches, at
least 32 branches, at least 34 branches, at least 36 branches, at
least 38 branches, or at least 40 branches. Molecules often exhibit
a `power of 2` number of branches, such as 2, 4, 8, 16, 32, 64, or
128 branches.
[0290] In some instances, the resulting functional end groups
distal from the surface following the deposition of one or more
layers, e.g., polymer layers can include, but are not limited to,
biotin, methoxy ether, carboxylate, amine, NHS ester, maleimide,
and bis-silane.
[0291] Linear, branched, or multi-branched polymers used to create
one or more layers of any of the multi-layered surfaces disclosed
herein may have a molecular weight of at least 500 Daltons, at
least 1,000 Daltons, at least 1,500 Daltons, at least 2,000
Daltons, at least 2,500 Daltons, at least 3,000 Daltons, at least
3,500 Daltons, at least 4,000 Daltons, at least 4,500 Daltons, at
least 5,000 Daltons, at least 7,500 Daltons, at least 10,000
Daltons, at least 12,500 Daltons, at least 15,000 Daltons, at least
17,500 Daltons, at least 20,000 Daltons, at least 25,000 Daltons,
at least 30,000 Daltons, at least 35,000 Daltons, at least 40,000
Daltons, at least 45,000 Daltons, or at least 50,000 Daltons. In
some instances, the linear, branched, or multi-branched polymers
used to create one or more layers of any of the multi-layered
surfaces disclosed herein may have a molecular weight of at most
50,000 Daltons, at most 45,000 Daltons, at most 40,000 Daltons, at
most 35,000 Daltons, at most 30,000 Daltons, at most 25,000
Daltons, at most 20,000 Daltons, at most 17,500 Daltons, at most
15,000 Daltons, at most 12,500 Daltons, at most 10,000 Daltons, at
most 7,500 Daltons, at most 5,000 Daltons, at most 4,500 Daltons,
at most 4,000 Daltons, at most 3,500 Daltons, at most 3,000
Daltons, at most 2,500 Daltons, at most 2,000 Daltons, at most
1,500 Daltons, at most 1,000 Daltons, or at most 500 Daltons. Any
of the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the molecular weight of linear,
branched, or multi-branched polymers used to create one or more
layers of any of the multi-layered surfaces disclosed herein may
range from about 1,500 Daltons to about 20,000 Daltons. Those of
skill in the art will recognize that the molecular weight of
linear, branched, or multi-branched polymers used to create one or
more layers of any of the multi-layered surfaces disclosed herein
may have any value within this range, e.g., about 1,260
Daltons.
[0292] In some instances, two or more layers may be covalently
coupled to each other or internally cross-linked to improve the
stability of the resulting surface. In some instances, e.g.,
wherein at least one layer of a multi-layered surface comprises a
branched polymer, the number of covalent bonds between a branched
polymer molecule of the layer being deposited and molecules of the
previous layer may range from about one covalent linkage per
molecule and about 32 covalent linkages per molecule. In some
instances, the number of covalent bonds between a branched polymer
molecule of the new layer and molecules of the previous layer may
be at least 1, at least 2, at least 3, at least 4, at least 5, at
least 6, at least 7, at least 8, at least 9, at least 10, at least
12, at least 14, at least 16, at least 18, at least 20, at least
22, at least 24, at least 26, at least 28, at least 30, or at least
32, or more than 32 covalent linkages per molecule. In some
instances, the number of covalent bonds between a branched polymer
molecule of the new layer and molecules of the previous layer may
be at most 32, at most 30, at most 28, at most 26, at most 24, at
most 22, at most 20, at most 18, at most 16, at most 14, at most
12, at most 10, at most 9, at most 8, at most 7, at most 6, at most
5, at most 4, at most 3, at most 2, or at most 1. Any of the lower
and upper values described in this paragraph may be combined to
form a range included within the present disclosure, for example,
in some instances the number of covalent bonds between a branched
polymer molecule of the new layer and molecules of the previous
layer may range from about 4 to about 16. Those of skill in the art
will recognize that the number of covalent bonds between a branched
polymer molecule of the new layer and molecules of the previous
layer may have any value within this range, e.g., about 11 in some
instances, or an average number of about 4.6 in other
instances.
[0293] Any reactive functional groups that remain following the
coupling of a material layer to the interior flow cell device
surfaces may optionally be blocked by coupling a small, inert
molecule using a high yield coupling chemistry. For example, in the
case that amine coupling chemistry is used to attach a new material
layer to the previous one, any residual amine groups may
subsequently be acetylated or deactivated by coupling with a small
amino acid such as glycine.
[0294] In order to scale binding site surface density, e.g.,
oligonucleotide adapter/primer surface density, and add additional
dimensionality to hydrophilic or amphoteric surfaces, substrates
comprising multi-layer coatings of PEG and other hydrophilic
polymers have been developed. By using hydrophilic and amphoteric
surface layering approaches that include, but are not limited to,
the polymer/co-polymer materials described below, it is possible to
increase adapter/primer loading density on the surface
significantly. Traditional PEG coating approaches use monolayer
primer deposition, which has been tested and reported for single
molecule sequencing applications but do not yield high copy numbers
for nucleic acid amplification applications. As described herein,
"layering" can be accomplished using traditional crosslinking
approaches with any compatible polymer or monomer subunits such
that a surface comprising two or more highly crosslinked layers can
be built sequentially. Examples of suitable polymers include, but
are not limited to, streptavidin, polyacrylamide, polyester,
dextran, poly-lysine, and copolymers of poly-lysine and PEG. In
some instances, the different layers may be cross-linked to each
other through any of a variety of conjugation reactions including,
but not limited to, biotin-streptavidin binding, azide-alkyne click
reaction, amine-NETS ester reaction, thiol-maleimide reaction, and
ionic interactions between positively charged polymer and
negatively charged polymer. In some instances, high adapter/primer
density materials may be constructed in solution and subsequently
layered onto the surface in multiple steps.
[0295] Exemplary PEG multilayers include PEG (8 arm, 16 arm, 8 arm)
on PEG-amine-APTES. Similar concentrations were observed for
3-layer multi-arm PEG (8 arm, 16 arm, 8 arm) and (8 arm, 64 arm, 8
arm) on PEG-amine-APTES exposed to 8 uM primer, and 3-layer
multi-arm PEG (8 arm, 8 arm, 8 arm) using star-shape PEG-amine to
replace 16 arm and 64 arm. PEG multilayers having comparable first,
second and third PEG layers are also contemplated.
[0296] In some instances, the resultant surface density of binding
sites on the interior flow cell device surfaces, e.g.,
oligonucleotide adapter/primer surface densities, may range from
about 100 primer molecules per .mu.m.sup.2 to about 1,000,000
primer molecules per .mu.m.sup.2. In some instances, the surface
density of binding sites may be at least 100, at least 200, at
least 300, at least 400, at least 500, at least 600, at least 700,
at least 800, at least 900, at least 1,000, at least 1,500, at
least 2,000, at least 2,500, at least 3,000, at least 3,500, at
least 4,000, at least 4,500, at least 5,000, at least 5,500, at
least 6,000, at least 6,500, at least 7,000, at least 7,500, at
least 8,000, at least 8,500, at least 9,000, at least 9,500, at
least 10,000, at least 15,000, at least 20,000, at least 25,000, at
least 30,000, at least 35,000, at least 40,000, at least 45,000, at
least 50,000, at least 55,000, at least 60,000, at least 65,000, at
least 70,000, at least 75,000, at least 80,000, at least 85,000, at
least 90,000, at least 95,000, at least 100,000, at least 150,000,
at least 200,000, at least 250,000, at least 300,000, at least
350,000, at least 400,000, at least 450,000, at least 500,000, at
least 550,000, at least 600,000, at least 650,000, at least
700,000, at least 750,000, at least 800,000, at least 850,000, at
least 900,000, at least 950,000, or at least 1,000,000 molecules
per .mu.m.sup.2. In some instances, the surface density of binding
sites may be at most 1,000,000, at most 950,000, at most 900,000,
at most 850,000, at most 800,000, at most 750,000, at most 700,000,
at most 650,000, at most 600,000, at most 550,000, at most 500,000,
at most 450,000, at most 400,000, at most 350,000, at most 300,000,
at most 250,000, at most 200,000, at most 150,000, at most 100,000,
at most 95,000, at most 90,000, at most 85,000, at most 80,000, at
most 75,000, at most 70,000, at most 65,000, at most 60,000, at
most 55,000, at most 50,000, at most 45,000, at most 40,000, at
most 35,000, at most 30,000, at most 25,000, at most 20,000, at
most 15,000, at most 10,000, at most 9,500, at most 9,000, at most
8,500, at most 8,000, at most 7,500, at most 7,000, at most 6,500,
at most 6,000, at most 5,500, at most 5,000, at most 4,500, at most
4,000, at most 3,500, at most 3,000, at most 2,500, at most 2,000,
at most 1,500, at most 1,000, at most 900, at most 800, at most
700, at most 600, at most 500, at most 400, at most 300, at most
200, or at most 100 molecules per .mu.m.sup.2. Any of the lower and
upper values described in this paragraph may be combined to form a
range included within the present disclosure, for example, in some
instances the surface density of binding sites may range from about
10,000 molecules per .mu.m.sup.2 to about 100,000 molecules per
.mu.m.sup.2. Those of skill in the art will recognize that the
surface density of binding sites may have any value within this
range, e.g., about 3,800 molecules per .mu.m.sup.2 in some
instances, or about 455,000 molecules per .mu.m.sup.2 in other
instances. In some instances, as will be discussed further below
for nucleic acid sequencing applications, the surface density of
template library nucleic acid sequences (e.g., sample DNA
molecules) initially hybridized to adapter or primer sequences
tethered to the interior flow cell device surfaces may be less than
or equal to that indicated for the surface density of binding
sites. In some instances, as will also be discussed further below,
the surface density of clonally-amplified template library nucleic
acid sequences hybridized to adapter or primer sequences on the
interior flow cell device surfaces may span the same range or a
different range as that indicated for the surface density of
tethered oligonucleotide adapters or primers.
[0297] Local surface densities of binding sites on the interior
flow cell device surfaces as listed above do not preclude variation
in density across a surface, such that a surface may comprise a
region having a binding site density of, for example,
500,000/um.sup.2, while also comprising at least a second region
having a substantially different local surface density.
[0298] In some instances, capture probes, e.g., oligonucleotide
primers with different base sequences and base modifications (or
other biomolecules, e.g., enzymes or antibodies) may be tethered to
one or more layers of the resulting surface at various surface
densities. In some instances, for example, both surface functional
group density and the capture probe concentration used for coupling
may be varied to target a certain capture probe surface density
range. Additionally, capture probe surface density may be
controlled by diluting capture probes with other "inert" molecules
that carry the same reactive functional group for coupling to the
surface. For example, amine-labeled oligonucleotide probes can be
diluted with amine-labeled polyethylene glycol in a reaction with
an NETS-ester coated surface to reduce the final primer density. In
the case of oligonucleotide adapters/primers, probe sequences with
different lengths of linker between the hybridization region and
the surface attachment functional group may also be applied to vary
surface density. Example of suitable linkers include poly-T and
poly-A strands at the 5' end of the primer (e.g., 0 to 20 bases),
PEG linkers (e.g., 3 to 20 monomer units), and carbon-chain (e.g.,
C6, C12, C18, etc.). To measure or estimate the capture probe
surface density, fluorescently-labeled capture probes may be
tethered to the surface and a fluorescence reading then compared
with that for a calibration solution comprising a known
concentration of the fluorophore.
[0299] In some instances, the degree of hydrophilicity (or
"wettability" with aqueous solutions) of the disclosed support
surfaces, e.g., interior flow cell device surfaces, may be
assessed, for example, through the measurement of water contact
angles in which a small droplet of water is placed on the surface
and its angle of contact with the surface is measured using, e.g.,
an optical tensiometer. In some instances, a static contact angle
may be determined. In some instances, an advancing or receding
contact angle may be determined. In some instances, the water
contact angle for the hydrophilic, low-binding support surfaced
disclosed herein may range from about 0 degrees to about 50
degrees. In some instances, the water contact angle for the
hydrophilic, low-binding support surfaced disclosed herein may no
more than 50 degrees, 45 degrees, 40 degrees, 35 degrees, 30
degrees, 25 degrees, 20 degrees, 18 degrees, 16 degrees, 14
degrees, 12 degrees, 10 degrees, 8 degrees, 6 degrees, 4 degrees, 2
degrees, or 1 degree. In many cases the contact angle is no more
than any value within this range, e.g., no more than 40 degrees.
Those of skill in the art will realize that a given hydrophilic,
low-binding support surface of the present disclosure may exhibit a
water contact angle having a value of anywhere within this range,
e.g., about 27 degrees. In some instances, the disclosed low
nonspecific binding surfaces have a water contact angle of less
than 45 degrees. In some instances, the disclosed low nonspecific
binding surfaces have a water contact angle of less than 35
degrees.
[0300] As noted, the hydrophilic coated interior flow cell device
surfaces of the present disclosure exhibit reduce non-specific
binding of proteins, nucleic acids, fluorophores, and other
components of biological and biochemical assay methods. The degree
of non-specific binding exhibited by a given support surface, e.g.,
an interior flow cell device surface, may be assessed either
qualitatively or quantitatively. For example, in some instances,
exposure of the surface to fluorescent dyes (e.g., cyanine dye 3
(Cy3), cyanine dye 5 (Cy5), etc.), fluorescently-labeled
nucleotides, fluorescently-labeled oligonucleotides, and/or
fluorescently-labeled proteins (e.g. polymerases) under a
standardized set of conditions, followed by a specified rinse
protocol and fluorescence imaging may be used as a qualitative tool
for comparison of non-specific binding on supports comprising
different surface formulations. In some instances, exposure of the
surface to fluorescent dyes, fluorescently-labeled nucleotides,
fluorescently-labeled oligonucleotides, and/or
fluorescently-labeled proteins (e.g. polymerases) under a
standardized set of conditions, followed by a specified rinse
protocol and fluorescence imaging may be used as a quantitative
tool for comparison of non-specific binding on supports comprising
different surface formulations--provided that care has been taken
to ensure that the fluorescence imaging is performed under
conditions where fluorescence signal is linearly related (or
related in a predictable manner) to the number of fluorophores on
the support surface (e.g., under conditions where signal saturation
and/or self-quenching of the fluorophore is not an issue) and
suitable calibration standards are used. In some instances, other
techniques known to those of skill in the art, for example,
radioisotope labeling and counting methods may be used for
quantitative assessment of the degree to which non-specific binding
is exhibited by the different support surface formulations of the
present disclosure.
[0301] In some instances, the degree of non-specific binding
exhibited by the disclosed low nonspecific binding support surfaces
may be assessed using a standardized protocol for contacting the
surface with a labeled protein (e.g., bovine serum albumin (BSA),
streptavidin, a DNA polymerase, a reverse transcriptase, a
helicase, a single-stranded binding protein (SSB), etc., or any
combination thereof), a labeled nucleotide, a labeled
oligonucleotide, etc., under a standardized set of incubation and
rinse conditions, followed be detection of the amount of label
remaining on the surface and comparison of the signal resulting
therefrom to an appropriate calibration standard. In some
instances, the label may comprise a fluorescent label. In some
instances, the label may comprise a radioisotope. In some
instances, the label may comprise any other detectable label known
to one of skill in the art. In some instances, the degree of
non-specific binding exhibited by a given support surface
formulation may thus be assessed in terms of the number of
non-specifically bound protein molecules (or other molecules) per
unit area. In some instances, the low nonspecific binding supports
of the present disclosure may exhibit nonspecific protein binding
(or nonspecific binding of other specified molecules, e.g., cyanine
dye 3 (Cy3) of less than 0.001 molecule per .mu.m.sup.2, less than
0.01 molecule per .mu.m.sup.2, less than 0.1 molecule per
.mu.m.sup.2, less than 0.25 molecule per .mu.m.sup.2, less than 0.5
molecule per .mu.m.sup.2, less than 1 molecule per .mu.m.sup.2,
less than 10 molecules per .mu.m.sup.2, less than 100 molecules per
.mu.m.sup.2, or less than 1,000 molecules per .mu.m.sup.2. Those of
skill in the art will realize that a given support surface of the
present disclosure may exhibit nonspecific binding falling anywhere
within this range, for example, of less than 86 molecules per
.mu.m.sup.2. For example, some modified surfaces disclosed herein
exhibit nonspecific protein binding of less than 0.5
molecule/.mu.m.sup.2 following contact with a 1 uM solution of Cy3
labeled streptavidin (GE Amersham) in phosphate buffered saline
(PBS) buffer for 15 minutes, followed by 3 rinses with deionized
water. Some modified surfaces disclosed herein exhibit nonspecific
binding of Cy3 dye molecules of less than 0.25 molecules per
.mu.m.sup.2. In independent nonspecific binding assays, 1 .mu.M
labeled Cy3 SA (ThermoFisher), 1 uM Cy5 SA dye (ThermoFisher), 10
uM Aminoallyl-dUTP--ATTO-647N (Jena Biosciences), 10 uM
Aminoallyl-dUTP--ATTO-Rho11 (Jena Biosciences), 10 uM
Aminoallyl-dUTP--ATTO-Rho11 (Jena Biosciences), 10 uM
7-Propargylamino-7-deaza-dGTP--Cy5 (Jena Biosciences, and 10 uM
7-Propargylamino-7-deaza-dGTP--Cy3 (Jena Biosciences) were
incubated on the low nonspecific binding substrates at 37.degree.
C. for 15 minutes in a 384 well plate format. Each well was rinsed
2-3.times. with 50 ul deionized RNase/DNase Free water and
2-3.times. with 25 mM ACES buffer pH 7.4. The 384 well plates were
imaged on a GE Typhoon(GE Healthcare Lifesciences, Pittsburgh, Pa.)
instrument using the Cy3, AF555, or Cy5 filter sets (according to
dye test performed) as specified by the manufacturer at a PMT gain
setting of 800 and resolution of 50-100 .mu.m. For higher
resolution imaging, images were collected on an Olympus IX83
microscope (Olympus Corp., Center Valley, Pa.) with a total
internal reflectance fluorescence (TIRF) objective (20.times., 0.75
NA or 100.times., 1.5 NA, Olympus), an sCMOS Andor camera (Zyla
4.2. Dichroic mirrors were purchased from Semrock (IDEX Health
& Science, LLC, Rochester, N.Y.), e.g., 405, 488, 532, or 633
nm dichroic reflectors/beamsplitters, and band pass filters were
chosen as 532 LP or 645 LP concordant with the appropriate
excitation wavelength. Some modified surfaces disclosed herein
exhibit nonspecific binding of dye molecules of less than 0.25
molecules per .mu.m.sup.2.
[0302] In some instances, the coated flow cell device surfaces
disclosed herein may exhibit a ratio of specific to nonspecific
binding of a fluorophore such as Cy3 of at least 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40,
50, 75, 100, or greater than 100, or any intermediate value spanned
by the range herein.
[0303] In some instances, one or more surface modification and/or
polymer layers may be applied to the interior flow cell device
surfaces using a technique such as chemical vapor deposition (CVD).
In some instances, one or more surface modification and/or polymer
layers may be applied to the interior flow cell device surfaces by
flowing one or more appropriate chemical coupling or coating
reagents through the capillaries or fluid channels prior to use for
their intended application. In some instances, one or more coating
reagents may be added to a buffer used, e.g., a nucleic acid
hybridization, amplification reaction, and/or sequencing reaction
buffer to provide for dynamic coating of the interior flow cell
device surfaces.
[0304] In some instances, the chemical modification layers may be
applied uniformly across the surface of the substrate or support
structure. Alternately, the surface of the substrate or support
structure may be non-uniformly distributed or patterned, such that
the chemical modification layers are confined to one or more
discrete regions of the substrate. For example, the substrate
surface may be patterned using photolithographic techniques to
create an ordered array or random pattern of chemically-modified
regions on the surface. Alternately or in combination, the
substrate surface may be patterned using, e.g., contact printing
and/or ink-jet printing techniques. In some instances, an ordered
array or random patter of chemically-modified discrete regions may
comprise at least 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100,
200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000,
5000, 6000, 7000, 8000, 9000, or 10,000 or more discrete regions,
or any intermediate number of discrete regions spanned by the range
herein.
[0305] In some instances, fluorescence images of the disclosed low
nonspecific binding surfaces when used, e.g., in nucleic acid
hybridization or amplification applications to create clusters of
hybridized or clonally-amplified nucleic acid molecules (e.g.,
"discrete regions" that have been directly or indirectly labeled
with a fluorophore) exhibit contrast-to-noise ratios (CNRs) of at
least 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130,
140, 150, 160, 170, 180, 190, 20, 210, 220, 230, 240, 250, or
greater than 250 when the nucleic acid molecules are labeled with
Cy3 and the images are acquired using an Olympus IX83 inverted
fluorescence microscope equipped with a 20.times., 0.75 NA
objective, a 532 nm light source, a bandpass and dichroic mirror
filter set adapted or optimized for 532 nm long-pass excitation and
Cy3 fluorescence emission filter, a Semrock 532 nm dichroic
reflector, and a camera (Andor sCMOS, Zyla 4.2) where the
excitation light intensity is adjusted to avoid signal saturation,
and the surface is immersed in a buffer (e.g., 25 mM ACES, pH 7.4
buffer) while the image is acquired. As used herein,
contrast-to-noise ratio (CNR) is calculated as:
CNR=(S-B)/Noise
[0306] where S=foreground signal (e.g., the fluorescence signal as
measured in the image that arises from a labeled nucleic acid
colony or cluster on a sample support surface), B=background signal
(where B=B.sub.inter+B.sub.intra), B.sub.inter=background signal
measured at a location on the sample support surface that is
between labeled nucleic acid colonies or clusters,
B.sub.intra=background signal measured at the location of a nucleic
acid colony or cluster (determined, e.g., by contacting the sample
support surface with a labeled, non-complementary oligonucleotide
and measuring the resulting fluorescence), and Noise=the signal
noise. The contrast-to-noise ratio (CNR) of images of sequencing
surfaces, for example, provides a key metric in assessing nucleic
acid amplification specificity and non-specific binding on the
support. While signal-to-noise ratio (SNR) is often considered to
be a benchmark of overall signal quality, it can be shown that
improved CNR can provide a significant advantage over SNR as a
benchmark for signal quality in imaging applications that require
rapid image capture (e.g., nucleic acid sequencing applications for
which cycle times must be minimized).
[0307] In some instances, polymer-coated sample support structures,
e.g., interior flow cell device surfaces comprising the disclosed
hydrophilic polymer coatings, may exhibit improved stability to
repetitive exposure to solvents, changes in temperature, changes in
pH, or long-term storage.
[0308] Fluidics systems and fluid flow control modules: in some
implementations, the disclosed imaging and/or analysis systems may
provide fluid flow control capability for delivering samples or
reagents to the one or more flow cell devices or flow cell
cartridges (e.g., single capillary flow cell device or microfluidic
channel flow cell device) connected to the system. Reagents and
buffers may be stored in bottles, reagent and buffer cartridges, or
other suitable containers that are connected to the flow cell
inlets by means of tubing and valve manifolds. The disclosed
systems may also include processed sample and waste reservoirs in
the form of bottles, cartridges, or other suitable containers for
collecting fluids downstream of the capillary flow cell devices or
capillary flow cell cartridges. In some embodiments, the fluid flow
(or "fluidics") control module may provide programmable switching
of flow between different sources, e.g. sample or reagent
reservoirs or bottles located in the instrument, and the inlet(s)
to a central region (e.g., a capillary flow cell or microfluidic
device, or a large fluid chamber such as a large fluid chamber
within a microfluidic device). In some instances, the fluid flow
control module may provide programmable switching of flow between
outlet(s) from the central region (e.g., a capillary flow cell or
microfluidic device) and different collection points, e.g.,
processed sample reservoirs, waste reservoirs, etc., connected to
the system. In some instances, samples, reagents, and/or buffers
may be stored within reservoirs that are integrated into the flow
cell cartridge or microfluidic cartridge itself. In some instances,
processed samples, spent reagents, and/or used buffers may be
stored within reservoirs that are integrated into the flow cell
cartridge or microfluidic device cartridge itself.
[0309] In some implementations, one or more fluid flow control
modules may be configured to control the delivery of fluids to one
or more capillary flow cells, capillary flow cell cartridges,
microfluidic devices, microfluidic cartridges, or any combination
thereof. In some instances, the one or more fluidics controllers
may be configured to control volumetric flow rates for one or more
fluids or reagents, linear flow velocities for one or more fluids
or reagents, mixing ratios for one or more fluids or reagents, or
any combination thereof. Control of fluid flow through the
disclosed systems will typically be performed using pumps (or other
fluid actuation mechanisms) and valves (e.g., programmable pumps
and valves). Examples of suitable pumps include, but are not
limited to, syringe pumps, programmable syringe pumps, peristaltic
pumps, diaphragm pumps, and the like. Examples of suitable valves
include, but are not limited to, check valves, electromechanical
two-way or three-way valves, pneumatic two-way and three-way
valves, and the like. In some instances, fluid flow through the
system may be controlled by means of applying positive pneumatic
pressure to one or more inlets of the reagent and buffer
containers, or to inlets incorporated into flow cell cartridge(s)
(e.g., capillary flow cell or microfluidic cartridges). In some
embodiments, fluid flow through the system may be controlled by
means of drawing a vacuum at one or more outlets of waste
reservoir(s), or at one or more outlets incorporated into flow cell
cartridge(s) (e.g., capillary flow cell or microfluidic
cartridges).
[0310] In some instances, different modes of fluid flow control are
utilized at different points in an assay or analysis procedure,
e.g. forward flow (relative to the inlet and outlet for a given
capillary flow cell device), reverse flow, oscillating or pulsatile
flow, or combinations thereof. In some applications, oscillating or
pulsatile flow may be applied, for example, during assay wash/rinse
steps to facilitate complete and efficient exchange of fluids
within the one or more flow cell devices or flow cell cartridges
(e.g., capillary flow cell devices or cartridges, and microfluidic
devices or cartridges).
[0311] Similarly, in some cases different fluid flow rates may be
utilized at different locations within a flow cell device or at
different points in the assay or analysis process workflow, for
example, in some instances, the volumetric flow rate may vary from
-100 ml/sec to +100 ml/sec. In some embodiment, the absolute value
of the volumetric flow rate may be at least 0.001 ml/sec, at least
0.01 ml/sec, at least 0.1 ml/sec, at least 1 ml/sec, at least 10
ml/sec, or at least 100 ml/sec. In some embodiments, the absolute
value of the volumetric flow rate may be at most 100 ml/sec, at
most 10 ml/sec, at most 1 ml/sec, at most 0.1 ml/sec, at most 0.01
ml/sec, or at most 0.001 ml/sec. The volumetric flow rate at a
given location with the flow cell device or at a given point in
time may have any value within this range, e.g. a forward flow rate
of 2.5 ml/sec, a reverse flow rate of -0.05 ml/sec, or a value of 0
ml/sec (i.e., stopped flow).
[0312] In some implementations, the fluidics system may be designed
to minimize the consumption of key reagents (e.g., expensive
reagents) required for performing, e.g., genomic analysis
applications. For example, in some implementations the disclosed
fluidics systems may comprise a first reservoir housing a first
reagent or solution, a second reservoir housing a second reagent or
solution, and a central region, e.g., a central capillary flow cell
or microfluidic device, where an outlet from the first reservoir
and an outlet from the second reservoir are fluidically coupled to
an inlet of the central capillary flow cell or microfluidic device
through at least one valve such that the volume of the first
reagent or solution flowing per unit time from the outlet of the
first reservoir to the inlet of the central capillary flow cell or
microfluidic device is less than the volume of the second reagent
or solution flowing per unit time from the outlet of the second
reservoir to the inlet of the central region. In some
implementations, the first reservoir and second reservoir may be
integrated into a capillary flow cell cartridge or microfluidic
cartridge. In some instances, the at least one valve may also be
integrated into the capillary flow cell cartridge or microfluidic
cartridge.
[0313] In some instances, the first reservoir is fluidically
coupled to the central capillary flow cell or microfluidic device
through a first valve, and the second reservoir is fluidically
coupled to the central capillary flow cell or microfluidic device
through a second valve. In some instances, the first and/or second
valves may be, e.g., a diaphragm valve, pinch valve, gate valve, or
other suitable valve. In some instances, the first reservoir is
positioned in close proximity to the inlet of the central capillary
flow cell or microfluidic device to reduce dead volume for delivery
of the first reagent solution. In some instances, the first
reservoir is placed in closer proximity to the inlet of the central
capillary flow cell or microfluidic device than is the second
reservoir. In some instances, the first reservoir is positioned in
close proximity to the second valve so as to reduce the dead volume
for delivery of the first reagent relative to that for delivery of
a plurality of "second" reagents (e.g., two, three, four, five, or
six or more "second" reagents) from a plurality of "second"
reservoirs (e.g., two, three, four, five, or six or more "second"
reservoirs).
[0314] The first and second reservoirs described above may be used
to house the same or different reagents or solutions. In some
instances, the first reagent that is housed in the first reservoir
is different from the second reagent that is housed in the second
reservoir, and the second reagent comprises at least one reagent
that is used in common by a plurality of reactions occurring in the
central a central capillary flow cell or microfluidic device. In
some instances, e.g., in fluidics systems configured for performing
nucleic acid sequencing chemistry within the central capillary flow
cell or microfluidic device, the first reagent comprises at least
one reagent selected from the group consisting of a polymerase,
nucleotide, and a nucleotide analog. In some instances, the second
reagent comprises a low-cost reagent, e.g., a solvent.
[0315] In some instances, the interior volume of the central
region, e.g., a central capillary flow cell cartridge, or
microfluidic device comprising one or more fluid channels or fluid
chambers, can be adjusted based on the specific application to be
performed, e.g., nucleic acid sequencing. In some embodiments, the
central region comprises an interior volume suitable for sequencing
a eukaryotic genome. In some embodiments, the central region
comprises an interior volume suitable for sequencing a prokaryotic
genome. In some embodiments, the central region comprises an
interior volume suitable for sequencing a viral genome. In some
embodiments, the central region comprises an interior volume
suitable for sequencing a transcriptome. For example, in some
embodiments, the interior volume of the central region may comprise
a volume of less than 0.05 between 0.05 .mu.l and 0.1 .mu.l,
between 0.05 .mu.l and 0.2 .mu.l, between 0.05 .mu.l and 0.5 .mu.l,
between 0.05 .mu.l and 0.8 .mu.l, between 0.05 .mu.l and 1 .mu.l,
between 0.05 .mu.l and 1.2 .mu.l, between 0.05 .mu.l and 1.5 .mu.l,
between 0.1 .mu.l and 1.5 .mu.l, between 0.2 .mu.l and 1.5 .mu.l,
between 0.5 .mu.l and 1.5 .mu.l, between 0.8 .mu.l and 1.5 .mu.l,
between 1 .mu.l and 1.5 .mu.l, between 1.2 .mu.l and 1.5 .mu.l or
greater than 1.5 .mu.l, or a range defined by any two of the
foregoing. In some embodiments, the interior volume of the central
region may comprise a volume of less than 0.5 .mu.l, between 0.5
.mu.l and 1 .mu.l, between 0.5 .mu.l and 2 .mu.l, between 0.5 .mu.l
and 5 .mu.l, between 0.5 .mu.l and 8 .mu.l, between 0.5 .mu.l and
10 .mu.l, between 0.5 .mu.l and 12 .mu.l, between 0.5 .mu.l and
between 1 .mu.l and 15 .mu.l, between 2 .mu.l and 15 .mu.l, between
5 .mu.l and 15 .mu.l, between 8 .mu.l and 15 .mu.l, between 10
.mu.l and 15 .mu.l, between 12 .mu.l and 15 .mu.l, or greater than
15 .mu.l, or a range defined by any two of the foregoing. In some
embodiments, the interior volume of the central region may comprise
a volume of less than 5.mu.l, between 5 .mu.l and 10 .mu.l, between
5 .mu.l and 20 .mu.l, between 5 .mu.l and 500 .mu.l, between 5
.mu.l and 80 .mu.l, between 5 .mu.l and 100 .mu.l, between 5 .mu.l
and 120 .mu.l, between 5 .mu.l and 150 .mu.l, between 10 .mu.l and
150 .mu.l, between 20 .mu.l and 150 .mu.l, between 50 .mu.l and 150
.mu.l, between 80 .mu.l and 150 .mu.l, between 100 .mu.l and 150
.mu.l, between 120 .mu.l and 150 .mu.l, or greater than 150 .mu.l,
or a range defined by any two of the foregoing. In some
embodiments, the interior volume of the central region may comprise
a volume of less than 50 .mu.l, between 50 .mu.l and 100 .mu.l,
between 50 .mu.l and 200 .mu.l, between 50 .mu.l and 500 .mu.l,
between 50 .mu.l and 800 .mu.l, between 50 .mu.l and 1000 .mu.l,
between 50 .mu.l and 1200 .mu.l, between 50 .mu.l and 1500 .mu.l,
between 100 .mu.l and 1500 .mu.l, between 200 .mu.l and 1500 .mu.l,
between 500 .mu.l and 1500 .mu.l, between 800 .mu.l and 1500 .mu.l,
between 1000 .mu.l and 1500 .mu.l, between 1200 .mu.l and 1500
.mu.l, or greater than 1500 .mu.l, or a range defined by any two of
the foregoing. In some embodiments, the interior volume of the
central region may comprise a volume of less than 500 .mu.l between
500 .mu.l and 1000 .mu.l, between 500 .mu.l and 2000 .mu.l, between
500 .mu.l and 5 ml, between 500 .mu.l and 8 ml, between 500 .mu.l
and 10 ml, between 500 .mu.l and 12 ml, between 500 .mu.l and 15
ml, between 1 ml and 15 ml, between 2 ml and 15 ml, between 5 ml
and 15 ml, between 8 ml and 15 ml, between 10 ml and 15 ml, between
12 ml and 15 ml, or greater than 15 ml, or a range defined by any
two of the foregoing. In some embodiments, the interior volume of
the central region may comprise a volume of less than 5 ml, between
5 ml and 10 ml, between 5 ml and 20 ml, between 5 ml and 50 ml,
between 5 ml and 80 ml, between 5 ml and 100 ml, between 5 ml and
120 ml, between 5 ml and 150 ml, between 10 ml and 150 ml, between
20 ml and 150 ml, between 50 ml and 150 ml, between 80 ml and 150
ml, between 100 ml and 150 ml, between 120 ml and 150 ml, or
greater than 150 ml, or a range defined by any two of the
foregoing. In some embodiments, the systems described herein
comprise an array or collection of flow cell devices or systems
comprising multiple discrete capillaries, microfluidic channels,
fluidic channels, chambers, or lumenal regions, wherein the
combined interior volume is, comprises, or includes one or more of
the values within a range disclosed herein.
[0316] In some instances, the ratio of volumetric flow rate for the
delivery of the first reagent to the central capillary flow cell or
microfluidic device to that for delivery of the second reagent to
the central capillary flow cell or microfluidic device may be less
than 1:20, less than 1:16, least than 1:12, less than 1:10, less
than 1:8, less than 1:6, or less than 1:2. In some instances, the
ratio of volumetric flow rate for the delivery of the first reagent
to the central capillary flow cell or microfluidic device to that
for delivery of the second reagent to the central capillary flow
cell or microfluidic device may have any value with the range
spanned by these values, e.g., less than 1:15.
[0317] As noted, the flow cell devices and/or fluidics systems
disclosed herein may be configured to achieve a more efficient use
of the reagents than that achieved by, e.g., other sequencing
devices and systems, particularly for the costly reagents used in a
variety of sequencing chemistry steps. In some instances, the first
reagent comprises a reagent that is more expensive than the second
reagent. In some instances, the first reagent comprises a
reaction-specific reagent and the second reagent comprises a
nonspecific reagent common to all reactions performed in the
central capillary flow cell or microfluidic device region, and
wherein the reaction specific reagent is more expensive than the
nonspecific reagent.
[0318] In some instances, utilization of the flow cell devices
and/or fluidic systems disclosed herein may convey advantages in
terms of reduced consumption of costly reagents. In some instances,
for example, utilization of the flow cell devices and/or fluidic
systems disclosed herein may results in at least a 5%, at least a
7.5%, at least a 10%, at least a 12.5%, at least a 15%, at least a
17.5%, at least a 20%, at least a 22.5%, at least a 25%, at least a
30%, at least a 35%, at least a 40%, at least a 45%, or at least a
50% reduction in reagent consumption compared to the reagent
consumption encountered when operating, e.g., current
commercially-available nucleic acid sequencing systems.
[0319] FIG. 31 illustrates a non-limiting example of a simple
fluidics system comprising a single capillary flow cell connected
to various fluid flow control components, where the single
capillary is optically accessible and compatible with mounting on a
microscope stage or in a custom imaging instrument for use in
various imaging applications. A plurality of reagent reservoirs is
fluidically-coupled with the inlet end of the single capillary flow
cell device, where the reagent flowing through the capillary at any
given point in time is controlled by means of a programmable rotary
valve that allows the user to control the timing and duration of
reagent flow. In this non-limiting example, fluid flow is
controlled by means of a programmable syringe pump that provides
precise control and timing of volumetric fluid flow and fluid flow
velocity.
[0320] FIG. 32 illustrates a non-limiting example of a fluidics
system that comprises a capillary flow cell cartridge having
integrated diaphragm valves to reduce or minimize dead volume and
conserve certain key reagents. The integration of miniature
diaphragm valves into the cartridge allows the valve to be
positioned in close proximity to the inlet of the capillary,
thereby reducing or minimizing dead volume within the device and
reducing the consumption of costly reagents. The integration of
valves and other fluid control components within the capillary flow
cell cartridge also allows greater fluid flow control functionality
to be incorporated into the cartridge design.
[0321] FIG. 33 illustrates a non-limiting example of a capillary
flow cell cartridge-based fluidics system used in combination with
a microscope setup, where the cartridge incorporates or mates with
a temperature control component such as a metal plate that makes
contact with the capillaries within the cartridge and serves as a
heat source/sink. The microscope setup consists of an illumination
system (e.g., including a laser, LED, or halogen lamp, etc., as a
light source), an objective lens, an imaging system (e.g., a CMOS
or CCD camera), and a translation stage to move the cartridge
relative to the optical system, which allows, e.g., fluorescence
and/or bright field images to be acquired for different regions of
the capillary flow cells as the stage is moved.
[0322] Temperature control modules: In some implementations the
disclosed systems will include temperature control functionality
for the purpose of facilitating the accuracy and reproducibility of
assay or analysis results. Examples of temperature control
components that may be incorporated into the instrument system (or
capillary flow cell cartridge) design include, but are not limited
to, resistive heating elements, infrared light sources, Peltier
heating or cooling devices, heat sinks, thermistors, thermocouples,
and the like. In some instances, the temperature control module (or
"temperature controller") may provide for a programmable
temperature change at a specified, adjustable time prior to
performing specific assay or analysis steps. In some instances, the
temperature controller may provide for programmable changes in
temperature over specified time intervals. In some embodiments, the
temperature controller may further provide for cycling of
temperatures between two or more set temperatures with specified
frequency and ramp rates so that thermal cycling for amplification
reactions may be performed.
[0323] FIG. 34 illustrates one non-limiting example for temperature
control of the flow cells (e.g., capillary flow cells or
microfluidic device-based flow cells) through the use of a metal
plate that is placed in contact with the flow cell cartridge. In
some instances, the metal plate may be integrated with the
cartridge chassis. In some instances, the metal plate may be
temperature controlled using a Peltier or resistive heater.
[0324] FIG. 35 illustrates one non-limiting approach for
temperature control of the flow cells (e.g., capillary or
microfluidic channel flow cells) that comprises a non-contact
thermal control mechanism. In this approach, a stream of
temperature-controlled air is directed through the flow cell
cartridge (e.g., towards a single capillary flow cell device or a
microfluidic channel flow cell device) using an air temperature
control system. The air temperature control system comprises a heat
exchanger, e.g., a resistive heater coil, fins attached to a
Peltier device, etc., that is capable of heating and/or cooling the
air and holding it at a constant, user-specified temperature. The
air temperature control system also comprises an air delivery
device, such as a fan, that directs the stream of heated or cooled
air to the capillary flow cell cartridge. In some instances, the
air temperature control system may be set to a constant temperature
T1 so that the air stream, and consequently the flow cell or
cartridge (e.g., capillary flow cell or microfluidic channel flow
cell) is kept at a constant temperature T2, which in some cases may
differ from the set temperature T1 depending on the environment
temperature, air flow rate, etc. In some instances, two or more
such air temperature control systems may be installed around the
capillary flow cell device or flow cell cartridge so that the
capillary or cartridge may be rapidly cycled between several
different temperatures by controlling which one of the air
temperature control systems is active at a given time. In another
approach, the temperature setting of the air temperature control
system may be varied so the temperature of the capillary flow cell
or cartridge may be changed accordingly.
[0325] Fluid dispensing robotics: In some implementations, the
disclosed systems may comprise an automated, programmable
fluid-dispensing (or liquid-dispensing) system for use in
dispensing reagents or other solutions into, e.g., microplates,
capillary flow cell devices and cartridges, microfluidic devices
and cartridges, etc. Suitable automated, programmable
fluid-dispensing systems are commercially available from a number
of vendors, e.g. Beckman Coulter, Perkin Elmer, Tecan, Velocity 11,
and many others. In a preferred aspect of the disclosed systems,
the fluid-dispensing system further comprises a multichannel
dispense head, e.g. a 4 channel, 8 channel, 16 channel, 96 channel,
or 384 channel dispense head, for simultaneous delivery of
programmable volumes of liquid (e.g. ranging from about 1
microliter to several milliliters) to multiple wells or locations
on a flow cell cartridge or microfluidic cartridge.
[0326] Cartridge- and/or microplate-handling (pick-and-place)
robotics: In some implementations, the disclosed system may
comprise a cartridge- and/or microplate-handling robotic system for
automated replacement and positioning of microplates, capillary
flow cell cartridges, or microfluidic device cartridges in relation
to the optical imaging system, or for optionally moving
microplates, capillary flow cell cartridges, or microfluidic device
cartridges between the optical imaging system and a
fluid-dispensing system. Suitable automated, programmable
microplate-handling robotic systems are commercially available from
a number of vendors, including Beckman Coulter, Perkin Elemer,
Tecan, Velocity 11, and many others. In a preferred aspect of the
disclosed systems, an automated microplate-handling robotic system
is configured to move collections of microwell plates comprising
samples and/or reagents to and from, e.g., refrigerated storage
units.
[0327] Spectroscopy or imaging modules: As indicated above, in some
implementations the disclosed analysis systems will include optical
imaging capabilities and may also include other spectroscopic
measurement capabilities. For example, the disclosed imaging
modules may be configured to operate in any of a variety of imaging
modes known to those of skill in the art including, but not limited
to, bright-field, dark-field, fluorescence, luminescence, or
phosphorescence imaging. In some instances, the one or more
capillary flow cells or microfluidic devices of a fluidics
sub-system comprise a window that allows at least a section of one
or more capillaries or one or more fluid channels in each flow cell
or microfluidic device to be illuminated and imaged.
[0328] In some embodiments, single wavelength excitation and
emission fluorescence imaging may be performed. In some
embodiments, dual wavelength excitation and emission (or
multi-wavelength excitation or emission) fluorescence imaging may
be performed. In some instances, the imaging module is configured
to acquire video images. The choice of imaging mode may impact the
design of the flow cells devices or cartridges in that all or a
portion of the capillaries or cartridge will necessarily need to be
optically transparent over the spectral range of interest. In some
instances, a plurality of capillaries within a capillary flow cell
cartridge may be imaged in their entirety within a single image. In
some instances, only a single capillary or a subset of capillaries
within a capillary flow cell cartridge, or portions thereof, may be
imaged within a single image. In some instances, a series of images
may be "tiled" to create a single high-resolution image of one,
two, several, or the entire plurality of capillaries within a
cartridge. In some instances, a plurality of fluid channels within
a microfluidic chip may be imaged in their entirety within a single
image. In some instances, only a single fluid channel or a subset
of fluid channels within a microfluidic chip, or portions thereof,
may be imaged within a single image. In some instances, a series of
images may be "tiled" to create a single high-resolution image of
one, two, several, or the entire plurality of fluid channels within
a cartridge.
[0329] A spectroscopy or imaging module may comprise, e.g., a
microscope equipped with a CMOS of CCD camera. In some instances,
the spectroscopy or imaging module may comprise, e.g., a custom
instrument such as one of the imaging modules described herein that
is configured to perform a specific spectroscopic or imaging
technique of interest. In general, the hardware associated with the
spectroscopy or imaging module may include light sources,
detectors, and other optical components, as well as processors or
computers.
[0330] Light sources: Any of a variety of light sources may be used
to provide the imaging or excitation light, including but not
limited to, tungsten lamps, tungsten-halogen lamps, arc lamps,
lasers, light emitting diodes (LEDs), or laser diodes. In some
instances, a combination of one or more light sources, and
additional optical components, e.g. lenses, filters, apertures,
diaphragms, mirrors, and the like, may be configured as an
illumination system (or sub-system).
[0331] Detectors: Any of a variety of image sensors may be used for
imaging purposes, including but not limited to, photodiode arrays,
charge-coupled device (CCD) cameras, or complementary
metal-oxide-semiconductor (CMOS) image sensors. As used herein,
"imaging sensors" may be one-dimensional (linear) or
two-dimensional array sensors. In many instances, a combination of
one or more image sensors, and additional optical components, e.g.
lenses, filters, apertures, diaphragms, mirrors, and the like, may
be configured as an imaging system (or sub-system). In some
instances, e.g., where spectroscopic measurements are performed by
the system rather than imaging, suitable detectors may include, but
are not limited to, photodiodes, avalanche photodiodes, and
photomultipliers.
[0332] Other optical components: The hardware components of the
spectroscopic measurement or imaging module may also include a
variety of optical components for steering, shaping, filtering, or
focusing light beams through the system. Examples of suitable
optical components include, but are not limited to, lenses,
mirrors, prisms, apertures, diffraction gratings, colored glass
filters, long-pass filters, short-pass filters, bandpass filters,
narrowband interference filters, broadband interference filters,
dichroic reflectors, optical fibers, optical waveguides, and the
like. In some instances, as noted above, the spectroscopic
measurement or imaging module may further comprise one or more
translation stages or other motion control mechanisms for the
purpose of moving capillary flow cell devices and cartridges
relative to the illumination and/or detection/imaging sub-systems,
or vice versa.
[0333] Total internal reflection: In some instances, the optical
module or sub-system may be designed to use all or a portion of an
optically transparent wall of the capillaries or microfluidic
channels in flow cell devices and cartridges as a waveguide for
delivering excitation light to the capillary or channel lumen(s)
via total internal reflection. When incident excitation light
strikes the surface of the capillary or channel lumen at an angle
with respect to a normal to the surface that is larger than the
critical angle (determined by the relative refractive indices of
the capillary or channel wall material and the aqueous buffer
within the capillary or channel), total internal reflection occurs
at the surface and the light propagates through the capillary or
channel wall along the length of the capillary or channel. Total
internal reflection generates an evanescent wave at the lumen
surface which penetrates the lumen interior for extremely short
distances, and which may be used to selectively excite fluorophores
at the surface, e.g., labeled nucleotides that have been
incorporated by a polymerase into a growing oligonucleotide through
a solid-phase primer extension reaction.
[0334] Light-tight housings and environmental control chambers: In
some implementations, the disclosed systems may comprise a
light-tight housing to prevent stray ambient light from creating
glare and obscuring, e.g., relatively faint fluorescence signals.
In some implementations, the disclosed systems may comprise an
environmental control chamber that enables the system to operate
under a tightly controlled temperature, humidity level, etc.
[0335] Processors and computers: In some instances, the disclosed
systems may comprise one or more processors or computers. The
processor may be a hardware processor such as a central processing
unit (CPU), a graphic processing unit (GPU), a general-purpose
processing unit, or a computing platform. The processor may be
comprised of any of a variety of suitable integrated circuits,
microprocessors, logic devices, field-programmable gate arrays
(FPGAs) and the like. In some instances, the processor may be a
single core or multi core processor, or a plurality of processors
may be configured for parallel processing. Although the disclosure
is described with reference to a processor, other types of
integrated circuits and logic devices are also applicable. The
processor may have any suitable data operation capability. For
example, the processor may perform 512 bit, 256 bit, 128 bit, 64
bit, 32 bit, or 16 bit data operations.
[0336] The processor or CPU can execute a sequence of
machine-readable instructions, which can be embodied in a program
or software. The instructions may be stored in a memory location.
The instructions can be directed to the CPU, which can subsequently
program or otherwise configure the CPU to implement, e.g., the
system control methods of the present disclosure. Examples of
operations performed by the CPU can include fetch, decode, execute,
and write back.
[0337] Some processors may comprise a processing unit of a computer
system. The computer system may enable cloud-based data storage
and/or computing. In some instances, the computer system may be
operatively coupled to a computer network ("network") with the aid
of a communication interface. The network may be the internet, an
intranet and/or extranet, an intranet and/or extranet that is in
communication with the internet, or a local area network (LAN). The
network in some cases is a telecommunication and/or data network.
The network may include one or more computer servers, which may
enable distributed computing, such as cloud-based computing.
[0338] The computer system may also include computer memory or
memory locations (e.g., random-access memory, read-only memory,
flash memory), electronic storage units (e.g., hard disk),
communication interfaces (e.g., network adapters) for communicating
with one or more other systems, and peripheral devices, such as
cache, other memory units, data storage units and/or electronic
display adapters. In some instances, the communication interface
may allow the computer to be in communication with one or more
additional devices. The computer may be able to receive input data
from the coupled devices for analysis. Memory units, storage units,
communication interfaces, and peripheral devices may be in
communication with the processor or CPU through a communication bus
(solid lines), such as may be incorporated into a motherboard. A
memory or storage unit may be a data storage unit (or data
repository) for storing data. The memory or storage units may store
files, such as drivers, libraries and saved programs. The memory or
storage units may store user data, e.g., user preferences and user
programs.
[0339] The system control, image processing, and/or data analysis
methods as described herein can be implemented by way of
machine-executable code stored in an electronic storage location of
the computer system, such as, for example, in the memory or
electronic storage unit. The machine-executable or machine-readable
code can be provided in the form of software. During use, the code
can be executed by the processor. In some cases, the code can be
retrieved from the storage unit and stored in memory for ready
access by the processor. In some situations, the electronic storage
unit can be precluded, and machine-executable instructions are
stored in memory.
[0340] In some instances, the code may be pre-compiled and
configured for use with a machine having a processer adapted to
execute the code. In some instances, the code may be compiled
during runtime. The code can be supplied in a programming language
that can be selected to enable the code to execute in a
pre-compiled or as-compiled fashion.
[0341] Some aspects of the systems and methods provided herein can
be embodied in software. Various aspects of the technology may be
thought of as "products" or "articles of manufacture" typically in
the form of machine (or processor) executable code and/or
associated data that is carried on or embodied in a type of
machine-readable medium. Machine-executable code can be stored on
an electronic storage unit, such as memory (e.g., read-only memory,
random-access memory, flash memory) or a hard disk. "Storage" type
media can include any or all of the tangible memory of the
computers, processors or the like, or associated modules thereof,
such as various semiconductor memories, tape drives, disk drives
and the like, which may provide non-transitory storage at any time
for the software programming. All or portions of the software may
at times be communicated through the Internet or various other
telecommunication networks. Such communications, for example, may
enable loading of the software from one computer or processor into
another, for example, from a management server or host computer
into the computer platform of an application server. Thus, another
type of media that may bear the software elements includes optical,
electrical and electromagnetic waves, such as used across physical
interfaces between local devices, through wired and optical
landline networks and over various air-links. The physical elements
that carry such waves, such as wired or wireless links, optical
links or the like, also may be considered as media bearing the
software. As used herein, unless restricted to non-transitory,
tangible "storage" media, terms such as computer or machine
"readable medium" refer to any medium that participates in
providing instructions to a processor for execution.
[0342] In some instances, the system control, image processing,
and/or data analysis methods of the present disclosure may be
implemented by way of one or more algorithms. An algorithm may be
implemented by way of software upon execution by the central
processing unit.
[0343] System control software: In some instances, the system may
comprise a computer (or processor) and a computer-readable medium
that includes code for providing a user interface as well as
manual, semi-automated, or fully-automated control of all system
functions, e.g., control of the fluid flow control module(s), the
temperature control module(s), and/or the spectroscopy or imaging
module(s), as well as other data analysis and display options. The
system computer or processor may be an integrated component of the
system (e.g. a microprocessor or mother board embedded within the
instrument) or may be a stand-alone module, for example, a main
frame computer, a personal computer, or a laptop computer. Examples
of fluid flow control functions provided by the system control
software include, but are not limited to, volumetric fluid flow
rates, fluid flow velocities, the timing and duration for sample
and reagent addition, buffer addition, and rinse steps. Examples of
temperature control functions provided by the system control
software include, but are not limited to, specifying temperature
set point(s) and control of the timing, duration, and ramp rates
for temperature changes. Examples of spectroscopic measurement or
imaging control functions provided by the system control software
include, but are not limited to, autofocus capability, control of
illumination or excitation light exposure times and intensities,
control of image acquisition rate, exposure time, and data storage
options.
[0344] Image processing software: In some instances, the system may
further comprise a computer (or processor) and computer-readable
medium that includes code for providing image processing and
analysis capability. Examples of image processing and analysis
capability that may be provided by the software include, but are
not limited to, manual, semi-automated, or fully-automated image
exposure adjustment (e.g. white balance, contrast adjustment,
signal-averaging and other noise reduction capability, etc.),
automated edge detection and object identification (e.g., for
identifying clonally-amplified clusters of fluorescently-labeled
oligonucleotides on the lumen surface of capillary flow cell
devices), automated statistical analysis (e.g., for determining the
number of clonally-amplified clusters of oligonucleotides
identified per unit area of the capillary lumen surface, or for
automated nucleotide base-calling in nucleic acid sequencing
applications), and manual measurement capabilities (e.g. for
measuring distances between clusters or other objects, etc.).
Optionally, instrument control and image processing/analysis
software may be written as separate software modules. In some
embodiments, instrument control and image processing/analysis
software may be incorporated into an integrated package.
[0345] Any of a variety of image processing methods known to those
of skill in the art may be used for image
processing/pre-processing. Examples include, but are not limited
to, Canny edge detection methods, Canny-Deriche edge detection
methods, first-order gradient edge detection methods (e.g., the
Sobel operator), second order differential edge detection methods,
phase congruency (phase coherence) edge detection methods, other
image segmentation algorithms (e.g., intensity thresholding,
intensity clustering methods, intensity histogram-based methods,
etc.), feature and pattern recognition algorithms (e.g., the
generalized Hough transform for detecting arbitrary shapes, the
circular Hough transform, etc.), and mathematical analysis
algorithms (e.g., Fourier transform, fast Fourier transform,
wavelet analysis, auto-correlation, etc.), or any combination
thereof.
[0346] Nucleic acid sequencing systems & applications: Nucleic
acid sequencing provides one non-limiting example of an application
for the disclosed flow cell devices (e.g., capillary flow cell
devices or cartridges and microfluidic devices and cartridges) and
imaging systems. Many "second generation" and "third generation"
sequencing technologies utilize a massively parallel, cyclic array
approach to perform sequencing-by-nucleotide incorporation, in
which accurate decoding of a single-stranded template
oligonucleotide sequence tethered to a solid support relies on
successfully classifying signals that arise from the stepwise
addition of A, G, C, and T nucleotides by a polymerase to a
complementary oligonucleotide strand. These methods typically
require the oligonucleotide template to be modified with a known
adapter sequence of fixed length, affixed to a solid support (e.g.,
the lumen surface(s) of the disclosed capillary flow cell devices
or microfluidic chips) in a random or patterned array by
hybridization to surface-tethered capture probes (also referred to
herein as "adapters" or "primers" tethered to the interior flow
cell surfaces) of known sequence that are complementary to that of
the adapter sequence, and then probed through a cyclic series of
single base addition primer extension reactions that use, e.g.,
fluorescently-labeled nucleotides to identify the sequence of bases
in the template oligonucleotides. These processes thus require the
use of miniaturized fluidics systems that offer precise,
reproducible control of the timing of reagent introduction to the
flow cell in which the sequencing reactions are performed, and
small volumes to reduce or minimize the consumption of costly
reagents.
[0347] Existing commercially-available NGS flow cells are
constructed from layers of glass that have been etched, lapped,
and/or processed by other methods to meet the tight dimensional
tolerances required for imaging, cooling, and/or other
requirements. When flow cells are used as consumables, the costly
manufacturing processes required for their fabrication result in
costs per sequencing run that are too high to make sequencing
routinely accessible to scientists and medical professionals in the
research and clinical fields.
[0348] This disclosure provides an example of a low-cost flow cell
architecture that includes low cost glass or polymer capillaries or
microfluidic channels, fluidics adapters, and cartridge chassis.
Utilizing glass or polymer capillaries that are extruded in their
final cross-sectional geometry may eliminate the need for multiple
high-precision and costly glass manufacturing processes. Robustly
constraining the orientation of the capillaries or microfluidic
channels and providing convenient fluidic connections using molded
plastic and/or elastomeric components further reduces cost. Laser
bonding the components of the polymer cartridge chassis provides a
fast and efficient means of sealing the capillary or the
microfluidic channels and structurally-stabilizing the capillaries
or channels and flow cell cartridge without requiring the use of
fasteners or adhesives.
[0349] The disclosed devices and systems may be configured to
perform nucleic acid sequencing using any of a variety of
"sequencing-by-nucleotide incorporation", "sequencing-by-nucleotide
binding", "sequencing-by-nucleotide base-pairing", and
"sequencing-by-avidity" sequencing biochemistries. The improvements
in flow cell device design disclosed herein, e.g., comprising
hydrophilic coated surfaces that maximize foreground signals for,
e.g., fluorescently-labeled nucleic acid clusters disposed thereon,
while minimizing background signal may give rise to improvements in
CNR for images used for base-calling purposes, in combination with
improvements in optical imaging system design for fast dual-surface
flow cell imaging (comprising simultaneous or near-simultaneous
imaging of the interior flow cell surfaces) achieved through
improved objective lens and/or tube lens designs that provide for
larger depth of field and larger fields-of-view, and reduced
reagent consumption (achieved through improved flow cell design)
may give rise to dramatic improvements in base-calling accuracy,
shortened imaging cycle times, shortened overall sequencing
reaction cycle times, and higher throughput nucleic acid sequencing
at reduced cost per base.
[0350] In some instances, the disclosed hydrophilic, polymer coated
flow cell devices used in combination with the optical imaging
systems disclosed herein may confer one or more of the following
additional advantages for a nucleic acid sequencing system: (i)
decreased fluidic wash times (due to reduced non-specific binding,
and thus faster sequencing cycle times), (ii) decreased imaging
times (and thus faster turnaround times for assay readout and
sequencing cycles), (iii) decreased overall work flow time
requirements (due to decreased cycle times), (iv) decreased
detection instrumentation costs (due to the improvements in CNR),
(v) improved readout (base-calling) accuracy (due to improvements
in CNR), (vi) improved reagent stability and decreased reagent
usage requirements (and thus reduced reagents costs), and (vii)
fewer run-time failures due to nucleic acid amplification
failures.
[0351] The methods, devices, and systems disclosed herein for
performing nucleic acid sequencing are suitable for a variety of
sequencing applications and for sequencing nucleic acid molecules
derived from any of a variety of samples and sources. Nucleic
acids, in some instances, may be extracted from any of a variety of
biological samples, e.g., blood samples, saliva samples, urine
samples, cell samples, tissue samples, and the like. For example,
the disclosed devices and systems may be used for the analysis of
nucleic acid molecules derived from any of a variety of different
cell, tissue, or sample types known to those of skill in the art.
For example, nucleic acids may be extracted from cells, or tissue
samples comprising one or more types of cells, derived from
eukaryotes (such as animals, plants, fungi, protista),
archaebacteria, or eubacteria. In some cases, nucleic acids may be
extracted from prokaryotic or eukaryotic cells, such as adherent or
non-adherent eukaryotic cells. Nucleic acids are variously
extracted from, for example, primary or immortalized rodent,
porcine, feline, canine, bovine, equine, primate, or human cell
lines. Nucleic acids may be extracted from any of a variety of
different cell, organ, or tissue types (e.g., white blood cells,
red blood cells, platelets, epithelial cells, endothelial cells,
neurons, glial cells, astrocytes, fibroblasts, skeletal muscle
cells, smooth muscle cells, gametes, or cells from the heart,
lungs, brain, liver, kidney, spleen, pancreas, thymus, bladder,
stomach, colon, or small intestine). Nucleic acids may be extracted
from normal or healthy cells. Alternately or in combination, acids
are extracted from diseased cells, such as cancerous cells, or from
pathogenic cells that are infecting a host. Some nucleic acids may
be extracted from a distinct subset of cell types, e.g., immune
cells (such as T cells, cytotoxic (killer) T cells, helper T cells,
alpha beta T cells, gamma delta T cells, T cell progenitors, B
cells, B-cell progenitors, lymphoid stem cells, myeloid progenitor
cells, lymphocytes, granulocytes, Natural Killer cells, plasma
cells, memory cells, neutrophils, eosinophils, basophils, mast
cells, monocytes, dendritic cells, and/or macrophages, or any
combination thereof), undifferentiated human stem cells, human stem
cells that have been induced to differentiate, rare cells (e.g.,
circulating tumor cells (CTCs), circulating epithelial cells,
circulating endothelial cells, circulating endometrial cells, bone
marrow cells, progenitor cells, foam cells, mesenchymal cells, or
trophoblasts). Other cells are contemplated and consistent with the
disclosure herein.
[0352] Nucleic acids may optionally be attached to one or more
non-nucleotide moieties such as labels and other small molecules,
large molecules (such as proteins, lipids, sugars, etc.), and solid
or semi-solid supports, for example through covalent or
non-covalent linkages with either the 5' or 3' end of the nucleic
acid. Labels include any moiety that is detectable using any of a
variety of detection methods known to those of skill in the art,
and thus renders the attached oligonucleotide or nucleic acid
similarly detectable. Some labels, e.g., fluorophores, emit
electromagnetic radiation that is optically detectable or visible.
Alternately or in combination, some labels comprise a mass tag that
renders the labeled oligonucleotide or nucleic acid visible in mass
spectral data, or a redox tag that renders the labeled
oligonucleotide or nucleic acid detectable by amperometry or
voltametry. Some labels comprise a magnetic tag that facilitates
separation and/or purification of the labeled oligonucleotide or
nucleic acid. The nucleotide or polynucleotide is often not
attached to a label, and the presence of the oligonucleotide or
nucleic acid is directly detected.
[0353] Flow cell devices configured for sequencing: In some
instances, one or more flow cell devices according to the present
disclosure may be configured for nucleic acid sequencing
applications, e.g., wherein two or more interior flow cell device
surfaces comprise hydrophilic polymer coatings that further
comprise one or more capture oligonucleotides, e.g., adapter/primer
oligonucleotides, or any other oligonucleotides as disclosed
herein. In some instances, the hydrophilic, polymer-coated surfaces
of the disclosed flow cell devices may comprise a plurality of
oligonucleotides tethered thereto that have been selected for use
in sequencing a eukaryotic genome. In some instances, the
hydrophilic, polymer-coated surfaces of the disclosed flow cell
devices may comprise a plurality of oligonucleotides tethered
thereto that have been selected for use in sequencing a prokaryotic
genome or portion thereof. In some instances, the hydrophilic,
polymer-coated surfaces of the disclosed flow cell devices may
comprise a plurality of oligonucleotides tethered thereto that have
been selected for use in sequencing a viral genome or portion
thereof. In some instances, the hydrophilic, polymer-coated
surfaces of the disclosed flow cell devices may comprise a
plurality of oligonucleotides tethered thereto that have been
selected for use in sequencing a transcriptome.
[0354] In some instances, a flow cell device of the present
disclosure may comprise a first surface in an orientation generally
facing the interior of the flow channel, a second surface in an
orientation generally facing the interior of the flow channel and
further generally facing or parallel to the first surface, a third
surface generally facing the interior of a second flow channel, and
a fourth surface, generally facing the interior of the second flow
channel and generally opposed to or parallel to the third surface;
wherein said second and third surfaces may be located on or
attached to opposite sides of a generally planar substrate which
may be a reflective, transparent, or translucent substrate. In some
instances, an imaging surface or imaging surfaces within a flow
cell may be located within the center of a flow cell or within or
as part of a division between two subunits or subdivisions of a
flow cell, wherein said flow cell may comprise a top surface and a
bottom surface, one or both of which may be transparent to such
detection mode as may be utilized; and wherein a surface comprising
oligonucleotides adapters/primers tethered to one or more polymer
coatings may be placed or interposed within the lumen of the flow
cell. In some instances, the top and/or bottom surfaces do not
include attached oligonucleotide adapters/primers. In some
instances, said top and/or bottom surfaces do comprise attached
oligonucleotide adapters/primers. In some instances, either said
top or said bottom surface may comprise attached oligonucleotide
adapters/primers. A surface or surfaces placed or interposed within
the lumen of a flow cell may be located on or attached to one side,
to an opposite side, or to both sides of a generally planar
substrate which may be a reflective, transparent, or translucent
substrate.
[0355] In general, at least one layer of the one or more layers of
low nonspecific binding coating on the flow cell device surfaces
may comprise functional groups for covalently or non-covalently
attaching oligonucleotide molecules, e.g., adapter or primer
sequences, or the at least one layer may already comprise
covalently or non-covalently attached oligonucleotide adapter or
primer sequences at the time that it is deposited on the support
surface. In some instances, the oligonucleotides tethered to the
polymer molecules of at least one third layer may be distributed at
a plurality of depths throughout the layer.
[0356] In some instances, the oligonucleotide adapter or primer
molecules are covalently coupled to the polymer in solution, i.e.,
prior to coupling or depositing the polymer on the surface. In some
instances, the oligonucleotide adapter or primer molecules are
covalently coupled to the polymer after it has been coupled to or
deposited on the surface. In some instances, at least one
hydrophilic polymer layer comprises a plurality of
covalently-attached oligonucleotide adapter or primer molecules. In
some instances, at least two, at least three, at least four, or at
least five layers of hydrophilic polymer comprise a plurality of
covalently-attached adapter or primer molecules.
[0357] In some instances, the oligonucleotide adapter or primer
molecules may be coupled to the one or more layers of hydrophilic
polymer using any of a variety of suitable conjugation chemistries
known to those of skill in the art. For example, the
oligonucleotide adapter or primer sequences may comprise moieties
that are reactive with amine groups, carboxyl groups, thiol groups,
and the like. Examples of suitable amine-reactive conjugation
chemistries that may be used include, but are not limited to,
reactions involving isothiocyanate, isocyanate, acyl azide, NHS
ester, sulfonyl chloride, aldehyde, glyoxal, epoxide, oxirane,
carbonate, aryl halide, imidoester, carbodiimide, anhydride, and
fluorophenyl ester groups. Examples of suitable carboxyl-reactive
conjugation chemistries include, but are not limited to, reactions
involving carbodiimide compounds, e.g., water soluble EDC
(1-ethyl-3-(3-dimethylaminopropyl)carbodiimide.HCL). Examples of
suitable sulfydryl-reactive conjugation chemistries include
maleimides, haloacetyls and pyridyl disulfides.
[0358] One or more types of oligonucleotide molecules may be
attached or tethered to the support surface. In some instances, the
one or more types of oligonucleotide adapters or primers may
comprise spacer sequences, adapter sequences for hybridization to
adapter-ligated template library nucleic acid sequences, forward
amplification primers, reverse amplification primers, sequencing
primers, and/or molecular barcoding sequences, or any combination
thereof. In some instances, 1 primer or adapter sequence may be
tethered to at least one layer of the surface. In some instances,
at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 different
primer or adapter sequences may be tethered to at least one layer
of the surface.
[0359] In some instances, the tethered oligonucleotide adapter
and/or primer sequences may range in length from about 10
nucleotides to about 100 nucleotides. In some instances, the
tethered oligonucleotide adapter and/or primer sequences may be at
least 10, at least 20, at least 30, at least 40, at least 50, at
least 60, at least 70, at least 80, at least 90, or at least 100
nucleotides in length. In some instances, the tethered
oligonucleotide adapter and/or primer sequences may be at most 100,
at most 90, at most 80, at most 70, at most 60, at most 50, at most
40, at most 30, at most 20, or at most 10 nucleotides in length.
Any of the lower and upper values described in this paragraph may
be combined to form a range included within the present disclosure,
for example, in some instances the length of the tethered
oligonucleotide adapter and/or primer sequences may range from
about 20 nucleotides to about 80 nucleotides. Those of skill in the
art will recognize that the length of the tethered oligonucleotide
adapter and/or primer sequences may have any value within this
range, e.g., about 24 nucleotides.
[0360] In some instances, the number of coating layers and/or the
material composition of each layer is chosen so as to adjust the
resultant surface density of oligonucleotide adapters/primers (or
other attached molecules) on the coated interior flow cell
surfaces. In some instances, the surface density of oligonucleotide
adapters/primers may range from about 1,000 primer molecules per
.mu.m.sup.2 to about 1,000,000 primer molecules per .mu.m.sup.2. In
some instances, the surface density of oligonucleotide primers may
be at least 1,000, at least 10,000, at least 100,000, or at least
1,000,000 molecules per .mu.m.sup.2. In some instances, the surface
density of oligonucleotide primers may be at most 1,000,000, at
most 100,000, at most 10,000, or at most 1,000 molecules per
.mu.m.sup.2. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the surface
density of primers may range from about 10,000 molecules per
.mu.m.sup.2 to about 100,000 molecules per .mu.m.sup.2. Those of
skill in the art will recognize that the surface density of primer
molecules may have any value within this range, e.g., about 455,000
molecules per .mu.m.sup.2. In some instances, the surface
properties of the capillary or channel lumen coating, including the
surface density of tethered oligonucleotide primers, may be
adjusted to improve or optimize, e.g., solid-phase nucleic acid
hybridization specificity and efficiency, and/or solid-phase
nucleic acid amplification rate, specificity, and efficiency.
[0361] In some instances, the tethered adapter or primer sequences
may comprise modifications designed to facilitate the specificity
and efficiency of nucleic acid amplification as performed on the
low-binding supports. For example, in some instances the primer may
comprise polymerase stop points such that the stretch of primer
sequence between the surface conjugation point and the modification
site is always in single-stranded form and functions as a loading
site for 5' to 3' helicases in some helicase-dependent isothermal
amplification methods. Other examples of primer modifications that
may be used to create polymerase stop points include, but are not
limited to, an insertion of a PEG chain into the backbone of the
primer between two nucleotides towards the 5' end, insertion of an
abasic nucleotide (i.e., a nucleotide that has neither a purine nor
a pyrimidine base), or a lesion site which can be bypassed by the
helicase.
[0362] Nucleic acid hybridization: In some instances, the
hydrophilic, polymer coated flow cell device surfaces disclosed
herein may provide advantages when used alone or in combination
with improved buffer formulations for performing solid-phase
nucleic acid hybridization and/or solid-phase nucleic acid
amplification reactions as part of genotyping or nucleic acid
sequencing applications. In some instances, the polymer-coated flow
cell devices disclosed herein may provide advantages in terms of
improved nucleic acid hybridization rate and specificity, and
improved nucleic acid amplification rates and specificity that may
be achieved through one or more of the following additional aspects
of the present disclosure: (i) primer design (e.g., sequence and/or
modifications), (ii) control of tethered primer density on the
solid support, (iii) the surface composition of the solid support,
(iv) the surface polymer density of the solid support, (v) the use
of improved hybridization conditions before and during
amplification, and/or (vi) the use of improved amplification
formulations that decrease non-specific primer amplification or
increase template amplification efficiency.
[0363] In some instances, it may be desirable to vary the surface
density of tethered oligonucleotide adapters or primers on the
coated flow cell surfaces and/or the spacing of the tethered
adapters or primers away from the coated flow cell surface (e.g.,
by varying the length of a linker molecule used to tether the
adapter or primers to the surface) in order to "tune" the support
for optimal performance when, e.g., using a given amplification
method. In some instances, adjusting the surface density of
tethered oligonucleotide adapters or primers may impact the level
of specific and/or non-specific amplification observed on the
surface in a manner that varies according to the amplification
method selected. In some instances, the surface density of tethered
oligonucleotide adapters or primers may be varied by adjusting the
ratio of molecular components used to create the support surface.
For example, in the case that an oligonucleotide primer--PEG
conjugate is used to create the final layer of a low-binding
support, the ratio of the oligonucleotide primer--PEG conjugate to
a non-conjugated PEG molecule may be varied. The resulting surface
density of tethered primer molecules may then be estimated or
measured using any of a variety of techniques known to those of
skill in the art. Examples include, but are not limited to, the use
of radioisotope labeling and counting methods, covalent coupling of
a cleavable molecule that comprises an optically-detectable tag
(e.g., a fluorescent tag) that may be cleaved from a support
surface of defined area, collected in a fixed volume of an
appropriate solvent, and then quantified by comparison of
fluorescence signals to that for a calibration solution of known
optical tag concentration, or using fluorescence imaging techniques
provided that care has been taken with the labeling reaction
conditions and image acquisition settings to ensure that the
fluorescence signals are linearly related to the number of
fluorophores on the surface (e.g., that there is no significant
self-quenching of the fluorophores on the surface).
[0364] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, either alone or in combination
with improved or optimized buffer formulations, may yield relative
hybridization rates that range from about 2.times. to about
20.times. faster than that for a conventional hybridization
protocol. In some instances, the relative hybridization rate may be
at least 2.times., at least 3.times., at least 4.times., at least
5.times., at least 6.times., at least 7.times., at least 8.times.,
at least 9.times., at least 10.times., at least 12.times., at least
14.times., at least 16.times., at least 18.times., at least
20.times., at least 25.times., at least 30.times., or at least
40.times. that for a conventional hybridization protocol.
[0365] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, either alone or in combination
with improved or optimized buffer formulations, may yield total
hybridization reaction times (i.e., the time required to reach 90%,
95%, 98%, or 99% completion of the hybridization reaction) of less
than 60 minutes, 50 minutes, 40 minutes, 30 minutes, 20 minutes, 15
minutes, 10 minutes, or 5 minutes for any of these completion
metrics.
[0366] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, either alone or in combination
with improved or optimized buffer formulations, may yield improved
hybridization specificity compared to that for a conventional
hybridization protocol. In some instances, the hybridization
specificity that may be achieved is better than 1 base mismatch in
10 hybridization events, 1 base mismatch in 20 hybridization
events, 1 base mismatch in 30 hybridization events, 1 base mismatch
in 40 hybridization events, 1 base mismatch in 50 hybridization
events, 1 base mismatch in 75 hybridization events, 1 base mismatch
in 100 hybridization events, 1 base mismatch in 200 hybridization
events, 1 base mismatch in 300 hybridization events, 1 base
mismatch in 400 hybridization events, 1 base mismatch in 500
hybridization events, 1 base mismatch in 600 hybridization events,
1 base mismatch in 700 hybridization events, 1 base mismatch in 800
hybridization events, 1 base mismatch in 900 hybridization events,
1 base mismatch in 1,000 hybridization events, 1 base mismatch in
2,000 hybridization events, 1 base mismatch in 3,000 hybridization
events, 1 base mismatch in 4,000 hybridization events, 1 base
mismatch in 5,000 hybridization events, 1 base mismatch in 6,000
hybridization events, 1 base mismatch in 7,000 hybridization
events, 1 base mismatch in 8,000 hybridization events, 1 base
mismatch in 9,000 hybridization events, or 1 base mismatch in
10,000 hybridization events.
[0367] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, either alone or in combination
with improved or optimized buffer formulations, may yield improved
hybridization efficiency (e.g., the fraction of available
oligonucleotide primers on the support surface that are
successfully hybridized with target oligonucleotide sequences)
compared to that for a conventional hybridization protocol. In some
instances, the hybridization efficiency that may be achieved is
better than 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, or 99% for any
of the input target oligonucleotide concentrations specified below
and in any of the hybridization reaction times specified above. In
some instances, e.g., wherein the hybridization efficiency is less
than 100%, the resulting surface density of target nucleic acid
sequences hybridized to the support surface may be less than the
surface density of oligonucleotide adapter or primer sequences on
the surface.
[0368] In some instances, use of the disclosed hydrophilic,
polymer-coated flow cell devices for nucleic acid hybridization (or
nucleic acid amplification) applications using conventional
hybridization (or amplification) protocols, or improved or
optimized hybridization (or amplification) protocols, may lead to a
reduced requirement for the input concentration of target (or
sample) nucleic acid molecules contacted with the support surface.
For example, in some instances, the target (or sample) nucleic acid
molecules may be contacted with the support surface at a
concentration ranging from about 10 pM to about 1 .mu.M (i.e.,
prior to annealing or amplification). In some instances, the target
(or sample) nucleic acid molecules may be administered at a
concentration of at least 10 pM, at least 20 pM, at least 30 pM, at
least 40 pM, at least 50 pM, at least 100 pM, at least 200 pM, at
least 300 pM, at least 400 pM, at least 500 pM, at least 600 pM, at
least 700 pM, at least 800 pM, at least 900 pM, at least 1 nM, at
least 10 nM, at least 20 nM, at least 30 nM, at least 40 nM, at
least 50 nM, at least 60 nM, at least 70 nM, at least 80 nM, at
least 90 nM, at least 100 nM, at least 200 nM, at least 300 nM, at
least 400 nM, at least 500 nM, at least 600 nM, at least 700 nM, at
least 800 nM, at least 900 nM, or at least 1 .mu.M. In some
instances, the target (or sample) nucleic acid molecules may be
administered at a concentration of at most 1 .mu.M, at most 900 nM,
at most 800 nm, at most 700 nM, at most 600 nM, at most 500 nM, at
most 400 nM, at most 300 nM, at most 200 nM, at most 100 nM, at
most 90 nM, at most 80 nM, at most 70 nM, at most 60 nM, at most 50
nM, at most 40 nM, at most 30 nM, at most 20 nM, at most 10 nM, at
most 1 nM, at most 900 pM, at most 800 pM, at most 700 pM, at most
600 pM, at most 500 pM, at most 400 pM, at most 300 pM, at most 200
pM, at most 100 pM, at most 90 pM, at most 80 pM, at most 70 pM, at
most 60 pM, at most 50 pM, at most 40 pM, at most 30 pM, at most 20
pM, or at most 10 pM. Any of the lower and upper values described
in this paragraph may be combined to form a range included within
the present disclosure, for example, in some instances the target
(or sample) nucleic acid molecules may be administered at a
concentration ranging from about 90 pM to about 200 nM. Those of
skill in the art will recognize that the target (or sample) nucleic
acid molecules may be administered at a concentration having any
value within this range, e.g., about 855 nM.
[0369] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, either alone or in combination
with improved or optimized hybridization buffer formulations, may
result in a surface density of hybridized target (or sample)
oligonucleotide molecules (i.e., prior to performing any subsequent
solid-phase or clonal amplification reaction) ranging from about
from about 0.0001 target oligonucleotide molecules per .mu.m.sup.2
to about 1,000,000 target oligonucleotide molecules per
.mu.m.sup.2. In some instances, the surface density of hybridized
target oligonucleotide molecules may be at least 0.0001, at least
0.0005, at least 0.001, at least 0.005, at least 0.01, at least
0.05, at least 0.1, at least 0.5, at least 1, at least 5, at least
10, at least 20, at least 30, at least 40, at least 50, at least
60, at least 70, at least 80, at least 90, at least 100, at least
200, at least 300, at least 400, at least 500, at least 600, at
least 700, at least 800, at least 900, at least 1,000, at least
1,500, at least 2,000, at least 2,500, at least 3,000, at least
3,500, at least 4,000, at least 4,500, at least 5,000, at least
5,500, at least 6,000, at least 6,500, at least 7,000, at least
7,500, at least 8,000, at least 8,500, at least 9,000, at least
9,500, at least 10,000, at least 15,000, at least 20,000, at least
25,000, at least 30,000, at least 35,000, at least 40,000, at least
45,000, at least 50,000, at least 55,000, at least 60,000, at least
65,000, at least 70,000, at least 75,000, at least 80,000, at least
85,000, at least 90,000, at least 95,000, at least 100,000, at
least 150,000, at least 200,000, at least 250,000, at least
300,000, at least 350,000, at least 400,000, at least 450,000, at
least 500,000, at least 550,000, at least 600,000, at least
650,000, at least 700,000, at least 750,000, at least 800,000, at
least 850,000, at least 900,000, at least 950,000, or at least
1,000,000 molecules per .mu.m.sup.2. In some instances, the surface
density of hybridized target oligonucleotide molecules may be at
most 1,000,000, at most 950,000, at most 900,000, at most 850,000,
at most 800,000, at most 750,000, at most 700,000, at most 650,000,
at most 600,000, at most 550,000, at most 500,000, at most 450,000,
at most 400,000, at most 350,000, at most 300,000, at most 250,000,
at most 200,000, at most 150,000, at most 100,000, at most 95,000,
at most 90,000, at most 85,000, at most 80,000, at most 75,000, at
most 70,000, at most 65,000, at most 60,000, at most 55,000, at
most 50,000, at most 45,000, at most 40,000, at most 35,000, at
most 30,000, at most 25,000, at most 20,000, at most 15,000, at
most 10,000, at most 9,500, at most 9,000, at most 8,500, at most
8,000, at most 7,500, at most 7,000, at most 6,500, at most 6,000,
at most 5,500, at most 5,000, at most 4,500, at most 4,000, at most
3,500, at most 3,000, at most 2,500, at most 2,000, at most 1,500,
at most 1,000, at most 900, at most 800, at most 700, at most 600,
at most 500, at most 400, at most 300, at most 200, at most 100, at
most 90, at most 80, at most 70, at most 60, at most 50, at most
40, at most 30, at most 20, at most 10, at most 5, at most 1, at
most 0.5, at most 0.1, at most 0.05, at most 0.01, at most 0.005,
at most 0.001, at most 0.0005, or at most 0.0001 molecules per
.mu.m.sup.2. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the surface
density of hybridized target oligonucleotide molecules may range
from about 3,000 molecules per .mu.m.sup.2 to about 20,000
molecules per .mu.m.sup.2. Those of skill in the art will recognize
that the surface density of hybridized target oligonucleotide
molecules may have any value within this range, e.g., about 2,700
molecules per .mu.m2.
[0370] Stated differently, in some instances the use of the
disclosed low-binding supports alone or in combination with
improved or optimized hybridization buffer formulations may result
in a surface density of hybridized target (or sample)
oligonucleotide molecules (i.e., prior to performing any subsequent
solid-phase or clonal amplification reaction) ranging from about
100 hybridized target oligonucleotide molecules per mm.sup.2 to
about 1.times.10.sup.12 hybridized target oligonucleotide molecules
per mm.sup.2. In some instances, the surface density of hybridized
target oligonucleotide molecules may be at least 100, at least 500,
at least 1,000, at least 4,000, at least 5,000, at least 6,000, at
least 10,000, at least 15,000, at least 20,000, at least 25,000, at
least 30,000, at least 35,000, at least 40,000, at least 45,000, at
least 50,000, at least 55,000, at least 60,000, at least 65,000, at
least 70,000, at least 75,000, at least 80,000, at least 85,000, at
least 90,000, at least 95,000, at least 100,000, at least 150,000,
at least 200,000, at least 250,000, at least 300,000, at least
350,000, at least 400,000, at least 450,000, at least 500,000, at
least 550,000, at least 600,000, at least 650,000, at least
700,000, at least 750,000, at least 800,000, at least 850,000, at
least 900,000, at least 950,000, at least 1,000,000, at least
5,000,000, at least 1.times.10.sup.7, at least 5.times.10.sup.7, at
least 1.times.10.sup.8, at least 5.times.10.sup.8, at least
1.times.10.sup.9, at least 5.times.10.sup.9, at least
1.times.10.sup.10, at least 5.times.10.sup.10, at least
1.times.10.sup.11, at least 5.times.10.sup.11, or at least
1.times.10.sup.12 molecules per mm.sup.2. In some instances, the
surface density of hybridized target oligonucleotide molecules may
be at most 1.times.10.sup.12, at most 5.times.10.sup.11, at most
1.times.10.sup.11, at most 5.times.10.sup.10, at most
1.times.10.sup.10, at most 5.times.10.sup.9, at most
1.times.10.sup.9, at most 5.times.10.sup.8, at most
1.times.10.sup.8, at most 5.times.10.sup.7, at most
1.times.10.sup.7, at most 5,000,000, at most 1,000,000, at most
950,000, at most 900,000, at most 850,000, at most 800,000, at most
750,000, at most 700,000, at most 650,000, at most 600,000, at most
550,000, at most 500,000, at most 450,000, at most 400,000, at most
350,000, at most 300,000, at most 250,000, at most 200,000, at most
150,000, at most 100,000, at most 95,000, at most 90,000, at most
85,000, at most 80,000, at most 75,000, at most 70,000, at most
65,000, at most 60,000, at most 55,000, at most 50,000, at most
45,000, at most 40,000, at most 35,000, at most 30,000, at most
25,000, at most 20,000, at most 15,000, at most 10,000, at most
5,000, at most 1,000, at most 500, or at most 100 molecules per
mm.sup.2. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the surface
density of hybridized target oligonucleotide molecules may range
from about 5,000 molecules per mm.sup.2 to about 50,000 molecules
per mm.sup.2. Those of skill in the art will recognize that the
surface density of hybridized target oligonucleotide molecules may
have any value within this range, e.g., about 50,700 molecules per
mm.sup.2.
[0371] In some instances, the target (or sample) oligonucleotide
molecules (or nucleic acid molecules) hybridized to the
oligonucleotide adapter or primer molecules attached to the
low-binding support surface may range in length from about 0.02
kilobases (kb) to about 20 kb or from about 0.1 kilobases (kb) to
about 20 kb. In some instances, the target oligonucleotide
molecules may be at least 0.001 kb, at least 0.005 kb, at least
0.01 kb, at least 0.02 kb, at least 0.05 kb, at least 0.1 kb in
length, at least 0.2 kb in length, at least 0.3 kb in length, at
least 0.4 kb in length, at least 0.5 kb in length, at least 0.6 kb
in length, at least 0.7 kb in length, at least 0.8 kb in length, at
least 0.9 kb in length, at least 1 kb in length, at least 2 kb in
length, at least 3 kb in length, at least 4 kb in length, at least
5 kb in length, at least 6 kb in length, at least 7 kb in length,
at least 8 kb in length, at least 9 kb in length, at least 10 kb in
length, at least 15 kb in length, at least 20 kb in length, at
least 30 kb in length, or at least 40 kb in length, or any
intermediate value spanned by the range described herein, e.g., at
least 0.85 kb in length.
[0372] In some instances, the target (or sample) oligonucleotide
molecules (or nucleic acid molecules) may comprise single-stranded
or double-stranded, multimeric nucleic acid molecules (e.g.,
concatamers) further comprising repeats of a regularly occurring
monomer unit. In some instances, the single-stranded or
double-stranded, multimeric nucleic acid molecules may be at least
0.001 kb, at least 0.005 kb, at least 0.01 kb, at least 0.02 kb, at
least 0.05 kb, at least 0.1 kb in length, at least 0.2 kb in
length, at least 0.3 kb in length, at least 0.4 kb in length, at
least 0.5 kb in length, at least 1 kb in length, at least 2 kb in
length, at least 3 kb in length, at least 4 kb in length, at least
5 kb in length, at least 6 kb in length, at least 7 kb in length,
at least 8 kb in length, at least 9 kb in length, at least 10 kb in
length, at least 15 kb in length, or at least 20 kb in length, at
least 30 kb in length, or at least 40 kb in length, or any
intermediate value spanned by the range described herein, e.g.,
about 2.45 kb in length.
[0373] In some instances, the target (or sample) oligonucleotide
molecules (or nucleic acid molecules) may comprise single-stranded
or double-stranded multimeric nucleic acid molecules (e.g.,
concatamers) comprising from about 2 to about 100 copies of a
regularly repeating monomer unit. In some instances, the number of
copies of the regularly repeating monomer unit may be at least 2,
at least 3, at least 4, at least 5, at least 10, at least 15, at
least 20, at least 25, at least 30, at least 35, at least 40, at
least 45, at least 50, at least 55, at least 60, at least 65, at
least 70, at least 75, at least 80, at least 85, at least 90, at
least 95, and at least 100. In some instances, the number of copies
of the regularly repeating monomer unit may be at most 100, at most
95, at most 90, at most 85, at most 80, at most 75, at most 70, at
most 65, at most 60, at most 55, at most 50, at most 45, at most
40, at most 35, at most 30, at most 25, at most 20, at most 15, at
most 10, at most 5, at most 4, at most 3, or at most 2. Any of the
lower and upper values described in this paragraph may be combined
to form a range included within the present disclosure, for
example, in some instances the number of copies of the regularly
repeating monomer unit may range from about 4 to about 60. Those of
skill in the art will recognize that the number of copies of the
regularly repeating monomer unit may have any value within this
range, e.g., about 17. Thus, in some instances, the surface density
of hybridized target sequences in terms of the number of copies of
a target sequence per unit area of the support surface may exceed
the surface density of oligonucleotide primers even if the
hybridization efficiency is less than 100%.
[0374] Nucleic acid surface amplification (NASA): As used herein,
the phrase "nucleic acid surface amplification" (NASA) is used
interchangeably with the phrase "solid-phase nucleic acid
amplification" (or simply "solid-phase amplification"). In some
aspects of the present disclosure, nucleic acid amplification
formulations are described which, in combination with the disclosed
hydrophilic, polymer-coated flow cell devices, provide for improved
amplification rates, amplification specificity, and amplification
efficiency. As used herein, specific amplification refers to
amplification of template library oligonucleotide strands that have
been tethered to the solid support either covalently or
non-covalently. As used herein, non-specific amplification refers
to amplification of primer-dimers or other non-template nucleic
acids. As used herein, amplification efficiency is a measure of the
percentage of tethered oligonucleotides on the support surface that
are successfully amplified during a given amplification cycle or
amplification reaction. Nucleic acid amplification performed on
surfaces disclosed herein may obtain amplification efficiencies of
at least 50%, 60%, 70%, 80%, 90%, 95%, or greater than 95%, such as
98% or 99%.
[0375] Any of a variety of thermal cycling or isothermal nucleic
acid amplification schemes may be used with the disclosed
low-binding supports. Examples of nucleic acid amplification
methods that may be utilized with the disclosed low-binding
supports include, but are not limited to, polymerase chain reaction
(PCR), multiple displacement amplification (MDA),
transcription-mediated amplification (TMA), nucleic acid
sequence-based amplification (NASBA), strand displacement
amplification (SDA), real-time SDA, bridge amplification,
isothermal bridge amplification, rolling circle amplification,
circle-to-circle amplification, helicase-dependent amplification,
recombinase-dependent amplification, or single-stranded binding
(SSB) protein-dependent amplification.
[0376] In some instances, improvements in amplification rate,
amplification specificity, and amplification efficiency may be
achieved using the disclosed hydrophilic, polymer-coated flow cell
devices, either alone or in combination with formulations of the
amplification reaction components. In addition to inclusion of
nucleotides, one or more polymerases, helicases, single-stranded
binding proteins, etc. (or any combination thereof), the
amplification reaction mixture may be adjusted in a variety of ways
to achieve improved performance including, but are not limited to,
choice of buffer type, buffer pH, organic solvent mixtures, buffer
viscosity, detergents and zwitterionic components, ionic strength
(including adjustment of both monovalent and divalent ion
concentrations), antioxidants and reducing agents, carbohydrates,
BSA, polyethylene glycol, dextran sulfate, betaine, other
additives, and the like.
[0377] The use of the disclosed hydrophilic, polymer-coated flow
cell devices, alone or in combination with improved or optimized
amplification reaction formulations, may yield increased
amplification rates compared to those obtained using conventional
supports and amplification protocols. In some instances, the
relative amplification rates that may be achieved may be at least
2.times., at least 3.times., at least 4.times., at least 5.times.,
at least 6.times., at least 7.times., at least 8.times., at least
9.times., at least 10.times., at least 12.times., at least
14.times., at least 16.times., at least 18.times., or at least
20.times. that for use of conventional supports and amplification
protocols for any of the amplification methods described above.
[0378] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, alone or in combination with
improved or optimized buffer formulations, may yield total
amplification reaction times (i.e., the time required to reach 90%,
95%, 98%, or 99% completion of the amplification reaction) of less
than 180 mins, 120 mins, 90 min, 60 minutes, 50 minutes, 40
minutes, 30 minutes, 20 minutes, 15 minutes, 10 minutes, 5 minutes,
3 minutes, 1 minute, 50 s, 40 s, 30 s, 20 s, or 10 s for any of
these completion metrics.
[0379] In some instances, the use of the disclosed low-binding
supports alone or in combination with improved or optimized
amplification buffer formulations may enable faster amplification
reaction times (i.e., the times required to reach 90%, 95%, 98%, or
99% completion of the amplification reaction) of no more than 60
minutes, 50 minutes, 40 minutes, 30 minutes, 20 minutes, or 10
minutes. Similarly, use of the disclosed low-binding supports alone
or in combination with improved or optimized buffer formulations
may enable amplification reactions to be completed in some cases in
no more than 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or no more than 30
cycles.
[0380] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, alone or in combination with
improved or optimized amplification reaction formulations, may
yield increased specific amplification and/or decreased
non-specific amplification compared to that obtained using
conventional supports and amplification protocols. In some
instances, the resulting ratio of specific
amplification-to-non-specific amplification that may be achieved is
at least 4:1 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 20:1, 30:1, 40:1, 50:1,
60:1, 70:1, 80:1, 90:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1,
700:1, 800:1, 900:1, or 1,000:1.
[0381] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, alone or in combination with
improved or optimized amplification reaction formulations, may
yield increased amplification efficiency compared to that obtained
using conventional supports and amplification protocols. In some
instances, the amplification efficiency that may be achieved is
better than 50%, 60%, 70% 80%, 85%, 90%, 95%, 98%, or 99% in any of
the amplification reaction times specified above.
[0382] In some instances, the clonally-amplified target (or sample)
oligonucleotide molecules (or nucleic acid molecules) hybridized to
the oligonucleotide adapter or primer molecules attached to the
hydrophilic, polymer-coated flow cell device surfaces may range in
length from about 0.02 kilobases (kb) to about 20 kb or from about
0.1 kilobases (kb) to about 20 kb. In some instances, the
clonally-amplified target oligonucleotide molecules may be at least
0.001 kb, at least 0.005 kb, at least 0.01 kb, at least 0.02 kb, at
least 0.05 kb, at least 0.1 kb in length, at least 0.2 kb in
length, at least 0.3 kb in length, at least 0.4 kb in length, at
least 0.5 kb in length, at least 1 kb in length, at least 2 kb in
length, at least 3 kb in length, at least 4 kb in length, at least
5 kb in length, at least 6 kb in length, at least 7 kb in length,
at least 8 kb in length, at least 9 kb in length, at least 10 kb in
length, at least 15 kb in length, or at least 20 kb in length, or
any intermediate value spanned by the range described herein, e.g.,
at least 0.85 kb in length.
[0383] In some instances, the clonally-amplified target (or sample)
oligonucleotide molecules (or nucleic acid molecules) may comprise
single-stranded or double-stranded, multimeric nucleic acid
molecules (e.g., concatamers) further comprising repeats of a
regularly occurring monomer unit. In some instances, the
clonally-amplified single-stranded or double-stranded, multimeric
nucleic acid molecules may be at least 0.1 kb in length, at least
0.2 kb in length, at least 0.3 kb in length, at least 0.4 kb in
length, at least 0.5 kb in length, at least 1 kb in length, at
least 2 kb in length, at least 3 kb in length, at least 4 kb in
length, at least 5 kb in length, at least 6 kb in length, at least
7 kb in length, at least 8 kb in length, at least 9 kb in length,
at least 10 kb in length, at least 15 kb in length, or at least 20
kb in length, or any intermediate value spanned by the range
described herein, e.g., about 2.45 kb in length.
[0384] In some instances, the clonally-amplified target (or sample)
oligonucleotide molecules (or nucleic acid molecules) may comprise
single-stranded or double-stranded multimeric nucleic acid (e.g.,
concatamers) molecules comprising from about 2 to about 100 copies
of a regularly repeating monomer unit. In some instances, the
number of copies of the regularly repeating monomer unit may be at
least 2, at least 3, at least 4, at least 5, at least 10, at least
15, at least 20, at least 25, at least 30, at least 35, at least
40, at least 45, at least 50, at least 55, at least 60, at least
65, at least 70, at least 75, at least 80, at least 85, at least
90, at least 95, and at least 100. In some instances, the number of
copies of the regularly repeating monomer unit may be at most 100,
at most 95, at most 90, at most 85, at most 80, at most 75, at most
70, at most 65, at most 60, at most 55, at most 50, at most 45, at
most 40, at most 35, at most 30, at most 25, at most 20, at most
15, at most 10, at most 5, at most 4, at most 3, or at most 2. Any
of the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the number of copies of the
regularly repeating monomer unit may range from about 4 to about
60. Those of skill in the art will recognize that the number of
copies of the regularly repeating monomer unit may have any value
within this range, e.g., about 12. Thus, in some instances, the
surface density of clonally-amplified target sequences in terms of
the number of copies of a target sequence per unit area of the
support surface may exceed the surface density of oligonucleotide
primers even if the hybridization and/or amplification efficiencies
are less than 100%.
[0385] In some instances, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, alone or in combination with
improved or optimized amplification reaction formulations, may
yield increased clonal copy number compared to that obtained using
conventional supports and amplification protocols. In some
instances, e.g., wherein the clonally-amplified target (or sample)
oligonucleotide molecules comprise concatenated, multimeric repeats
of a monomeric target sequence, the clonal copy number may be
substantially smaller than compared to that obtained using
conventional supports and amplification protocols. Thus, in some
instances, the clonal copy number may range from about 1 molecule
to about 100,000 molecules (e.g., target sequence molecules) per
amplified colony. In some instances, the clonal copy number may be
at least 1, at least 5, at least 10, at least 50, at least 100, at
least 500, at least 1,000, at least 2,000, at least 3,000, at least
4,000, at least 5,000, at least 6,000, at least 7,000, at least
8,000, at least 9,000, at least 10,000, at least 15,000, at least
20,000, at least 25,000, at least 30,000, at least 35,000, at least
40,000, at least 45,000, at least 50,000, at least 55,000, at least
60,000, at least 65,000, at least 70,000, at least 75,000, at least
80,000, at least 85,000, at least 90,000, at least 95,000, or at
least 100,000 molecules per amplified colony. In some instances,
the clonal copy number may be at most 100,000, at most 95,000, at
most 90,000, at most 85,000, at most 80,000, at most 75,000, at
most 70,000, at most 65,000, at most 60,000, at most 55,000, at
most 50,000, at most 45,000, at most 40,000, at most 35,000, at
most 30,000, at most 25,000, at most 20,000, at most 15,000, at
most 10,000, at most 9,000, at most 8,000, at most 7,000, at most
6,000, at most 5,000, at most 4,000, at most 3,000, at most 2,000,
at most 1,000, at most 500, at most 100, at most 50, at most 10, at
most 5, or at most 1 molecule per amplified colony. Any of the
lower and upper values described in this paragraph may be combined
to form a range included within the present disclosure, for
example, in some instances the clonal copy number may range from
about 2,000 molecules to about 9,000 molecules. Those of skill in
the art will recognize that the clonal copy number may have any
value within this range, e.g., about 2,220 molecules in some
instances, or about 2 molecules in others.
[0386] As noted above, in some instances the amplified target (or
sample) oligonucleotide molecules (or nucleic acid molecules) may
comprise concatenated, multimeric repeats of a monomeric target
sequence. In some instances, the amplified target (or sample)
oligonucleotide molecules (or nucleic acid molecules) may comprise
a plurality of molecules each of which comprises a single monomeric
target sequence. Thus, the use of the disclosed hydrophilic,
polymer-coated flow cell devices, alone or in combination with
improved or optimized amplification reaction formulations, may
result in a surface density of target sequence copies that ranges
from about 100 target sequence copies per mm.sup.2 to about
1.times.10.sup.12 target sequence copies per mm.sup.2. In some
instances, the surface density of target sequence copies may be at
least 100, at least 500, at least 1,000, at least 5,000, at least
10,000, at least 15,000, at least 20,000, at least 25,000, at least
30,000, at least 35,000, at least 40,000, at least 45,000, at least
50,000, at least 55,000, at least 60,000, at least 65,000, at least
70,000, at least 75,000, at least 80,000, at least 85,000, at least
90,000, at least 95,000, at least 100,000, at least 150,000, at
least 200,000, at least 250,000, at least 300,000, at least
350,000, at least 400,000, at least 450,000, at least 500,000, at
least 550,000, at least 600,000, at least 650,000, at least
700,000, at least 750,000, at least 800,000, at least 850,000, at
least 900,000, at least 950,000, at least 1,000,000, at least
5,000,000, at least 1.times.10.sup.7, at least 5.times.10.sup.7, at
least 1.times.10.sup.8, at least 5.times.10.sup.8, at least
1.times.10.sup.9, at least 5.times.10.sup.9, at least
1.times.10.sup.10, at least 5.times.10.sup.10, at least
1.times.10.sup.11, at least 5.times.10.sup.11, or at least
1.times.10.sup.12 of clonally amplified target sequence molecules
per mm.sup.2. In some instances, the surface density of target
sequence copies may be at most 1.times.10.sup.12, at most
5.times.10.sup.11, at most 1.times.10.sup.11, at most
5.times.10.sup.10, at most 1.times.10.sup.10, at most
5.times.10.sup.9, at most 1.times.10.sup.9, at most
5.times.10.sup.8, at most 1.times.10.sup.8, at most
5.times.10.sup.7, at most 1.times.10.sup.7, at most 5,000,000, at
most 1,000,000, at most 950,000, at most 900,000, at most 850,000,
at most 800,000, at most 750,000, at most 700,000, at most 650,000,
at most 600,000, at most 550,000, at most 500,000, at most 450,000,
at most 400,000, at most 350,000, at most 300,000, at most 250,000,
at most 200,000, at most 150,000, at most 100,000, at most 95,000,
at most 90,000, at most 85,000, at most 80,000, at most 75,000, at
most 70,000, at most 65,000, at most 60,000, at most 55,000, at
most 50,000, at most 45,000, at most 40,000, at most 35,000, at
most 30,000, at most 25,000, at most 20,000, at most 15,000, at
most 10,000, at most 5,000, at most 1,000, at most 500, or at most
100 target sequence copies per mm.sup.2. Any of the lower and upper
values described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the surface density of target sequence copies may range
from about 1,000 target sequence copies per mm.sup.2 to about
65,000 target sequence copies mm.sup.2. Those of skill in the art
will recognize that the surface density of target sequence copies
may have any value within this range, e.g., about 49,600 target
sequence copies per mm.sup.2.
[0387] In some instances, the use of the disclosed low-binding
supports alone or in combination with improved or optimized
amplification buffer formulations may result in a surface density
of clonally-amplified target (or sample) oligonucleotide molecules
(or clusters) ranging from about from about 100 molecules per mm2
to about 1.times.10.sup.12 colonies per mm.sup.2. In some
instances, the surface density of clonally-amplified molecules may
be at least 100, at least 500, at least 1,000, at least 5,000, at
least 10,000, at least 15,000, at least 20,000, at least 25,000, at
least 30,000, at least 35,000, at least 40,000, at least 45,000, at
least 50,000, at least 55,000, at least 60,000, at least 65,000, at
least 70,000, at least 75,000, at least 80,000, at least 85,000, at
least 90,000, at least 95,000, at least 100,000, at least 150,000,
at least 200,000, at least 250,000, at least 300,000, at least
350,000, at least 400,000, at least 450,000, at least 500,000, at
least 550,000, at least 600,000, at least 650,000, at least
700,000, at least 750,000, at least 800,000, at least 850,000, at
least 900,000, at least 950,000, at least 1,000,000, at least
5,000,000, at least 1.times.10.sup.7, at least 5.times.10.sup.7, at
least 1.times.10.sup.8, at least 5.times.10.sup.8, at least
1.times.10.sup.9, at least 5.times.10.sup.9, at least
1.times.10.sup.10, at least 5.times.10.sup.10, at least
1.times.10.sup.11, at least 5.times.10.sup.11, or at least
1.times.10.sup.12 molecules per mm.sup.2. In some instances, the
surface density of clonally-amplified molecules may be at most
1.times.10.sup.12, at most 5.times.10.sup.11, at most
1.times.10.sup.11, at most 5.times.10.sup.10, at most
1.times.10.sup.10, at most 5.times.10.sup.9, at most
1.times.10.sup.9, at most 5.times.10.sup.8, at most
1.times.10.sup.8, at most 5.times.10.sup.7, at most
1.times.10.sup.7, at most 5,000,000, at most 1,000,000, at most
950,000, at most 900,000, at most 850,000, at most 800,000, at most
750,000, at most 700,000, at most 650,000, at most 600,000, at most
550,000, at most 500,000, at most 450,000, at most 400,000, at most
350,000, at most 300,000, at most 250,000, at most 200,000, at most
150,000, at most 100,000, at most 95,000, at most 90,000, at most
85,000, at most 80,000, at most 75,000, at most 70,000, at most
65,000, at most 60,000, at most 55,000, at most 50,000, at most
45,000, at most 40,000, at most 35,000, at most 30,000, at most
25,000, at most 20,000, at most 15,000, at most 10,000, at most
5,000, at most 1,000, at most 500, or at most 100 molecules per
mm.sup.2. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the surface
density of clonally-amplified molecules may range from about 5,000
molecules per mm.sup.2 to about 50,000 molecules per mm.sup.2.
Those of skill in the art will recognize that the surface density
of clonally-amplified colonies may have any value within this
range, e.g., about 48,800 molecules per mm.sup.2.
[0388] In some instances. the use of the disclosed hydrophilic,
polymer-coated flow cell devices, alone or in combination with
improved or optimized amplification reaction formulations, may
yield signal from the amplified and labeled nucleic acid
populations (e.g., a fluorescence signal) that has a coefficient of
variance of no greater than 50%, such as 50%, 40%, 30%, 20%, 15%,
10%, 5%, or less than 5%.
[0389] Similarly, in some instances the use of the disclosed
hydrophilic, polymer-coated flow cell devices, alone or in
combination with improved or optimized amplification reaction
formulations, may yield signal from the amplified and non-labeled
nucleic acid populations that has a coefficient of variance of no
greater than 50%, such as 50%, 40%, 30%, 20%, 10%, 5%, or less than
5%.
[0390] Fluorescence imaging of hydrophilic, polymer-coated flow
cell device surfaces: The disclosed hydrophilic, polymer-coated
flow cell devices comprising, e.g., clonal clusters of labeled
target nucleic acid molecules disposed thereon may be used in any
of a variety of nucleic acid analysis applications, e.g., nucleic
acid base discrimination, nucleic acid base classification, nucleic
acid base calling, nucleic acid detection applications, nucleic
acid sequencing applications, and nucleic acid-based (genetic and
genomic) diagnostic applications. In many of these applications,
fluorescence imaging techniques may be used to monitor
hybridization, amplification, and/or sequencing reactions performed
on the low-binding supports. Fluorescence imaging may be performed
using any of the optical imaging modules disclosed herein, as well
as a variety of fluorophores, fluorescence imaging techniques, and
other fluorescence imaging instruments known to those of skill in
the art.
[0391] In some instances, the performance of nucleic acid
hybridization and/or amplification reactions using the disclosed
hydrophilic, polymer-coated flow cell devices and reaction buffer
formulations may be assessed using fluorescence imaging techniques,
where the contrast-to-noise ratio (CNR) of the images provides a
key metric in assessing amplification specificity and non-specific
binding on the support. CNR is commonly defined as:
CNR=(Signal-Background)/Noise. The background term is commonly
taken to be the signal measured for the interstitial regions
surrounding a particular feature (diffraction limited spot, DLS) in
a specified region of interest (ROI). As noted above, while
signal-to-noise ratio (SNR) is often considered to be a benchmark
of overall signal quality, it can be shown that improved CNR can
provide a significant advantage over SNR as a benchmark for signal
quality in applications that require rapid image capture (e.g.,
sequencing applications for which cycle times should be reduced or
minimized). At high CNR, the imaging time required to reach
accurate signal discrimination (and thus accurate base-calling in
the case of sequencing applications) can be drastically reduced
even with moderate improvements in CNR.
[0392] In most ensemble-based sequencing approaches, the background
term is typically measured as the signal associated with
`interstitial` regions. In addition to "interstitial" background
(B.sub.inter), "intrastitial" background (B.sub.intra) exists
within the discrete regions occupied by amplified DNA colonies. The
combination of these two background signal terms dictates the
achievable CNR in the image, and subsequently directly impacts the
optical instrument requirements, architecture costs, reagent costs,
run-times, cost/genome, and ultimately the accuracy and data
quality for cyclic array-based sequencing applications. The
B.sub.inter background signal arises from a variety of sources; a
few examples include auto-fluorescence from consumable flow cells,
non-specific adsorption of detection molecules that yield spurious
fluorescence signals that may obscure the foreground signal from
the ROI, and the presence of non-specific DNA amplification
products (e.g., those arising from primer dimers). In typical next
generation sequencing (NGS) applications, this background signal in
the current field-of-view (FOV) is averaged over time and
subtracted. The signal arising from individual DNA colonies (i.e.,
(S)-B.sub.inter in the FOV) yields a discernable feature that can
be classified. In some instances, the intrastitial background
(B.sub.intra) can contribute a confounding fluorescence signal that
is not specific to the target of interest but is present in the
same ROI, thus making it far more difficult to average and
subtract.
[0393] The implementation of nucleic acid amplification on the
hydrophilic, polymer-coated substrate surfaces of the present
disclosure may decrease the B.sub.inter background signal by
reducing non-specific binding, may lead to improvements in specific
nucleic acid amplification, and may lead to a decrease in
non-specific amplification that can impact the background signal
arising from both the interstitial and intrastitial regions. In
some instances, the disclosed low nonspecific binding support
surfaces, optionally used in combination with improved
hybridization and/or amplification reaction buffer formulations,
may lead to improvements in CNR by a factor of 2, 5, 10, 100, 200,
500, or 1000-fold over those achieved using conventional supports
and hybridization, amplification, and/or sequencing protocols.
Although described here in the context of using fluorescence
imaging as the read-out or detection mode, the same principles
apply to the use of the disclosed low nonspecific binding supports
and nucleic acid hybridization and amplification formulations for
other detection modes as well, including both optical and
non-optical detection modes.
[0394] Alternative sequencing biochemistries: In addition to the
sequencing-by-nucleotide incorporation approach described above,
the disclosed flow cell devices and optical imaging systems are
compatible with other emerging nucleic acid sequencing
biochemistries as well. Examples include the
"sequencing-by-nucleotide binding" approach described in U.S. Pat.
No. 10,655,176 B2, and the "sequencing-by-avidity" approach
described in U.S. Pat. No. 10,768,173 B2.
[0395] The "sequencing-by-nucleotide binding" approach, as
currently being developed by Omniome, Inc. (San Diego, Calif.) is
based on performing repetitive cycles of detecting a stabilized
complex that forms at each position along the template (e.g. a
ternary complex that includes the primed template (tethered to a
sample support structure), a polymerase, and a cognate nucleotide
for the position), under conditions that prevent covalent
incorporation of the cognate nucleotide into the primer, and then
extending the primer to allow detection of the next position along
the template. In the sequencing-by-binding approach, detection of
the nucleotide at each position of the template occurs prior to
extension of the primer to the next position. Generally, the
methodology is used to distinguish the four different nucleotide
types that can be present at positions along a nucleic acid
template by uniquely labelling each type of ternary complex (i.e.
different types of ternary complexes differing in the type of
nucleotide it contains) or by separately delivering the reagents
needed to form each type of ternary complex. In some instances, the
labeling may comprise fluorescence labeling of, e.g., the cognate
nucleotide or the polymerase that participate in the ternary
complex. The approach is thus compatible with the disclosed flow
cell devices and imaging systems.
[0396] The "sequencing-by-avidity" approach, as currently being
developed by Element Biosciences, Inc. (San Diego, Calif.) relies
on the increased avidity (or "functional affinity") derived from
forming a complex comprising a plurality of individual non-covalent
binding interactions. Element's approach is based on the detection
of a multivalent binding complex formed between a
fluorescently-labeled polymer-nucleotide conjugate, a polymers, and
a plurality of primed target nucleic acid molecules tethered to a
sample support structure, which allows the detection/base-calling
step to be separated from the nucleotide incorporation step.
Fluorescence imaging is used to detect the bound complex and
thereby determine the identity of the N+1 nucleotide in the target
nucleic acid sequence (where the primer extension strand is N
nucleotides in length). Following the imaging step, the multivalent
binding complex is disrupted and washed away, the correct blocked
nucleotide is incorporated into the primer extension strand, and
the cycle is repeated.
[0397] Nucleic acid sequencing system performance: In some
instances, the disclosed nucleic acid sequencing systems,
comprising one or more of the disclosed flow cell devices used in
combination with one or more of the disclosed optical imaging
systems, and optionally utilizing one of the emerging sequencing
biochemistries such as the "sequencing-by-trapping" (or
"sequencing-by-avidity") approach described above, may provide
improved nucleic acid sequencing performance in terms of, e.g.,
reduced sample input requirements, reduced image acquisition cycle
time, reduced sequencing reaction cycle time, reduced sequencing
run time, improved base-calling accuracy, reduced reagent
consumption and cost, higher sequencing throughput, and reduced
sequencing cost.
[0398] Nucleic acid sample input (pM): In some instances, the
sample input requirements for the disclosed system may be
significantly reduced due to the improved hybridization and
amplification efficiencies that may be attained, and the high CNR
images that may be acquired for base-calling, using the disclosed
hydrophilic, polymer coated flow cell devices and imaging systems.
In some instances, the nucleic acid sample input requirement for
the disclosed systems may range from about 1 pM to about 10,000 pM.
In some instances, the nucleic acid sample input requirement may be
at least 1 pM, at least 2 pM, at least 5 pM, at least 10 pM, at
least 20 pM, at least 50 pM, at least 100 pM, at least 200 pM, at
least 500 pM, at least 1,000 pM, at least 2,000 pM, at least 5,000
pM, at least 10,000 pM. In some instances, the nucleic acid sample
input requirement for the disclosed systems may be at most 10,000
pM, at most 5,000 pM, at most 2,000 pM, at most 1,000 pM, at most
500 pM, at most 200 pM, at most 100 pM, at most 50 pM, at most 20
pM, at most 10 pM, at most 5 pM, at most 2 pM, or at most 1 pM. Any
of the lower and upper values described in this paragraph may be
combined to form a range included within the present disclosure,
for example, in some instances the nucleic acid sample input
requirement for the disclosed systems may range from about 5 pM to
about 500 pM. Those of skill in the art will recognize that the
nucleic acid sample input requirement may have any value within
this range, e.g., about 132 pM. In one exemplary instance, a
nucleic acid sample input of about 100 pM is sufficient to generate
signals for reliable base-calling.
[0399] Nucleic acid sample input (nanograms): In some instances,
the nucleic acid sample input requirement for the disclosed systems
may range from about 0.05 nanograms to about 1,000 nanograms. In
some instances, the nucleic acid sample input requirement may be at
least 0.05 nanograms, at least 0.1 nanograms, at least 0.2
nanograms, at least 0.4 nanograms, at least 0.6 nanograms, at least
0.8 nanograms, at least 1.0 nanograms, at least 2 nanograms, at
least 4 nanograms, at least 6 nanograms, at least 8 nanograms, at
least 10 nanograms, at least 20 nanograms, at least 40 nanograms,
at least 60 nanograms, at least 80 nanograms, at least 100
nanograms, at least 200 nanograms, at least 400 nanograms, at least
600 nanograms, at least 800 nanograms, or at least 1,000 nanograms.
In some instances, the nucleic acid sample input requirement may be
at most 1,000 nanograms, at most 800 nanograms, at most 600
nanograms, at most 400 nanograms, at most 200 nanograms, at most
100 nanograms, at most 80 nanograms, at most 60 nanograms, at most
40 nanograms, at most 20 nanograms, at most 10 nanograms, at most 8
nanograms, at most 6 nanograms, at most 4 nanograms, at most 2
nanograms, at most 1 nanograms, at most 0.8 nanograms, at most 0.6
nanograms, at most 0.4 nanograms, at most 0.2 nanograms, at most
0.1 nanograms, or at most 0.05 nanograms. Any of the lower and
upper values described in this paragraph may be combined to form a
range included within the present disclosure, for example, in some
instances the nucleic acid sample input requirement for the
disclosed systems may range from about 0.6 nanograms to about 400
nanograms. Those of skill in the art will recognize that the
nucleic acid sample input requirement may have any value within
this range, e.g., about 2.65 nanograms.
[0400] # FOV images required to tile flow cell: In some instances,
the field-of-view (FOV) of the disclosed optical imaging module is
sufficiently large that a multi-channel (or multi-lane) flow cell
(i.e., the fluid channel portions thereof) of the present
disclosure may be imaged by tiling from about 10 FOV images (or
"frames") to about 1,000 FOV images (or "frames"). In some
instances, an image of the entire multi-channel flow cell may
require tiling at least 10, at least 20, at least 30, at least 40,
at least 50, at least 60, at least 70, at least 80, at least 90, at
least 100, at least 150, at least 200, at least 250, at least 300,
at least 350, at least 400, at least 450, at least 500, at least
550, at least 600, at least 650, at least 700, at least 750, at
least 800, at least 850, at least 900, at least 950, or at least
1,000 FOV images (or "frames"). In some instances, an image of the
entire multi-channel flow cell may require tiling at most 1,000, at
most 950, at most 900, at most 850, at most 800, at most 750, at
most 700, at most 650, at most 600, at most 550, at most 500, at
most 450, at most 400, at most 350, at most 300, at most 250, at
most 200, at most 150, at most 100, at most 90, at most 80, at most
80, at most 70, at most 60, at most 50, at most 40, at most 30, at
most 20, or at most 10 FOV images (or "frames"). Any of the lower
and upper values described in this paragraph may be combined to
form a range included within the present disclosure, for example,
in some instances an image of the entire multi-channel flow cell
may require tiling from about 30 to about 100 FOV images. Those of
skill in the art will recognize that in some instances the number
of required FOV images may have any value within this range, e.g.,
about 54 FOV images.
[0401] Imaging cycle time: In some instances, the combination of
large FOV, image sensor response sensitivity, and/or fast FOV
translation times enables shortened imaging cycle times (i.e., the
time required to acquire a sufficient number of FOV images to tile
the entire multichannel flow cell (or the fluid channel portions
thereof). In some instances, the imaging cycle time may range from
about 10 seconds to about 10 minutes. In some instances, the
imaging cycle time may be at least 10 seconds at least 20 seconds,
at least 30 seconds, at least 40 seconds, at least 50 seconds, at
least 1 minute, at least 2 minutes, at least 3 minutes, at least 4
minutes, at least 5 minutes, at least 6 minutes, at least 7
minutes, at least 8 minutes, at least 9 minutes, or at least 10
minutes. In some instances, the imaging cycle time may be at most
10 minutes, at most 9 minutes, at most 8 minutes, at most 7
minutes, at most 6 minutes, at most 5 minutes, at most 4 minutes,
at most 3 minutes, at most 2 minutes, at most 1 minute, at most 50
second, at most 40 second, at most 30 seconds, at most 20 seconds,
or at most 10 seconds. Any of the lower and upper values described
in this paragraph may be combined to form a range included within
the present disclosure, for example, in some instances the imaging
cycle time may range from about 20 seconds to about 1 minute. Those
of skill in the art will recognize that in some instances the
imaging cycle time may have any value within this range, e.g.,
about 57 seconds.
[0402] Sequencing cycle time: In some instances, shortened
sequencing reaction steps, e.g., due to reduced wash time
requirements for the disclosed hydrophilic, polymer-coated flow
cells, may result in shortened overall sequencing cycle times. In
some instances, the sequencing cycle times for the disclosed
systems may range from about 1 minute to about 60 minutes. In some
instances, the sequencing cycle time may be at least 1 minute, at
least 2 minutes, at least 3 minutes, at least 4 minutes, at least 5
minutes, at least 6 minutes, at least 7 minutes, at least 8
minutes, at least 9 minutes, at least 10 minutes, at least 15
minutes, at least 20 minutes, at least 25 minutes, at least 30
minutes, at least 35 minutes, at least 40 minutes, at least 45
minutes, at least 50 minutes, at least 55 minutes, or at least 60
minutes. In some instances, the sequencing reaction cycle time may
be at most 60 minutes, at most 55 minutes, at most 50 minutes, at
most 45 minutes, at most 40 minutes, at most 35 minutes, at most 30
minutes, at most 25 minutes, at most 20 minutes, at most 15
minutes, at most 10 minutes, at most 9 minutes, at most 8 minutes,
at most 7 minutes, at most 6 minutes, at most 5 minutes, at most 4
minutes, at most 3 minutes, at most 2 minutes, or at most 1
minutes. Any of the lower and upper values described in this
paragraph may be combined to form a range included within the
present disclosure, for example, in some instances the sequencing
cycle time may range from about 2 minutes to about 15 minutes.
Those of skill in the art will recognize that in some instances the
sequencing cycle time may have any value within this range, e.g.,
about 1 minute, 12 seconds.
[0403] Sequencing read length: In some instances, the enhanced CNR
images that may be achieved using the disclosed hydrophilic,
polymer-coated flow cell devices in combination with the disclosed
imaging systems, and in some cases, the use of milder sequencing
biochemistries, may enable longer sequencing read lengths for the
disclosed systems. In some instances, the maximum (single read)
read length may range from about 50 bp to about 500 bp. In some
instances, the maximum (single read) read length may be at least 50
bp, at least 100 bp, at least 150 bp, at least 200 bp, at least 250
bp, at least 300 bp, at least 350 bp, at least 400 bp, at least 450
bp, or at least 500 bp. In some instances, the maximum (single
read) read length is at most 500 bp, at most 450 bp, at most 400
bp, at most 350 bp, at most 300 bp, at most 250 bp, at most 200 bp,
at most 150 bp, at most 100 bp, or at most 50 bp. Any of the lower
and upper values described in this paragraph may be combined to
form a range included within the present disclosure, for example,
in some instances the maximum (single read) read length may range
from about 100 bp to about 450 bp. Those of skill in the art will
recognize that in some instances the maximum (single read) read
length may have any value within this range, e.g., about 380
bp.
[0404] Sequencing run time: In some instances, the sequencing run
time for the disclosed nucleic acid sequencing systems may range
from about 8 hours to about 20 hours. In some instances, the
sequencing run time is at least 8 hours, at least 9 hours, at least
10 hours, at least 12 hours, at least 14 hours, at least 16 hours,
at least 18 hours, or at least 20 hours. In some instances, the
sequencing run time is at most 20 hours, at most 18 hours, at most
16 hours, at most 14 hours, at most 12 hours, at most 10 hours, at
most 9 hours, or at most 8 hours. Any of the lower and upper values
described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the sequencing run time may range from about 10 hours to
about 16 hours. Those of skill in the art will recognize that in
some instances the sequencing run time may have any value within
this range, e.g., about 7 hours, 35 minutes.
[0405] Average base-calling accuracy: In some instances, the
disclosed nucleic acid sequencing systems may provide an average
base-calling accuracy of at least 80%, at least 85%, at least 90%,
at least 92%, at least 94%, at least 96%, at least 98%, at least
99%, at least 99.5%, at least 99.8%, or at least 99.9% correct over
the course of a sequencing run. In some instances, the disclosed
nucleic acid sequencing systems may provide an average base-calling
accuracy of at least 80%, at least 85%, at least 90%, at least 92%,
at least 94%, at least 96%, at least 98%, at least 99%, at least
99.5%, at least 99.8%, or at least 99.9% correct per every 1,000
bases, 10,0000 bases, 25,000 bases, 50,000 bases, 75,000 bases, or
100,000 bases called.
[0406] Average Q-score: In some instances, the disclosed nucleic
acid sequencing systems may provide a more accurate base readout.
In some instances, for example, the disclosed nucleic acid
sequencing systems may provide an average Q-score for base-calling
accuracy over a sequencing run that ranges from about 20 to about
50. In some instances, the average Q-score may be at least 20, at
least 25, at least 30, at least 35, at least 40, at least 45, or at
least 50. Those of skill in the art will recognize that the average
Q-score may have any value within this range, e.g., about 32.
[0407] Q-score vs. % nucleotides identified: In some instances, the
disclosed nucleic acid sequencing systems may provide a Q-score of
greater than 30 for at least 50%, at least 60%, at least 70%, at
least 80%, at least 85%, at least 90%, at least 95%, at least 98%,
or at least 99% of the terminal (or N+1) nucleotides identified. In
some instances, the disclosed nucleic acid sequencing systems may
provide a Q-score of greater than 35 for at least 50%, at least
60%, at least 70%, at least 80%, at least 85%, at least 90%, at
least 95%, at least 98%, or at least 99% of the terminal (or N+1)
nucleotides identified. In some instances, the disclosed nucleic
acid sequencing systems may provide a Q-score of greater than 40
for at least 50%, at least 60%, at least 70%, at least 80%, at
least 85%, at least 90%, at least 95%, at least 98%, or at least
99% of the terminal (or N+1) nucleotides identified. In some
instances, the disclosed nucleic acid sequencing systems may
provide a Q-score of greater than 45 for at least 50%, at least
60%, at least 70%, at least 80%, at least 85%, at least 90%, at
least 95%, at least 98%, or at least 99% of the terminal (or N+1)
nucleotides identified. In some instances, the disclosed
compositions and methods for nucleic acid sequencing may provide a
Q-score of greater than 50 for at least 50%, at least 60%, at least
70%, at least 80%, at least 85%, at least 90%, at least 95%, at
least 98%, or at least 99% of the terminal (or N+1) nucleotides
identified.
[0408] Reagent consumption: In some instances, the disclosed
nucleic acid sequencing systems may have lower reagent consumption
rates and costs due to, e.g., the use of the disclosed flow cell
devices and fluidic systems that minimize fluid channel volumes and
dead volumes. In some instances, the disclosed nucleic acid
sequencing systems may thus require an average of at least 5% less,
at least 10% less, at least 15% less, at least 20% less, at least
25% less, at least 30% less, at least 35% less, at least 40% less,
at least 45% less, or at least 50% less reagent by volume per Gbase
sequenced that that consumed by an Illumina MiSeq sequencer.
[0409] Sequencing throughput: In some instances, the disclosed
nucleic acid sequencing systems may provide a sequencing throughput
ranging from about 50 Gbase/run to about 200 Gbase/run. In some
instances, the sequencing throughput may be at least 50 Gbase/run,
at least 75 Gbase/run, at least 100 Gbase/run, at least 125
Gbase/run, at least 150 Gbase/run, at least 175 Gbase/run, or at
least 200 Gbase/run. In some instances, the sequencing throughput
may be at most 200 Gbase/run, at most 175 Gbase/run, at most 150
Gbase/run, at most 125 Gbase/run, at most 100 Gbase/run, at most 75
Gbase/run, or at most 50 Gbase/run. Any of the lower and upper
values described in this paragraph may be combined to form a range
included within the present disclosure, for example, in some
instances the sequencing throughput may range from about 75
Gbase/run to about 150 Gbase/run. Those of skill in the art will
recognize that in some instances the sequencing throughput may have
any value within this range, e.g., about 119 Gbase/run.
[0410] Sequencing cost: In some instances, the disclosed nucleic
acid sequencing systems may provide nucleic acid sequencing at a
cost ranging from about $5 per Gbase to about $30 per Gbase. In
some instances, the sequencing cost may be at least $5 per Gbase,
at least $10 per Gbase, at least $15 per Gbase, at least $20 per
Gbase, at least $25 per Gbase, or at least $30 per Gbase. In some
instances, the sequencing cost may be at most $30 per Gbase, at
most $25 per Gbase, at most $20 per Gbase, at most $15 per Gbase,
at most $10 per Gbase, or at most $30 per Gbase. Any of the lower
and upper values described in this paragraph may be combined to
form a range included within the present disclosure, for example,
in some instances the sequencing cost may range from about $10 per
Gbase to about $15 per Gbase. Those of skill in the art will
recognize that in some instances the sequencing cost may have any
value within this range, e.g., about $7.25 per Gbase.
EXAMPLES
[0411] These examples are provided for illustrative purposes only
and not to limit the scope of the claims provided herein.
Example 1--Design Specifications for a Fluorescence Imaging Module
for Genomics Applications
[0412] A non-limiting example of design specifications for a
fluorescence imaging module of the present disclosure is provided
in Table 1.
TABLE-US-00001 TABLE 1 Examples of design specifications for a
fluorescence imaging module for genomics applications. Design
Parameter Specification Numerical aperture .gtoreq.0.3 Image
quality Diffraction limited Field-of-view (FOV) >2.0 mm.sup.2
Image plane curvature Best focal plane within 100 nm for >90% of
the FOV, within 150 nm for 99% of the FOV, and within 200 nm for
the entire FOV Image distortion <0.5% across the FOV
Magnification 2x to 20x Camera pixel size at sample plane .gtoreq.2
x optical system modulation transfer function (MTF) limit Coverslip
thickness >700 .mu.m Number of fluorescence imaging channels
.gtoreq.3 Chromatic focal plane difference at .ltoreq.100 nm
equivalent at sample plane camera between all imaging channels
Number of AF channels 1 Imaging time .ltoreq.2 seconds per FOV
Autofocus Single step autofocus with error correction Autofocus
accuracy <100 nm Scanning stage step and settle time <0.4
seconds Channel-specific optimized tube lens 1 per imaging channel
Illumination optical path Liquid light guide with underfilled
entrance aperture
Example 2--Fabrication of Glass Microfluidic Flow Cell Devices
[0413] Wafer-scale fabrication of microfluidic devices for use as
flow cells can be constructed from, for example, one, two, or three
layers of glass, e.g., borosilicate glass, fused-silica glass, or
quartz, using one of the processed illustrated in FIGS. 36A-36C and
a processing technique such as focused femtosecond laser
photoablation and/or laser glass bonding.
[0414] In FIG. 36A, a first wafer is processed with a laser (e.g.,
that produces femtosecond laser radiation) to ablate the wafer
material and provide a patterned surface. The patterned wafer
surface may comprise a plurality of microfluidic devices (e.g., 12
devices per 210 mm diameter wafer), each of which may comprise a
plurality of fluid channels. The processed wafer may then be diced
to create individual microfluidic chips comprising open fluid
channels that may optionally be subsequently sealed, e.g., by
sealing with a film or by clamping the device to another support
surface.
[0415] In FIG. 36B, a first wafer is processed to create a
patterned surface which may then be placed in contact with and
bonded to a second wafer to seal the fluid channels. Depending on
the materials used, e.g., glass wafers, silicon wafers, etc., the
bonding may be performed using, e.g., a thermal bonding process, an
anodic bonding process, a laser glass bonding process, etc. The
second wafer covers and/or seals the grooves, indentations, and/or
apertures on the wafer having the patterned surface to form fluid
channels and/or fluid chambers (e.g., the interior portion) of the
device at the interface of the two wafer components. The bonded
structure may then be diced into individual microfluidic chips,
e.g., 12 microfluidic chips per 210 mm diameter wafer.
[0416] In FIG. 36C, the first wafer is processed to create a
pattern of fluid channels that are cut or etched through the full
thickness of the wafer (i.e., open on either surface of the wafer).
The first wafer is then sandwiched between and bonded to a second
wafer on one side and a third wafer on the other side. Depending on
the materials used, e.g., glass wafers, silicon wafers, etc., the
bonding may be performed using, e.g., a thermal bonding process, an
anodic bonding process, a laser glass bonding process, etc. The
second and third wafers cover and/or seal the grooves,
indentations, and/or apertures in the first wafer to form fluid
channels and/or fluid chambers (e.g., the interior portions) of the
device. The bonded structure may then be diced into individual
microfluidic chips, e.g., 12 microfluidic chips per 210 mm diameter
wafer.
Example 3--Coating Flow Cell Surfaces with a Hydrophilic Polymer
Coating
[0417] Glass flow cell devices were coated by washing prepared
glass channels with KOH, followed by rinsing with ethanol and then
silanization for 30 minutes at 65.degree. C. Fluid channel surfaces
were activated with EDC-NHS for 30 min., followed by grafting of
oligonucleotide primers by incubation of the activated surface with
5 .mu.m primer for 20 min., and then passivation with 30 .mu.m of
an amino-terminated polyethylene glycol (PEG-NH2).
[0418] Multilayer surfaces are made following the approach
described above, where following the PEG-NH2 passivation step, a
multi-armed PEG-NETS is flowed through the fluid channels, followed
by another addition of the PEG-NH2, optionally followed by another
incubation with PEG-NETS, and optionally followed by another
incubation with multi-armed PEG-NH2. For these surfaces, the primer
may be grafted at any step, and especially following the last
addition of multi-armed PEG-NH2.
Example 4--Flow Cell Devices for Nucleic Acid Sequencing
[0419] FIG. 37A illustrates a non-limiting example of a one-piece
glass microfluidic chip/flow cell design. In this design, fluid
channels and inlet/outlet holes may be fabricated using, e.g.,
focused femtosecond laser radiation. There are two fluid channels
("lanes") in the flow cell device, and each fluid channel
comprises, e.g., 2 rows of 26 frames each (i.e., where a "frame" is
the image area equivalent to the field-of-view for a corresponding
imaging module) each, such that tiling 2.times.26=52 images
suffices to image an entire fluid channel. The fluid channel can
have, e.g., a depth of about 100 .mu.m. Fluid channel 1 has an
inlet hole A1 and an outlet hole A2, and fluid channel 2 has an
inlet hole B1 and an outlet hole B2. The flow cell device may also
comprise a 1D linear, human-readable and/or machine-readable
barcode, and optionally a 2D matrix barcode.
[0420] FIG. 37B illustrates a non-limiting example of a two-piece
glass microfluidic chip/flow cell design. In this design, fluid
channels and inlet/outlet holes may be fabricated using, e.g.,
focused femtosecond laser photoablation or photolithography and
chemical etching processes. The 2 pieces can be bonded together
using any of a variety of techniques as described above. The inlet
and outlet holes may be positioned on the top layer of the
structure and oriented in such a way that they are in fluid
communication with at least one of the fluid channels and/or fluid
chambers formed in the interior portion of the device. There are
two fluid channels in the flow cell device, and as with the device
illustrated in FIG. 37A, each fluid channel comprises, e.g., 2 rows
with 26 frames in each row. The fluid channels can have, e.g., a
depth of about 100 .mu.m. Fluid channel 1 has an inlet hole A1 and
an outlet hole A2, and fluid channel 2 has an inlet hole B1 and an
outlet hole B2. The flow cell device may also comprise a 1D linear,
human-readable and/or machine-readable barcode, and optionally a 2D
matrix barcode.
[0421] FIG. 37C illustrates a non-limiting example of a three-piece
glass microfluidic chip/flow cell design. In this design, fluid
channels and inlet/outlet holes may be fabricated using, e.g.,
focused femtosecond laser photoablation or photolithography and
chemical etching processes. The 3 pieces can be bonded together
using any of a variety of techniques as described above. The first
wafer (comprising a through-pattern of fluid channels or fluid
chambers) can be sandwiched between and bonded to a second wafer on
one side and a third wafer on the other side. The inlet and outlet
holes may be positioned on the top layer of the structure and
oriented in a way such that they are in fluid communication with at
least one of the fluid channels and/or fluid chambers formed in the
interior portion of the device. There are two fluid channels in the
flow cell device, and as with the devices illustrated in FIGS. 37A
and 37B, each fluid channel has 2 rows with 26 frames in each row.
The fluid channel can have a depth of, e.g., about 100 .mu.m. Fluid
channel 1 has an inlet hole A1 and an outlet hole A2, and fluid
channel 2 has an inlet hole B1 and an outlet hole B2. The flow cell
device may also comprise a 1D linear, human-readable and/or
machine-readable barcode, and optionally a 2D matrix barcode.
Example 5--Imaging of Nucleic Acid Clusters in a Capillary Flow
Cell
[0422] Nucleic acid clusters were established within a capillary
and subjected to fluorescence imaging. A flow device having a
capillary tube was used for the test. An example of the resulting
cluster images is presented in FIG. 38. The figure demonstrated
that nucleic acid clusters formed by amplification within the lumen
of a capillary flow cell device as disclosed herein can be reliably
formed and visualized.
Example 6--Plastic Sample Support Structures
[0423] In some instances, the disclosed samples support structures
may be fabricated from a polymer. Examples of materials from which
the sample support structure, e.g., a capillary flow cell device,
may be fabricated include, but are not limited to, polystyrene
(PS), macroporous polystyrene (MPPS), polymethylmethacrylate
(PMMA), polycarbonate (PC), polypropylene (PP), polyethylene (PE),
high density polyethylene (HDPE), cyclic olefin polymers (COP),
cyclic olefin copolymers (COC), polyethylene terephthalate (PET),
or any combination thereof. Various compositions comprising both
glass and plastic substrates are also contemplated.
[0424] Modification of a polymer surface for the surface coating
purposes disclosed herein involves making surfaces reactive with
other chemical groups (--R), including amines. When prepared on an
appropriate substrate, these reactive surfaces can be stored long
term at room temperature, for example, for at least 3 months or
more in some instances. Such surfaces can be further grafted with
R-PEG and R-primer oligomer for on-surface amplification of nucleic
acids, as described elsewhere herein. Plastic surfaces, such as
cyclic olefin polymer (COP), may be modified using any of a variety
of methods known in the art. For example, they can be treated with
Ti:Sapphire laser ablation, UV-mediated ethylene glycol
methacrylate photografting, plasma treatment, or mechanical
agitation (e.g., sand blasting, or polishing, etc.) to create
hydrophilic surfaces that can remain reactive for months towards a
variety of chemical groups, such as amines. These groups may then
allow conjugation of passivation polymers such as PEG, or
biomolecules such as DNA or proteins, without loss of biochemical
activity. For example, attachment of DNA primer oligomers allows
DNA amplification on a passivated plastic surface while reducing or
minimizing the non-specific adsorption of proteins, fluorophore
molecules, or other hydrophobic molecules.
[0425] Additionally, in some instances, surface modification can be
combined with, e.g., laser printing or UV masking, to create
patterned surfaces. This allows patterned attachment of DNA
oligomers, proteins, or other moieties, providing for surface-based
enzymatic activity, binding, detection, or processing. For example,
DNA oligomers may be used to amplify DNA only within patterned
features, or to capture amplified long DNA concatemers in a
patterned fashion. In some embodiments, enzyme islands may be
generated in the patterned areas that are capable of reacting with
solution-based substrates. Because plastic surfaces are especially
amenable to these processing modes, in some embodiments as
contemplated herein, plastic sample support surfaces or flow cell
devices may be recognized as being particularly advantageous.
[0426] Furthermore, plastic can be injection molded, embossed,
stamped, or 3D printed to form any shape, including microfluidic
devices, much more easily than glass substrates, and thus can be
used to create surfaces for the binding and analysis of biological
samples in multiple configurations, e.g., sample-to-result
microfluidic chips for biomarker detection or DNA sequencing.
[0427] Specific and localized DNA amplification on modified plastic
surfaces can be performed to produce nucleic acid spots with an
ultra-high contrast to noise ratio and very low background when
probed with fluorescent labels.
[0428] Hydrophilized and amine-reactive cyclic olefin polymer
surface with amine-primer and amine-PEG can be prepared and has
been demonstrated to support rolling circle amplification. When
probed with fluorophore labeled primers, or when labeled dNTPs were
added to the hybridized primers by a polymerase, bright spots of
DNA amplicons were observed that exhibited signal to noise ratios
greater than 100 with backgrounds that are extremely low,
indicating highly specific amplification, and ultra-low levels of
nonspecific protein and hydrophobic fluorophore binding, which are
hallmarks of the high accuracy detection required for systems such
as fluorescence-based DNA sequencers.
[0429] While preferred embodiments of the present invention have
been shown and described herein, it will be obvious to those
skilled in the art that such embodiments are provided by way of
example only. Numerous variations, changes, and substitutions will
now occur to those skilled in the art without departing from the
invention. It should be understood that various alternatives to the
embodiments of the invention described herein may be employed in
any combination in practicing the invention. It is intended that
the following claims define the scope of the invention and that
methods and structures within the scope of these claims and their
equivalents be covered thereby.
* * * * *