U.S. patent application number 09/817632 was filed with the patent office on 2001-10-18 for systems and methods for detection of labeled materials.
Invention is credited to Stern, David.
Application Number | 20010030290 09/817632 |
Document ID | / |
Family ID | 21781308 |
Filed Date | 2001-10-18 |
United States Patent
Application |
20010030290 |
Kind Code |
A1 |
Stern, David |
October 18, 2001 |
Systems and methods for detection of labeled materials
Abstract
Labeled targets on a support synthesized with polymer sequences
at known locations according to the methods disclosed in U.S. Pat.
No. 5,143,854 and PCT WO 92/10092 or others, can be detected by
exposing marked regions of sample to radiation from a source and
detecting the emission therefrom, and repeating the steps of
exposition and detection until the sample is completely
examined.
Inventors: |
Stern, David; (Mountain
View, CA) |
Correspondence
Address: |
Chief IP Counsel
Legal Department
AFFYMETRIX, INC.
3380 Central Expressway
Santa Clara
CA
95051
US
|
Family ID: |
21781308 |
Appl. No.: |
09/817632 |
Filed: |
March 26, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09817632 |
Mar 26, 2001 |
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09295214 |
Apr 21, 1999 |
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6207960 |
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09295214 |
Apr 21, 1999 |
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08856642 |
May 15, 1997 |
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5981956 |
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60017203 |
May 16, 1996 |
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Current U.S.
Class: |
250/458.1 |
Current CPC
Class: |
B01J 2219/00659
20130101; G02B 21/0084 20130101; B01J 2219/00608 20130101; G01N
21/6428 20130101; G02B 21/0076 20130101; C12Q 1/6883 20130101; C12Q
1/6876 20130101; B01J 2219/00529 20130101; G01N 21/6458 20130101;
B01J 2219/00637 20130101; B01J 2219/00621 20130101; C12Q 1/6834
20130101; G01N 21/6452 20130101; G02B 21/0072 20130101; B01J
2219/0061 20130101; B01J 2219/00612 20130101; B01J 2219/00626
20130101; G02B 21/0048 20130101 |
Class at
Publication: |
250/458.1 |
International
Class: |
G01N 021/64 |
Claims
What is claimed is:
1. A system for detecting marked regions on a surface of a
substrate, the system comprising: an excitation radiation source; a
focusing system for focusing radiation from said excitation
radiation source onto a selected region of said surface of said
substrate, said focusing system including an objective lens having
a ratio of scanning field diameter to focused spot diameter of
greater than about 2000, and a numerical aperture greater than
about 0.2; a radiation direction system for scanning said focused
excitation radiation across said surface of said substrate at a
rate of at least 5 image lines/second; a detector for detecting an
emission from said surface of said substrate in response to said
excitation is radiation, wherein said objective lens receives said
emission and transmits the emission to the detector; and a data
acquisition system for recording an amount of said emission
detected as a function of a position on said surface of said
substrate from which said emission was emitted.
2. The system of claim 1, wherein said focusing system has a ratio
of scanning field diameter to focused spot diameter of greater than
3000.
3. The system of claim 1, wherein said focusing system has a ratio
of scanning field diameter to focused spot diameter of greater than
4000.
4. The system of claim 1, wherein said focusing system focuses said
excitation radiation in a spot having a diameter of less than about
10 .mu.m.
5. The system of claim 1, wherein said focusing system focuses said
excitation radiation on said surface of said substrate in a spot
having a diameter of less than about 5 .mu.m.
6. The system of claim 1 wherein said focusing system focuses said
excitation radiation on said surface of said substrate in a spot
having a diameter of about 3 .mu.m.
7. The system of claim 1, wherein said scanning field diameter is
greater than about 10 mm.
8. The system of claim 1, wherein said scanning field diameter is
about 14 mm.
9. The system of claim 1, wherein said numerical aperture is
greater than about 0.25.
10. The system of claim 1, wherein said focusing system is
achromatic.
11. The system of claim 1, wherein said radiation direction system
is capable of scanning a spot across the substrate at a rate of at
least 10 image lines/second.
12. The system of claim 1, wherein said radiation direction system
is capable of scanning a spot across the substrate at a rate of at
least 30 image lines/second.
13. The system of claim 1, wherein said radiation direction system
comprises an angularly oscillating mirror or a rotating polyhedral
mirror.
14. The system of claim 1, further comprising a translation stage
upon which said substrate is mounted, said translation stage being
moveable in at least one dimension perpendicular to an optical axis
of said objective lens.
15. The system of claim 1, further comprising an autofocus system
for placing said surface of said substrate in a focal plane of said
focusing system.
16. The system of claim 1, further comprising a translation stage
upon which said substrate is mounted, said translation stage being
moveable in at least one dimension parallel to an optical axis of
said focusing system and at least one dimension perpendicular to
said optical axis of said focusing system.
17. The system of claim 1 further comprising a collection system
comprising: collection optics for collecting fluorescence emitted
from said surface of said substrate and for collecting an
excitation radiation reflected from said surface of said substrate;
separation optics for separating said emitted fluorescence from an
excitation radiation reflected from said surface of said substrate
and focusing said fluorescence through a confocal pinhole; and a
recorder responsive to said fluorescence, for recording an amount
of said fluorescence focused through said confocal pinhole.
18. The system of claim 1, wherein said surface of said substrate
comprises a plurality of distinct polymer sequences in different
known locations on said surface.
19. The system of claim 18, wherein each of said different polymer
sequences is contained in a feature having at least one of a width
or length dimension of less than about 50 .mu.m.
20. The system of claim 1 further comprising a processor for
processing and storing said signal so as to generate a
2-dimensional image of said sample.
21. The system of claim 1 further comprising a body for
immobilizing said substrate, the substrate having at least a first
surface with a sample thereon, the body comprising: a mounting
surface; a cavity in said mounting surface, said first surface
mated to said mounting surface for sealing said cavity, said sample
being in fluid communication with said cavity, said cavity having a
bottom surface comprising a light absorptive material; an inlet and
an outlet being in communication with said cavity such that fluid
flowing into said cavity for contacting said sample flows through
said inlet and fluid flowing out of said cavity flows through said
outlet; and a temperature controller for controlling the
temperature in said cavity.
22. The system of claim 21 wherein said temperature controller
comprises a thermoelectric cooler.
23. A system for detecting marked regions on a surface of a
substrate, the system comprising: an excitation radiation source;
first focusing optics for focusing said excitation radiation on
said surface of said substrate in a spot having a diameter no
greater than 5 .mu.m, said focusing optics including an objective
lens; a reciprocating radiation direction system for scanning said
spot linearly across said surface of said substrate, said spot
having a travel distance of at least 10 mm; an optical train for
separating emissions from said surface of said substrate from
excitation radiation reflected from said surface of said substrate,
said optical train including said objective lens; and an autofocus
system for automatically placing said surface of said substrate in
a focal plane of said first focusing optics.
24. The system of claim 23, wherein said optical train includes a
dichroic beam splitter for separating fluorescence emitted from
said surface of said substrate from excitation radiation reflected
from said surface of said substrate.
25. The system of claim 23, wherein said autofocus system
comprises: second focusing optics for focusing said excitation
radiation reflected from said surface of said substrate through a
confocal pinhole onto a photodiode; and a translation stage upon
which a substrate is mounted, said stage being capable of moving in
a direction parallel with an optical axis of said first focusing
optics for moving said substrate into a focal plane of said first
focusing optics.
26. The system of claim 23 further comprising a detector for
detecting an emission from said surface of said substrate in
response to said excitation radiation, and a data acquisition
system for recording an amount of said emission detected as a
function of a position on said surface of said substrate from which
said emission was emitted.
27. A method of scanning a polymer array having a plurality of
different polymer sequences, each of said different polymer
sequences being immobilized on a surface of a substrate in a
different known location, to identify which polymer sequence on
said array is bound by a target molecule, the method comprising:
focusing an excitation radiation source upon said surface of said
substrate with an objective lens; scanning said excitation
radiation across said surface of said substrate at a speed of at
least about 5 image lines/second; collecting emissions from said
surface of said substrate in response to said excitation radiation
with said objection lens; recording said emissions as a function of
a position on said surface of said substrate, said position
indicating the polymer sequence on said array is bound by a target
molecule.
28. The method of claim 27, wherein said polymer array comprises a
plurality of different oligonucleotide sequences immobilized on
said surface of said substrate in different known locations.
29. The method of claim 27 further comprising focusing the
excitation radiation source to a spot having a diameter of about 3
.mu.m and scanning the spot in linear direction across the
substrate for at least 14 mm.
30. The method of claim 27 further comprising the steps of:
immobilizing said substrate on a body; exciting said sample on said
substrate with an excitation radiation having a first wavelength
from an electromagnetic radiation source, said excitation radiation
detecting a response radiation having a second wavelength in
response to said excitation radiation, said response radiation
representing an image of said plurality of regions; exciting a
subsequent plurality of regions on said sample; processing and
storing said response radiation to generate a 2-dimensional image
of said sample; and auto-focusing said sample in a focal plane of
said excitation radiation.
31. The method as recited in claim 30 wherein said body comprises a
mounting surface having a cavity thereon, said substrate being
immobilized on said mounting surface such that said sample is in
fluid communication with said reaction chamber, said reaction
chamber comprising a inlet and a outlet for flowing fluids into and
through said reaction chamber.
32. The method as recited in claim 31 wherein said body further
comprises a temperature controller for controlling the temperature
in said cavity.
33. The method as recited in claim 27 wherein said excitation
radiation is scanned across said surface of said substrate at a
speed of at least about 10 image lines/second.
34. The method as recited in claim 27 wherein said excitation
radiation is scanned across said surface of said substrate at a
speed of at least about 30 image lines/second.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] The present application is a regular application of
provisional U.S. Patent Application Serial No. 60/017,203, filed
May 16, 1996 (Attorney Docket No. 16528X-018900), the complete
disclosure of which is hereby incorporated herein by reference for
all purposes. This application is also related to commonly
assigned, U.S. patent application Ser. No. 08/301,051, filed Sep.
9, 1994, now U.S. Pat. No. 5,578,832, and U.S. patent application
Ser. No. 08/195,889, filed Feb. 10, 1994 (Attorney Docket Nos.
16528X-003800 and 16528X-006000, respectively) the complete
disclosures of which are incorporated herein by reference for all
purposes.
BACKGROUND OF THE INVENTION
[0002] The present invention generally relates to the field of
imaging. In particular, the present invention provides scanning
systems and methods for high speed imaging of a sample containing
labeled materials, and particularly for scanning arrays of polymer
sequences, e.g., oligonucleotide arrays.
[0003] Methods and systems for imaging samples containing labeled
markers such as confocal microscopes are commercially available.
Confocal microscopes generally employ a pinhole that is confocal
with the illuminated spot on the specimen to reject light that is
not reflected or emitted from objects in the focal plane. This
rejection of out-of-focus light enables the microscope to collect
and combine a series of optical slices at different focus positions
to generate a two or three dimensional representation of the
specimen.
[0004] Some scanning microscopes employ radiation direction
systems, such as galvanometers that include servo-mounted mirrors,
to rapidly scan a laser spot across a substrate. Although these
microscopes have relatively high scan rates (e.g., on the order of
about 30 lines/second or greater), they generally do not achieve
both the resolution and field of view that is necessary for some
applications, such as imaging an array of sequenced materials on a
substrate. In fact, a galvanometer-based confocal microscope's
field of view is generally proportional to its resolution. For
example, a typical 40.times. microscope objective, which has a 0.25
.mu.m resolution, has a field size of only about 500 .mu.m. Thus,
conventional galvanometer-based confocal microscopes are inadequate
for applications requiring both high resolution and a large field
of view.
[0005] Scanning confocal microscope systems, such as those
discussed in U.S. Pat. No. 5,143,854 (Pirrung et al.), PCT WO
92/10092, and U.S. patent application Ser. No. 08/195,889 (Attorney
Docket Number 16528X-006000), incorporated herein by reference for
all purposes, are also known. These scanning systems include an
optical train which directs a monochromatic or polychromatic light
source to about a 5 micron (.mu.m) diameter spot at its focal
plane. In some cases, a photon counter detects the emission from
the device in response to the light. The data collected by the
photon counter represents one pixel or data point of the image.
Thereafter, the light scans another pixel as a translation stage
moves the device to a subsequent position.
[0006] As disclosed, these scanning confocal microscope systems
provide high resolution by using an appropriate objective lens and
large field of view by using appropriate translation stages. These
translation stage-based confocal microscopes, however, obtain high
resolution and field of view by sacrificing system throughput. As
an example, an array of sequenced material using the pioneering
fabrication techniques, such as those disclosed in U.S. Pat. No.
5,143,854 (Pirrung et al.) and U.S. patent application Ser. No.
08/143,312, incorporated herein by reference for all purposes, may
have a density of about 10.sup.5 sequences. Assuming that 36 pixels
are required for each sequence, the image can take over at least 10
minutes to acquire.
[0007] From the above, it is apparent that improved methods and
systems for imaging a sample are desired.
SUMMARY OF THE INVENTION
[0008] The present invention provides systems, methods and
apparatus for detecting marked regions on substrate surfaces. In
particular, the present invention provides methods and apparatus
for scanning a substrate to obtain an image with high sensitivity
and resolution at a high speed. The confocal scanning microscopes
of the present invention combine the high scan rate of galvanometer
based scanning microscopes with a sufficiently high resolution,
sensitivity and a large enough field of view for imaging high
density arrays of materials, such as those found in the fields of
combinatorial chemistry and genetic analysis.
[0009] In one aspect, the present invention provides a system for
detecting marked regions on a surface of a substrate, which
comprises an excitation radiation source, and focusing optics for
focusing the excitation radiation to regions on the surface of the
substrate. A radiation direction system is also included for
linearly scanning the focused excitation radiation across the
surface of the substrate. A detector is positioned for detecting an
emission from the substrate surface in response to the excitation
radiation, and a data acquisition system records the amount of
detected emission as a function of a position on the surface of the
substrate from which the emission was detected.
[0010] In one embodiment, the focusing optics comprises an
objective lens having a ratio of scanning field diameter to focused
spot diameter of greater than 2000, preferably greater than 3000
and more preferably greater than 4000. Thus, the microscope is, for
example, capable of focusing a laser beam to a spot having a
diameter of about 3 microns at any point within a flat field having
a length of about 14 mm. In addition, the objective lens has at
least a 0.2 numerical aperture, preferably a 0.25 numerical
aperture, which provides sufficient sensitivity to detect
fluorescently marked regions on the substrate.
[0011] The radiation direction system preferably comprises a
galvanometer mirror that scans the excitation radiation across the
surface of the substrate. The objective lens has an external
entrance pupil preferably located at or near the galvanometer
mirror's pivot location. The mirror usually oscillates at a
frequency of at least 7.5 Hz, preferably at least 20 Hz and more
preferably at least 30 Hz. In this manner, the laser spot can
usually be scanned across the substrate at velocities of about 5
image lines/second, preferably at least 10 images lines/second, and
more preferably at least about 30 image lines/second. This allows
the microscope to rapidly scan high density substrates, such as the
polymer array substrates disclosed by Pirrung. It should be noted
that the mirror may scan unidirectionally (e.g., with a sawtooth
wave) or bidirectionally (e.g., with a symmetric triangle wave). In
the latter case, the galvanometer frequency would generally be
about half of the data aquisition speed in image lines/second.
Accordingly, the frequency of the galvanometer in the latter case
may be lower than 7.5 Hz in order to scan 5 image lines/second.
[0012] In another embodiment, the present invention also provides a
system for detecting fluorescent regions on a surface of a
substrate, which comprises an excitation radiation source, and
first focusing optics for focusing the excitation radiation on the
surface of the substrate in a focused spot having a diameter no
greater than 10 .mu.m, preferably less than 5 .mu.m and more
preferably about 3 .mu.m. An oscillating or reciprocating radiation
direction system scans the spot linearly across the surface of the
substrate, with a focused travel distance of at least 10 mm and
preferably about 14 mm. In one embodiment, an optical train
separates fluorescence emitted from the surface of the substrate
from the excitation radiation reflected from the surface. An
autofocus system may also be included for automatically placing the
surface of the substrate in a focal plane of the focusing
optics.
[0013] The present invention also provides methods of scanning
substrates using the above systems. For example, in one aspect, the
invention provides a method of scanning a polymer array having a
plurality of different polymer sequences, each of the different
polymer sequences being immobilized on a surface of a substrate in
a different known location, to identify which polymer sequence on
the array is bound by a fluorescent target molecule. The method
comprises focusing an excitation radiation source upon the surface
of the substrate, and scanning the excitation radiation across the
surface of the substrate at a speed of at least 5 image
lines/second. Fluorescent emissions are collected from the surface
of the substrate in response to the excitation radiation. These
fluorescent emissions are recorded as a function of a position on
the surface of the substrate. The position on the surface indicates
the polymer sequence on the array that is bound by the fluorescent
target molecule.
[0014] A further understanding of the nature and advantages of the
inventions herein may be realized by reference to the remaining
portions of the specification and the attached drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0015] FIG. 1 is a schematic illustration of one embodiment of a
scanning system according to the present invention.
[0016] FIG. 2 illustrates one embodiment of a scanning system that
includes a flow cell on which a substrate is mounted.
[0017] FIG. 3 is a schematic illustration of a computer based
system for controlling and recording data from a scanning system
according to the present invention.
[0018] FIG. 4 is a schematic illustration of an alternate
embodiment of a scanning system according to the present
invention.
[0019] FIG. 5 is an enlarged view of a scanned image generated
using a scanning system of the present invention.
DESCRIPTION OF THE PREFERRED EMBODIMENT
Contents
[0020] I. Definitions
[0021] II. General
[0022] a. Introduction
[0023] b. Overview of the Imaging System
[0024] III. Detailed Description of One Embodiment of the Imaging
System
[0025] a. Detection Device
[0026] b. Data Acquisition
[0027] IV. Detailed Description of a Second Embodiment of the
Imaging System
[0028] I. Definitions
[0029] The following terms are intended to have the following
general meanings as they are used herein:
[0030] 1. Complementary: Refers to the topological compatibility or
matching together of interacting surfaces of a probe molecule and
its target. Thus, the target and its probe can be described as
complementary, and furthermore, the contact surface characteristics
are complementary to each other.
[0031] 2. Probe: A probe is a surface-immobilized molecule that is
recognized by a particular target. Examples of probes that can be
investigated by this invention include, but are not restricted to,
agonists and antagonists for cell membrane receptors, toxins and
venoms, viral epitopes, hormones (e.g., opioid peptides, steroids,
etc.), hormone receptors, peptides, enzymes, enzyme substrates,
cofactors, drugs, lectins, sugars, oligonucleotides, nucleic acids,
oligosaccharides, proteins, and monoclonal antibodies.
[0032] 3. Target: A molecule that has an affinity for a given
probe. Targets may be naturally-occurring or manmade molecules.
Also, they can be employed in their unaltered state or as
aggregates with other species. Targets may be attached, covalently
or noncovalently, to a binding member, either directly or via a
specific binding substance. Examples of targets which can be
employed by this invention include, but are not restricted to,
antibodies, cell membrane receptors, monoclonal antibodies and
antisera reactive with specific antigenic determinants (such as on
viruses, cells or other materials), drugs, polynucleotides, nucleic
acids, peptides, cofactors, lectins, sugars, polysaccharides,
cells, cellular membranes, and organelles. Targets are sometimes
referred to in the art as anti-probes. As the term targets is used
herein, no difference in meaning is intended. A "Probe Target Pair"
is formed when two macromolecules have combined through molecular
recognition to form a complex.
[0033] II. General
[0034] A. Introduction
[0035] The present invention provides methods and apparatus for
scanning a substrate to obtain a highly sensitive and resolved
image at a high speed. The invention will have a wide range of
uses, particularly, those requiring quantitative study of a
microscopic region from within a larger region, such as 2 or 3
.mu.m.sup.2 over 100 mm.sup.2. For example, the invention may find
application in the field of histology (for studying histochemical
stained and immunological fluorescent stained images), or
fluorescence in situ hybridization. In one application, the
invention herein is used to image an array of probe sequences
fabricated on a support.
[0036] High resolution scanning systems and methods, whether
microscopic or macroscopic, have routinely been used in the
electronics industries, e.g., in the semiconductor and
microfabrication industries, to scan microfabricated electronics,
e.g., microprocessors, microcircuitry, and the like. However, such
scanning also has great utility in the field of combinatorial
chemistry and genetic analysis. Specifically, high resolution
scanning methods and devices can be used in the application of
polymer arrays. These polymer arrays are generally made up of a
large number of different polymer sequences that are coupled to the
surface of a typically planar substrate.
[0037] The substrate on which the polymer sequences are formed may
be composed from a wide range of material, either biological,
nonbiological, organic, inorganic, or a combination of any of
these, existing as particles, strands, precipitates, gels, sheets,
tubing, spheres, containers, capillaries, pads, slices, films,
plates, slides, etc. The substrate may have any convenient shape,
such as a disc, square, sphere, circle, etc. The substrate is
preferably flat but may take on a variety of alternative surface
configurations. For example, the substrate may contain raised or
depressed regions on which a sample is located. The substrate and
its surface preferably form a rigid support on which the sample can
be formed. The substrate and its surface are also chosen to provide
appropriate light-absorbing characteristics. For instance, the
substrate may be a polymerized Langmuir Blodgett film,
functionalized glass, Si, Ge, GaAs, GaP, SiO.sub.2, SiN.sub.4,
modified silicon, or any one of a wide variety of gels or polymers
such as (poly)tetrafluoroethyle- ne, (poly)vinylidenedifluoride,
polystyrene, polycarbonate, or combinations thereof. Other
substrate materials will be readily apparent to those of skill in
the art upon review of this disclosure. In a preferred embodiment,
the substrate is flat glass or silica.
[0038] According to some embodiments, the surface of the substrate
is etched using well known techniques to provide for desired
surface features. For example, by way of the formation of trenches,
v-grooves, mesa structures, or the like, the synthesis regions may
be more closely placed within the focus point of impinging light.
The surface may also be provided with reflective "mirror"
structures for maximization of emission collected therefrom.
[0039] Surfaces on the solid substrate will usually, though not
always, be composed of the same material as the substrate. Thus,
the surface may be composed of any of a wide variety of materials,
for example, polymers, plastics, resins, polysaccharides, silica or
silica-based materials, carbon, metals, inorganic glasses,
membranes, or any of the above-listed substrate materials. In one
embodiment, the surface will be optically transparent and will have
surface Si--OH functionalities, such as those found on silica
surfaces.
[0040] These arrays are typically prepared in a manner that allows
groups of each different polymer sequence to be coupled in a
different known location on the substrate surface. The pioneering
methods for synthesizing these arrays have been previously
described. For example, methods of synthesizing arrays of polymers
using light directed synthesis methods are described in U.S. Pat.
No. 5,143,854 to Pirrung et al., and U.S. Pat. No. 5,405,783 to
Fodor et al., the complete disclosures of which are incorporated
herein by reference. Additionally, mechanical methods for
synthesizing these arrays are described in, e.g., U.S. Pat. No.
5,384,261 to Winkler et al., the complete disclosure of which is
incorporated herein by reference. Using these pioneering methods,
the combination of photolithograpic and fabrication techniques may,
for example, enable each probe sequence ("feature") to occupy a
very small area ("site") on the support. In some embodiments, this
feature site may be as small as a few microns or even a single
molecule. For example, about 10.sup.5 to 10.sup.6 features may be
fabricated in an area of only 12.8 mm.sup.2. Such probe arrays may
be of the type known as Very Large Scale Immobilized Polymer
Synthesis (VLSIPS.TM.). For ease of discussion, the arrays for use
with the present invention are described in terms of arrays of
different oligonucleotide sequences. However, it should be readily
understood that a variety of different polymer array types are
equally applicable to the devices of the invention. Furthermore,
the scanners of the present invention may also be used in the
reflectance mode to scan non-fluorescent surfaces.
[0041] In those applications using polymer arrays, such arrays may
be prepared having all nucleotide sequences of a given length,
composed of the basis set of monomers. For example, an array of
oligonucleotides containing all possible sequences of length n
which is made up of the basis set of four nucleotides contains up
to 4.sup.n oligonucleotides on its surface. For an array of 8mer or
10mer oligonucleotides, such arrays may include upwards of about
65,536 and 1,048,576 different oligonucleotides, respectively.
Generally, where it is desired to produce arrays having all
possible polymers of length n, a simple binary masking strategy can
be used, as described in U.S. Pat. No. 5,143,854 to Pirrung.
[0042] Alternate masking strategies can produce arrays of probes
which contain a subset of polymer sequences, i.e., polymers having
a given subsequence of monomers, but are systematically substituted
at each position with each member of the basis set of monomers. In
the context of oligonucleotide probes, these alternate synthesis
strategies may be used to lay down or "tile" a range of probes that
are complementary to, and span the length of a given known nucleic
acid segment. The tiling strategy will also include substitution of
one or more individual positions within the sequence of each of the
probe groups with each member of the basis set of nucleotides.
These positions are termed "interrogation positions." By reading
the hybridization pattern of the target nucleic acid, one can
determine if and where any mutations lie in the sequence, and also
determine what the specific mutation is by identifying which base
is contained within the interrogation position. Tiling methods and
strategies are discussed in substantial detail in Published PCT
Application No. 95/11995, the complete disclosure of which is
incorporated herein by reference in its entirety for all
purposes.
[0043] Tiled arrays may be used for a variety of applications, such
as identifying mutations within a known oligonucleotide sequence or
"target". Specifically, the probes on the array will have a
sub-sequence which is complementary to a known nucleic acid
sequence, but wherein at least one position in that sequence has
been systematically substituted with the other three nucleotides.
See, e.g., U.S. Pat. No. 5,527,681, the complete disclosure of
which is incorporated herein by reference.
[0044] Generally, the sample nucleic acid for which sequence
information is desired is contacted with the array. This "target"
sequence is typically labeled with a detectable group such as a
fluorescent moiety, i.e., fluorescein or rhodamine. Following
hybridization of the target to the array, one can detect the
position on the array to which the target sequence binds by
scanning the surface of the array for fluorescence.
[0045] The surface is typically scanned by directing excitation
radiation at the surface to activate the fluorescent labeling group
in the target, which in turn emits a fluorescent response
radiation. The fluorescent response radiation is detected and
assigned to the region from which it originated. By knowing the
position from which the fluorescence originates, one can identify
the sequence to which the target binds.
[0046] Although generally used herein to define separate regions
containing differing polymer sequences, the term "feature"
generally refers to any element, e.g., region, structure or the
like, on the surface of a substrate. Typically, substrates to be
scanned using the scanning systems described herein, will have
small feature sizes, and consequently, high feature densities on
substrate surfaces. For example, individual features will typically
have at least one of a length or width dimension that is no greater
than 100 .mu.m, and preferably, no greater than 50 .mu.m, and more
preferably greater than about 20 .mu.m. Thus, for embodiments
employing substrates having a plurality of polymer sequences on
their surfaces, each different polymer sequence will typically be
substantially contained within a single feature.
[0047] The probe arrays will have a wide range of applications. For
example, the probe arrays may be designed specifically to detect
genetic diseases, either from acquired or inherited mutations in an
individual DNA. These include genetic diseases such as cystic
fibrosis, diabetes, and muscular dystrophy, as well as acquired
diseases such as cancer (P53 gene relevant to some cancers), as
disclosed in U.S. patent application Ser. No. 08/143,312, already
incorporated by reference.
[0048] Genetic mutations may be detected by a method known as
sequencing by hybridization. In sequencing by hybridization, a
solution containing one or more targets to be sequenced (i.e.,
samples from patients) contacts the probe array. The targets will
bind or hybridize with complementary probe sequences. Generally,
the targets are labeled with a fluorescent marker, radioactive
isotopes, enzymes, or other types of markers. Accordingly,
locations at which targets hybridize with complimentary probes can
be identified by locating the markers. Based on the locations where
hybridization occur, information regarding the target sequences can
be extracted. The existence of a mutation may be determined by
comparing the target sequence with the wild type.
[0049] The interaction between targets and probes can be
characterized in terms of kinetics and thermodynamics. As such, it
may be necessary to interrogate the array while in contact with a
solution of labeled targets. Consequently, the detection system
must be extremely selective, with the capacity to discriminate
between surface-bound and solution-born targets. Also, in order to
perform a quantitative analysis, the high-density volume of the
probe sequences requires the system to have the capacity to
distinguish between each feature site.
[0050] B. Overview of the Imaging System
[0051] The devices of the present invention generally employ a
scanning device which rapidly sweeps an activation radiation beam
or spot across the surface of the substrate. The devices also
include focusing optics for focusing the excitation radiation onto
the surface of the substrate in a sufficiently small area to
provide high resolution of features on the substrate, while
simultaneously providing a wide scanning field. An image is
obtained by detecting the electromagnetic radiation emitted by the
labels on the sample when the labels are illuminated. In one
embodiment, fluorescent emissions are gathered by the focusing
optics and detected to generate an image of the fluorescence on the
substrate surface. In preferred aspects, the devices of the
invention further employ confocal detection systems to reduce or
eliminate unwanted signals from structures above and below the
plane of focus of the excitation radiation, as well as autofocus
systems to focus both the activation radiation on the substrate
surface and the emitted radiation from the surface. Generally, the
excitation radiation and response emission have different
wavelengths. Filters having high transmission in the label's
emission band and low transmission in the excitation wavelength may
be utilized to inhibit the detection of undesirable emission. These
generally include emission from out-of-focus planes or scattered
excitation illumination as potential sources of background
noise.
[0052] In operation, the devices of the present invention include
one or more sources of excitation radiation. Typically, these
source(s) are immobilized or stationary point light sources, e.g.,
lasers such as argon, helium-neon, diode, dye, titanium sapphire,
frequency-doubled diode pumped Nd:YAG and krypton. Typically, the
excitation source illuminates the sample with an excitation
wavelength that is within the visible spectrum, but other
wavelengths (i.e., near ultraviolet or near infrared spectrum) may
be used depending on the application (i.e., type of markers and/or
sample). In some embodiments, the sample is excited with
electromagnetic radiation having a wavelength at or near the
absorption maximum of the species of label used. Exciting the label
at such a wavelength produces the maximum number of photons
emitted. For example, if fluorescein (absorption maximum of 488 nm)
is used as a label, an excitation radiation having a wavelength of
about 488 nm would induce the strongest emission from the
labels.
[0053] In instances where a multi-labeling scheme is utilized, a
wavelength which approximates the mean of the various candidate
labels' absorption maxima may be used. Alternatively, multiple
excitations may be performed, each using a wavelength corresponding
to the absorption maximum of a specific label. Table I lists
examples of various types of fluorophores and their corresponding
absorption maxima.
1 TABLE 1 Candidate Fluorophores Absorption Maxima Fluorescein 488
nm Dichloro-fluorescein 525 nm Hexachloro-fluorescein 529 nm
Tetramethylrhodamine 550 nm Rodamine X 575 nm Cy3 .TM. 550 nm Cy5
.TM. 650 nm Cy7 .TM. 750 nm IRD40 785 nm
[0054] The excitation radiation from the point source is directed
at a movable radiation direction system which rapidly scans the
excitation radiation beam back and forth across the surface of the
substrate. A variety of devices may be employed to generate the
sweeping motion of the excitation radiation. For example, resonant
scanner or rotating polygons, may be employed to direct the
excitation radiation in this sweeping fashion. Generally, however,
galvanometer devices are preferred as the scanning system. As used
herein, the term "galvanometer" refers to devices that employ a
servo motor to oscillate or rotate a mirror over a restricted,
predefined range, which is typically less than 90.degree.. This
generates a rapidly sweeping or rastering beam reflecting from the
galvanometer mirror, which is then directed at and swept across the
surface of a substrate that is to be scanned. Typically, an optical
train may be employed between the activation source and the
galvanometer mirror to assist in directing, focusing or filtering
the radiation directed at and reflected from the galvanometer
mirror.
[0055] The galvanometers employed in the devices and systems of the
present invention typically sweep a scanning spot across the
substrate surface at an oscillating frequency that is typically
greater than about 7.5 Hz, preferably greater than about 20 Hz and
more preferably, greater than about 30 Hz. With this frequency, the
spot can typically be scanned across the substrate at a velocity of
at least about 20 lines/second, preferably in about 5 image
lines/second, preferably at least 10 images lines/second, and more
preferably at least about 30 image lines/second. It should be noted
that the mirror may scan unidirectionally (e.g., with a sawtooth
wave) or bidirectionally (e.g., with a symmetric triangle wave). In
the latter case, the galvanometer frequency would generally be
about half of the data aquisition speed in image lines/second.
Accordingly, the frequency of the galvanometer in the latter case
may be lower than 7.5 Hz in order to scan 5 image lines/second. The
activation radiation is then directed through focusing optics to
focus the sweeping beam at the surface of the array which is used
to interrogate the target sequence. These same focusing optics also
collect emitted fluorescence from the substrate surface for
subsequent detection.
[0056] The objective lens is preferably selected to provide high
resolution, as determined by the focused spot size, while still
allowing a wide scanning field. "Focused spot size" is defined by
the diameter of the focused activation spot on the surface of the
substrate at 1/e.sup.2 intensity points. "Scanning field" is
defined as the length of travel of the focused activation beam or
"spot," in one dimension parallel to the direction of travel of the
sweeping beam. The confocal system of the present invention
generally provides a focused spot size having a diameter no greater
than about 10 .mu.m, preferably no greater than about 5 .mu.m, and
more preferably about 3 .mu.m. In addition, these systems have a
scanning field with a dimension parallel to the direction of the
sweep of the activation beam that is usually greater than about 10
mm and more preferably about 14 mm.
[0057] For ease of discussion, the combined measurement of
resolution and effective scanning field are provided as a ratio of
the size of the effective field of view of the objective to the
size of the focused spot from the scanner. For example, a scanner
having a scanning field of 2 mm and a focused spot size of 10 .mu.m
would have a ratio of 200 (2 mm/0.010 mm). While a scanner having
an effective scanning field of 14 mm with a focused spot size of 3
.mu.m would have a ratio of 4666. In general, the scanning system
of the present invention usually has a ratio of size of effective
field of view to size of focused spot of at least about 2000,
preferably greater than about 3000, and more preferably greater
than about 4000. It should be noted that "scanning field" generally
refers to the direction in which the galvanometer mirror scans the
laser spot across the substrate. The translation stage moves the
substrate in the direction orthogonal to the scanned direction, and
this direction may be larger than 14 mm.
[0058] In one embodiment of the present invention, high
fluorescence collection efficiency is achieved by providing an
objective lens having a numerical aperture that is at least about
0.2. In particularly preferred aspects, the numerical aperture is
at least about 0.25. This translates to an F/number of about F/2.5
to F/2.
[0059] In addition to providing smaller spot size while not
sacrificing scanning field size, the focusing optics of the
scanning system may include a telecentric objective lens. This
allows the activation beam to strike the scanning surface at an
angle that is substantially normal to that surface, across the
entire scanning surface, i.e., regardless of where the input beam
is propagating through the lens relative to the lens axis. By
"substantially normal" is meant an angle of incidence of
approximately 0.degree., e.g., between 0.degree. and 5.degree., and
preferably from 0.degree. to 2.degree..
[0060] As the activation radiation spot is swept across the surface
of the substrate, it activates any fluorescent groups that remain
upon the surface, e.g., those that are bound to the surface. The
activated groups emit a response radiation or emission which is
then collected by the objective lens and directed back through the
optical train via the servo mounted mirror. In order to avoid the
detrimental effects of reflected excitation radiation upon the
detection of the fluorescence, dichroic mirrors or beam splitters
may be included in the optical train. These dichroic beam splitters
or mirrors are reflective to radiation in the wavelength of the
excitation radiation while transmissive to radiation in the
wavelength of the response radiation. For example, where an Argon
laser is used as the point energy source, it will typically
generate activation radiation having a wavelength of about 488 nm.
Fluorescence emitted from an activated fluorescein moiety on the
other hand will typically have a wavelength between about 515 and
545 nm. As such, dichroic mirrors may be included which transmit
light having a wavelength greater than 515 nm while reflecting
light of shorter wavelengths. This effectively separates the
excitation radiation reflected from the surface of the substrate
from the response radiation emitted from the surface of the
substrate. Similarly, additional dichroic mirrors may be used to
separate signals from label groups having different response
radiation wavelengths, thereby allowing simultaneous detection of
multiple fluorescent indicators, and thus, simultaneous
interrogation of a single array with multiple target sequences.
Specifically, a first target sequence may be labeled with a shorter
wavelength fluorescent label, e.g., fluorescein, while a second
target sequence is labeled with a longer wavelength fluorescent
label, e.g., carbocyanin dyes such as CY3 which emit response
radiation in the range of 550 to 600 nm. The response radiation
from each of these targets may be separated and individually
detected through the inclusion of additional dichroic beam
splitters and detectors.
[0061] Following separation of the response radiation from the
reflected excitation radiation, the response radiation or
fluorescence is then directed at a detector, e.g., a
photomultiplier tube, to measure the level of response radiation
and record that level as a function of the position on the
substrate from which that radiation originated. Typically, the
response radiation is focused upon the detector through a spatial
filter such as a confocal pinhole. Such spatial filters reduce or
eliminate unwanted signals from structures above and below the
plane of focus of the excitation radiation. Additionally, the
device may incorporate a bandpass filter between the dichroic
mirror and the detector to further restrict the wavelength of
radiation that is delivered to the detector.
[0062] As noted above, the reflected excitation radiation may
generally be used in an autofocusing system in the devices
described herein. In particular, the reflected excitation radiation
may also be directed at a detector, e.g., a photodiode, that is
preferably located behind another spatial filter, i.e., a confocal
pinhole.
[0063] The substrate surface may be moved closer to and further
from the objective lens using, e.g., a translation stage upon which
the substrate is mounted. As the substrate is moved out of focus,
the amount of reflected excitation radiation contacting the
photodiode will be reduced. As the substrate is brought back into
focus, this amount will increase, reaching a maximal value when the
substrate is in focus. Control for the autofocus system is
generally supplied by an appropriately programmed computer, which
moves the translation stage in response to the input from the
photodiode, until a maximum is reached. Generally, this computer is
the same computer which receives, compiles and stores the input
from the fluorescence detector or photomultiplier tube, to produce
an output of fluorescence as a function of position on the array,
typically in the form of a numerical representation or a scan
image. Examples of autofocus confocal systems for use in
fluorescent scanning devices are generally described in commonly
assigned, co-pending U.S. patent application Ser. No. 08/195,889,
filed Feb. 10, 1994, the complete disclosure of which is
incorporated herein by reference for all purposes. These autofocus
systems generally permit the focusing of light reflected from a
weakly reflecting surface, e.g., the wet side of a glass substrate,
even in the vicinity of a strongly reflecting surface, e.g., the
dry side of a glass substrate, as well as being capable of focusing
on a featureless surface, e.g., smooth glass.
[0064] III. Detailed Description of One Embodiment of the Imaging
System.
[0065] A. Detection Device
[0066] FIG. 1 is an optical block diagram illustrating the imaging
system 100 according to the present invention. Typically, imaging
system 100 is used to obtain images of oligonucleotide probe arrays
to which fluorescently labelled DNA or RNA is bound. It might also
be used for other applications, such as wafer or mask inspection,
or for imaging of polypeptide or other polymer arrays,
electrophoresis gels, or biological specimens. As shown in FIG. 1,
a beam of excitation radiation, e.g., 488-nm light, from a laser
102 is partially reflected and partially transmitted by a
beamsplitter 104. The reflected portion of the beam impinges upon a
photodetector 131 (optional), which is typically a photodiode used
as a laser power monitor. The portion of the beam that is
transmitted through beamsplitter 104 is reflected by dichroic
beamsplitters 106 and 108 and transmitted through lenses 111 and
112, which provide a telescope to expand the beam emitted by laser
102 and to demagnify the collimated fluorescence obtained from the
surface of the substrate. In an exemplary embodiment, lens 111 has
a focal length of 20 mm and lens 112 has a focal length of 80 mm.
Other focal lengths and focal length ratios can be used, but system
performance (confocality, resolution, etc.) may be affected. The
expanded laser beam is reflected by mirror 114 and focused by lens
116, which is described in more detail below.
[0067] Mirror 114, which typically is an 18 mm.times.28 mm octagon
or ellipse, is a galvanometer mirror that oscillates (i.e., scans)
at a rate of typically several Hertz or several tens of Hertz. In
preferred aspects, the galvanometer mirror oscillates at
frequencies greater than 7.5 Hz, preferably about 20 Hz and more
preferably about 30 Hz. A resonant scanner or rotating polygonal
mirror could be used instead of a galvanometer. Typically, imaging
system 100 obtains an image of a 2-dimensional area by scanning the
laser beam in one dimension while moving the sample in an
orthogonal direction.
[0068] Optimally, sample 118 is positioned such that the plane of
interest (e.g. the surface to which labelled target molecules are
bound) is located in the plane where the laser light is focused.
Light remitted by sample 118 is collected by lens 116, reflected by
mirror 114, and transmitted through lenses 112 and 111. Remitted
light may consist of fluorescence, phosphorescence, specular
reflection, diffuse reflection, Raman scattering, etc. Remitted
light having a wavelength greater than 555 nm passes through
dichroic beamsplitter 108 and is focused by lens 134 onto pinhole
136. Remitted light having a wavelength between 515 and 555 nm is
reflected by beamsplitter 108, passes through dichroic beamsplitter
106, and is focused by a lens 120 onto a pinhole 122. The light
that is transmitted through pinholes 136 and 122 impinges upon
filters 138 and 124, respectively; the light that passes through
these filters impinges upon photodetectors 140 and 126,
respectively. Filter 138 transmits light having wavelengths between
555 and 607 nm, and filter 124 transmits light having wavelengths
between 515 and 545 nm. Remitted light having wavelengths less that
515 nm is reflected by beamsplitters 108 and 106 and partially
reflected by beamsplitter 104; the light reflected by beamsplitter
104 is focused by a lens 132 onto a pinhole 128. The light that is
transmitted through pinhole 128 impinges upon a photodetector
130.
[0069] Pinholes 136, 122, and 128 are typically confocal pinholes.
Specifically, remitted light that originates from the location on
sample 118 where the laser beam is focused is maximally transmitted
through the pinholes, while light that originates from other
locations is not. Lenses 134, 120, and 132 preferably have focal
lengths of 50 mm. Pinholes 136 and 122 preferably have diameters of
100 microns; pinhole 128 preferably has a diameter of 50 microns.
Other lens focal lengths and pinhole diameters can be used, but
system performance (confocality, sensitivity to misalignment, etc.)
may be affected.
[0070] If lens 116 is not fully corrected for lateral color, the
remitted light that is focused onto pinholes 136 and 122 might move
laterally (across the plane of the pinhole) as mirror 114 is
scanned. In this case it might be advantageous to use pinholes that
are elliptical or rectangular rather than round, or to use slits
instead of pinholes. For example, lens 116 in the present scanner
has about 3 microns of lateral color at the edges of the scan
field; consequently, the remitted light can move laterally by about
40 microns across the pinholes. Reasonable sizes for pinholes 136
and 122 in this case might be approximately 75 microns by 125
microns.
[0071] Photodetectors 140 and 126 are typically photomultipliers
and are typically intended for the detection of relatively weak
signals such as fluorescence. Various light detectors may be used,
including photodiodes, avalanche photodiodes, phototransistors,
vacuum photodiodes, photomultiplier tubes, and other light
detectors.
[0072] Typically, photodetector 130 is used to aid in focusing the
sample prior to scanning or while it is being scanned. The amount
of reflected laser light reaching photodetector 130 is a maximum
when the laser beam is focused onto the surface of sample 118.
Focusing can be done either manually, or by a motorized translation
stage under computer control. Frequently, sample 118 is a glass
slide mounted in a liquid-filled flow cell (see FIG. 2) and the
surface of interest is the second surface of the glass, i.e. the
glass-liquid interface. Typically the reflection from this surface
is much weaker than the reflection from the first surface of the
glass, i.e. the glass-air interface, but the system is sufficiently
confocal that the reflection peaks from the 2 surfaces are well
separated.
[0073] The system described above is particularly useful in the
detection of fluorescence from targets that are labelled with dyes
such as fluorescein and phycoerythrin. Other dyes (rhodamines,
carbocyanines, etc.) can be used, but laser 102, beamsplitters 108
and 106, and filters 138 and 124 may need to be altered depending
on the dyes' absorption and emission spectra.
[0074] In some cases, target molecules may be labeled with
particles or very large molecules that scatter laser light but do
not fluoresce. In these cases, it may be desirable to detect
diffusely scattered light but not specularly reflected laser light.
An annular aperture can be placed between beamsplitter 104 and lens
132. If the inner diameter of the annulus is selected properly,
this aperture will block specularly reflected laser light while
transmitting diffusely scattered laser light, which can then be
detected by photodetector 130.
[0075] Objective lens 116 was designed to meet a number of
specifications, and may be obtained from, e.g., Special Optics,
Part No. 55-S30-15 (Wharton, N.J.). The objective lens is usable
with a galvanometer (or resonant scanner, rotating polygon, etc.),
i.e. with an entrance pupil that is external to the lens and is
located at or near the galvanometer mirror's pivot location. The
lens is also capable of focusing a TEM.sub.00-mode laser beam
having a wavelength of 488 nm to a spot having a diameter no
greater than 3 microns at the 1/e.sup.2 intensity points, and
should be capable of doing this at any point within a flat field
having a diameter no less than 14 mm.
[0076] Objective lens 116 is within 2 degrees of telecentric, i.e.
the transmitted laser beam should be parallel to the optical axis
of the lens to within 2 degrees. (If the lens is not telecentric or
nearly so, specularly reflected light from near the edges of the
field might miss the lens and therefore not be detected.) In
addition, lens 116 was designed so that the F/number would be no
greater than f/2, i.e. numerical aperture no less than 0.25, with
no vignetting even at the edges of the field. (F/number is a
measure of the lens's light-gathering ability and is important if
the lens is to be used for the detection of weak signals).
Objective lens 116 is capable of focusing a polychromatic beam,
having wavelengths between 488 and 600 nm and filling the entrance
pupil, to a spot having a diameter no greater than 10 microns, and
is capable of doing this at any point within a flat field having a
diameter no less than 14 mm.
[0077] Objective lens 116 preferably has a focal length of about 30
mm. A lens having a different focal length, but still meeting the
above specifications could be readily designed and would be
acceptable for the purposes described herein. Lens 116 can focus a
488 nm laser beam to a diffraction-limited spot when the ratio of
input beam diameter to lens focal length is less than approximately
0.21, e.g. it can focus a 6.2 mm diameter beam to a 3 micron
diameter spot. If a larger focal spot is desired, the input beam
diameter can be made smaller, e.g. by changing the ratio of the
focal lengths of lenses ill and 112 or by demagnifying the beam
between laser 102 and beamsplitter 104.
[0078] Lens 116 was designed to be able to image a 14 mm field with
3 micron resolution and 0.25 numerical aperture; however, the
design can easily be scaled up, e.g. to image a 28 mm field with 6
micron resolution and 0.25 numerical aperture (or potentially, to
image a 280 mm field with 60 micron resolution and 0.25 numerical
aperture, although the lens would be extremely large and costly).
This scale-up involves merely multiplying the thicknesses,
diameters, and radii of curvature of all of the elements of lens
116 by a constant. Similarly, the entire scanner can be scaled up
for imaging of larger areas by multiplying all of the lens
diameters and focal lengths, pinhole diameters, and mirror
diameters by the same factor.
[0079] B. Data Acquisition
[0080] As shown in FIG. 3, imaging system 300 includes a
galvanometer 306 (to which a mirror 114 is attached) and a
galvanometer driver board 305, which can be obtained from General
Scanning Inc. (Watertown, Mass.). Galvanometer 306 is a model M2T.
Other suitable galvanometers and driver boards are available, e.g.
from Cambridge Technology Inc. (Watertown, Mass.). The input to
driver board 305 is a voltage waveform from arbitrary waveform
generator 304 (Keithley Metrabyte model PCIP-AWFG, Taunton, Mass.),
which is installed in an ISA slot in computer 302. Circuitry on
board 305 attempts at every instant to force galvanometer 306 to
whatever angular position is commanded by waveform generator 304
(the desired angular position is linearly related to the waveform
voltage). Waveform generator 304, after being programmed, can
generate a waveform indefinitely without further intervention by
computer 302. The waveform used is typically a sawtooth wave: e.g.
if the waveform period is 33.3 msec, the voltage ramps up linearly
for 25 msec, during which time data are acquired as the laser beam
sweeps across the field; during the next 8.3 msec the voltage
returns to its initial value and the laser beam retraces. Other
waveforms such as sine waves or symmetric triangle waves could be
used. Various methods of waveform generation that do not require
the PCIP-AWFG waveform generator are known.
[0081] Currents from photomultipliers 320 and 321 and from
photodiode 322 are converted to voltages by either transimpedance
amplifiers or load resistors, optionally followed by voltage
amplifiers. Simple op-amp circuits for this purpose are well known.
The voltages are then low-pass filtered by filters 310, 311, and
312, e.g., programmable 4-pole Bessel filters (Frequency Devices
model 824L8L-6, Haverhill, Mass.). Filter cutoff frequencies are
digitally programmable in 400-Hz steps from 400 Hz to 102.4 kHz and
are set by digital input-output board 314 (Computer Boards Inc.
model CIO-DIO24, Mansfield, Mass.) installed in computer 302.
Similar digital I/O boards are available from several other
manufacturers. Filter cutoff frequencies are set by software so
that each filter's output rise time in response to a step input is
approximately equal to the time between A/D conversions. For
example, if A/D conversions are 6 microseconds apart, the cutoff
frequencies are set to 66 kHz. A variety of other types of filters
(filters with more or fewer poles of different transfer functions
(e.g. Butterworth), fixed-frequency filters, or simple RC filters)
could be used instead.
[0082] Filter outputs are digitized by a 12-bit, 330-kHz analog-to
digital converter on data acquisition board 308 (Computer Boards
Inc. model CIO-DAS16/330). Similar data acquisition boards are
available from several other manufacturers. Digitized data are
displayed by computer 302, typically in the form of a gray-scale
image, and are written to the computer's hard disk for subsequent
data analysis. If the internal clock on data acquisition board 308
is used to trigger A/D conversions, the images obtained may be
slightly distorted. A/D conversions that are equally far apart in
time are not equally far apart in space, i.e., the velocity of the
laser beam across sample 118 is not exactly constant, partly
because lens 116 is not an ideal f-theta lens, and partly because
of non-ideal behavior by driver board 305 and galvanometer 306.
Therefore, A/D conversions are preferably triggered by waveform
generator 304, which has digital output channels in addition to its
analog output channel. When waveform generator 304 is appropriately
programmed and its digital output pulses are appropriately spaced,
image distortion can be eliminated.
[0083] Typically 4096 A/D conversions are performed per scan line,
and if the user wants fewer than 4096 pixels/line the A/D
conversions are binned by software in groups of 2 or more. For
example, if the length of a scan line is 14 mm, the laser beam
moves 3.4 microns between one A/D conversion and the next; and if,
for example, the user chooses a pixel size of 13.6 microns,
software adds the numbers from 4 A/D conversions for each pixel.
One version of the software allows 8192 A/D conversions per scan
line. The utility of doing more A/D conversions per line diminishes
as the pixel size becomes less than the laser spot size.
[0084] Translation stages 332 (typically a 2-axis or 3-axis set of
stages) are controlled by indexer 330. Two axes of translation are
usually used: a scan axis (parallel to the plane of the sample and
perpendicular to the direction of motion of the laser spot), and a
focus axis (parallel to the optical axis of lens 116). A third axis
orthogonal to the other two may also be desirable. Computer 302
sends commands to indexer 330, and receives information about
translation-stage status from indexer 330, e.g., using an RS-232
interface. An indexer that communicates with computer 302 using
another interface, such as a GPIB or ISA interface, could be used
instead. Translation stage speed is set such that the distance that
sample 118 moves per scan line is equal to the desired pixel
size.
[0085] Software allows the user to control various scan parameters,
including the size of the area to be scanned, the pixel size, the
scan speed, and which output or outputs to digitize (either of the
photomultiplier outputs, or the photodiode output, or a combination
thereof). Default parameters are 14 mm.times.14 mm scan area, 10.2
micron pixel size, and scan speed of 30 lines/second. With these
parameters, an image contains 1365.times.1365 pixels and can be
acquired in about 45 seconds. These parameters are usually suitable
for users who need to image 12.8 mm.times.12.8 mm oligonucleotide
arrays having features that are approximately 100 .mu.m.times.100
.mu.m. Other scan parameters are suitable in other circumstances.
The source code for this software is enclosed in Appendix A, of
which is hereby incorporated herein by reference for all
purposes.
[0086] For example, if the features are 400 .mu.m.times.400 .mu.m
the user might choose a pixel size of 27.2 microns. In this case an
image of a 14 mm.times.14 mm area contains 512.times.512 pixels and
can be obtained in about 17 seconds. On the other hand, if the
features are 30 .mu.m.times.30 .mu.m, the user might choose a pixel
size of 3.4 microns. In this case an image of a 14 mm.times.14 mm
area contains 4096.times.4096 pixels and can be acquired in about 2
minutes and 16 seconds. If an image with adequate signal-to noise
ratio is not obtained at a scan speed of 30 lines/second, the user
might choose to reduce the scan speed, for example to 7.5
lines/second (quadrupling the scan time approximately quadruples
the number of photons detected per pixel, and therefore in many
cases approximately doubles the signal-to-noise ratio).
[0087] Scanned areas can vary from the 14 mm.times.14 mm dimensions
described above, and need not be square. For example, software
options can allow the user to reduce the length of a scan line,
e.g., to as little as 4 mm or smaller if a user so desired, with a
pixel size as small as 1 micron, and to set the number of lines per
scan independently of the other scan parameters. In the
galvanometer-scanned direction, a single scan can not cover a
region that is larger than the field of view of lens 116, e.g., 14
mm. However, the system may cover a region that is several inches
wide in the orthogonal direction (limited only by the length of
travel of the translation stage). Other software options allow
users automatically to scan a chip several times, with any desired
time interval between scans (useful for certain kinetics
experiments), and automatically to scan several different chips on
a wafer (useful for wafer inspection prior to dicing and
packaging). Another option allows users to choose between 2
different output file formats: one format which saves "raw" data,
with 2 bytes per pixel; and a space-saving format which saves
"scaled" data, with one byte per pixel. A scaled data value is
directly proportional to the square root of the raw data value. A
lookup table for converting from scaled data back to raw data is
stored in the file's header.
[0088] Referring to FIG. 2, a system and method for holding sample
118 within a flow cell will now be described. It should be clearly
understood that the present invention is not limited to a flow
cell. For example, the sample 118 may be part of a packaged chip,
such as a diced chip glued into a disposable plastic package. A
more complete description of a packaged chip can be found in
commonly assigned, co-pending applications Ser. No. 08/485,452,
filed Jun. 7, 1995 (Attorney Docket No. 16528X-006910), the
complete disclosures of which are incorporated herein by reference
for all purposes.
[0089] As shown, imaging system 100 further includes a body 422 for
holding a support 430 containing the sample on a surface 431. In
some embodiments, the support may be a microscope slide or any
surface which is adequate to hold the sample. The body 422,
depending on the application, may be a flow cell having a cavity
423. The flow cell, for example, may be employed to detect
reactions between targets and probes. In some embodiments, the
bottom of the cavity may comprise a light absorptive material so as
to minimize the scattering of incident light.
[0090] In embodiments utilizing the flow cell, surface 431 is mated
to body 422 and serves to seal cavity 423. The flow cell and the
substrate may be mated for sealing with one or more gaskets. In one
embodiment, the substrate is mated to the body by vacuum pressure
generated by a pump 452. Optionally, the flow cell is provided with
two concentric gaskets and the intervening space is held at a
vacuum to ensure mating of the substrate to the gaskets.
Alternatively, the substrate may be attached by using screws,
clips, or other mounting techniques.
[0091] When mated to the flow cell, the cavity encompasses the
sample. The cavity includes an inlet port 421 and an outlet port
420. A fluid, which in some embodiments contains fluorescently
labeled targets, is introduced into the cavity through inlet port
421. A pump 453, which may be a model no. B-120-S made by Eldex
Laboratories, circulates fluids into the cavity via inlet 421 port
and out through outlet port 420 for recirculation or disposal.
Alternatively, a syringe, gas pressure, or other fluid transfer
device may be used to flow fluids into and through the cavity.
[0092] Optionally, pump 453 may be replaced by an agitation system
that agitates and circulates fluids through the cavity. Agitating
the fluids shortens the incubation period between the probes and
targets. This can be best explained in terms of kinetics. A thin
layer, known as the depletion layer, is located above the probe
sample. Since targets migrate to the surface and bind with the
probe sequences, this layer is essentially devoid of targets.
However, additional targets are inhibited from flowing into the
depletion layer due to finite diffusion coefficients. As a result,
incubation period is significantly increased. By using the
agitation system to dissolve the depletion layer, additional
targets are presented at the surface for binding. Ultrasonic
radiation and/or heat, shaking the holder, magnetic beads, or other
agitating technique may also be employed.
[0093] In some embodiments, the flow cell is provided with a
temperature controller 450 for maintaining the flow cell at a
desired temperature. Since probe/target interaction is sensitive to
temperature, the ability to control it within the flow cell permits
hybridization to be conducted under optimal temperature. The
temperature controller 450 may include a circulating bath, a
refrigerated air circulating device, resistance heater, peltier
device (thermoelectric cooler), or other temperature controller may
be implemented.
[0094] As previously mentioned, the flow cell is oriented to
maintain the substrate perpendicular to the optical axis of the
collection optics. According to one embodiment, flow cell 422 may
mounted to a translation stage 424 for moving the flow cell in an
orthogonal direction relative to the optical path. The flow cell
may be mated to the translation stage by vacuum pressure generated
by pump 452. Alternatively, screws, clips or other mounting
techniques may be employed to mate the flow cell to the translation
stage.
[0095] IV. Detailed Description of an Alternative Embodiment of the
Imaging System.
[0096] An optical block diagram of a second embodiment of imaging
system 400 is shown in FIG. 4. As depicted, imaging system 400
comprises components which are common to the system described in
FIG. 1. In this scanner, lens 116 is intended for use at a finite
rather than an infinite conjugate ratio, and therefore lens 112 is
omitted. This scanner uses only a single pinhole 401, and all of
the remitted light passes through this pinhole 401 before being
separated by the various dichroic beamsplitters. This scanner has 2
additional dichroic beamsplitters, spectral filters, and
photomultipliers, and therefore can be used for 4-channel rather
than merely 2-channel fluorescent scanning.
[0097] As discussed above in the previous embodiment, a beam of
excitation radiation, e.g., 488-nm light, from a laser 102 is
partially reflected and partially transmitted by a beamsplitter
104. The reflected portion of the beam impinges upon a
photodetector 131 (optional), which is typically a photodiode used
as a laser power monitor. The portion of the beam that is
transmitted through beamsplitter 104 is reflected by dichroic
beamsplitter 106 and transmitted through lens 111, focused onto
pinhole 401, and expanded to the desired diameter at the entrance
pupil lens 116.
[0098] The beam of excitation radiation is focused by lens 116 and
scanned across the sample 118 by galvanometer mirror 114, as
discussed above. Light remitted by sample 118 is collected by lens
116, reflected by mirror 114, and focused onto confocal pinhole
401. Light that is transmitted through pinhole 401 is collimated by
lens 111. Remitted light having wavelengths less that 515 nm is
reflected by beamsplitter 106 and partially reflected by
beamsplitter 104; the light reflected by beamsplitter 104 impinges
upon a photodetector 130. Remitted light having a wavelength above
515 passes through beamsplitter 106 and is sent to one of the four
channels 402, 404, 406, 408 depending on its wavelength. For
example, imaging system 300 may be constructed such that remitted
light having a wavelength between 515 and 545 is reflected by
dichroic beamsplitter 410, and passes through a filter 412 onto
photodetector 414. Remitted light having a wavelength between 545
and 570 nm, for example, may be reflected by dichroic beamsplitter
416, where it passes through filter 418 and onto photodetector 420.
Similarly, beamsplitter 422 is constructed to reflect remitted
light having wavelengths between 570 and 595 nm through filter 423
onto photodetector 426. Remitted light having wavelengths greater
than 595 nm are transmitted through beamsplitter 422, to pass
through filter 425 onto photodetector 424.
[0099] The present invention is further illustrated by the
following example. This example is merely to illustrate aspects of
the present invention and is not intended as limitations of this
invention.
EXAMPLE
[0100] A tiling array was designed for the entire human
mitochondrial genome. See M. Chee et al., "Accessing genetic
information with high-density DNA arrays", Science vol. 274, pgs.
610-614 (1996). The array contained 134,688 different probe
sequences, each occupying a separate 35 .mu.m feature. The overall
array dimensions were 1.28 cm.times.1.28 cm. Using long range PCR
and RNA polymerase promoter tagged primers, a 16.3 kb fragment of
mtDNA was amplified directly from genomic DNA samples. Labeled 16.3
kb RNA targets were prepared by in vitro transcription from the PCR
amplicons and hybridized to the array.
[0101] A scanning system as described above was used to scan the
array and a 4096.times.4096 pixel image was obtained, each pixel
representing 3.4 .mu.m. The entire array was scanned in under three
minutes. A close-up view of a scanned image of this array is shown
in FIG. 5. The scanned image shown covers a 1.5 mm.times.1.5 mm
segment of 14 mm.times.14 mm image of a 12.8 mm.times.12.8 mm
array.
[0102] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. All publications and patent
documents cited in this application are incorporated by reference
in their entirety for all purposes to the same extent as if each
individual publication or patent document were so individually
denoted.
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