U.S. patent application number 15/941383 was filed with the patent office on 2018-08-09 for real-time optical system for polymerase chain reaction.
The applicant listed for this patent is Streck, Inc.. Invention is credited to Matthew R. Kreifels, Joel R. TerMaat, Scott E. Whitney.
Application Number | 20180223335 15/941383 |
Document ID | / |
Family ID | 48014369 |
Filed Date | 2018-08-09 |
United States Patent
Application |
20180223335 |
Kind Code |
A1 |
Kreifels; Matthew R. ; et
al. |
August 9, 2018 |
REAL-TIME OPTICAL SYSTEM FOR POLYMERASE CHAIN REACTION
Abstract
An improved device and system for facilitating polymerase chain
reaction including a light source, detector, waveguide, and filters
that occupy minimal space and facilitate reduced sample read time
and rapid reading of multiple light wavelengths.
Inventors: |
Kreifels; Matthew R.;
(Omaha, NE) ; Whitney; Scott E.; (Lincoln, NE)
; TerMaat; Joel R.; (Lincoln, NE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Streck, Inc. |
LaVista |
NE |
US |
|
|
Family ID: |
48014369 |
Appl. No.: |
15/941383 |
Filed: |
March 30, 2018 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
13833349 |
Mar 15, 2013 |
9932632 |
|
|
15941383 |
|
|
|
|
61752494 |
Jan 15, 2013 |
|
|
|
61681879 |
Aug 10, 2012 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 21/645 20130101;
G01N 2201/0627 20130101; G01N 2201/0833 20130101; G01N 2021/6484
20130101; G01N 2201/0826 20130101; C12Q 1/686 20130101; G01N
21/6452 20130101 |
International
Class: |
C12Q 1/686 20180101
C12Q001/686; G01N 21/64 20060101 G01N021/64 |
Claims
1. An instrument for performing polymerase chain reaction with
real-time detection comprising: a) a polymerase chain reaction
instrument that includes a sample holder having one or more sample
wells, wherein the one or more sample wells are configured to
receive one or more sample tubes that each have at least one
portion that is generally optically transparent, and that receives
a biological sample having a nucleic acid to be amplified and at
least one fluorescing agent that interacts with the nucleic acid
during amplification and that emits light upon excitation by light
of a known wavelength; b) at least one light emitting diode device
that is carried on at least one support substrate, is in electrical
communication with a power source, is adapted to emit light at a
plurality of different wavelengths, and is located below the sample
holder so that the sample holder receives light emitted from the at
least one light emitting diode device at a bottom of the sample
holder; c) at least one photodiode detector device located below
the sample holder and which is adapted to issue signals based upon
intensity of light it receives; d) a light transmission assembly
that includes at least one waveguide which is multi-branched and
extends towards or partially into the one or more sample wells of
the sample holder, wherein the al least one waveguide includes: i)
at least one first excitation fork portion that extends between the
sample holder and the at least one light emitting diode device for
transmitting light emitted from the at least one light emitting
diode device to the biological sample contained in the sample
holder to excite the at least one fluorescing agent; and ii) at
least one second emission fork portion that extends between the
sample holder and the at least one photodiode detector device for
transmitting light emitted by the at least one fluorescing agent
upon its excitation and having a first end that is proximate the
sample holder and a second end that is proximate the at least one
photodiode detector device; and e) one or more emission filters
disposed between the second end of the at least one second emission
fork portion and the at least one photodiode detector device and is
adapted to filter the light emitted by the at least one fluorescing
agent across a plurality of bandwidths so that the wavelengths of
light received by the at least one photodiode detector device are
known, wherein the one or more filters include a linear variable
band pass filter, series of bandpass filters, or multiple band
bandpass filter.
2-20. (canceled)
21. The instrument of claim 1, wherein the instrument includes one
or more excitation filters disposed between an end of the first
excitation fork portion and the at least one light emitting diode
device which are adapted to filter the light emitted by the at
least one light emitting diode device into multiple bandwidths for
excitation of the biological sample.
22. The instrument of claim 1, wherein the instrument includes a
rotatable filter wheel which includes the one or more emission
filters.
23. The instrument of claim 21, wherein the instrument includes a
rotatable filter wheel which includes the one or more excitation
filters.
24. The instrument of claim 21, wherein the instrument includes a
rotatable filter wheel which includes the one or more emission
filters and the one or more excitation filters.
25. The instrument of claim 1, wherein the instrument includes
opposing thermoelectric devices which sandwich the sample
holder.
26. The instrument of claim 1, wherein the instrument includes a
housing between the sample holder and the at least one support
substrate which receives the at least one waveguide.
27. The instrument of claim 26, wherein the housing includes one or
more chambers which isolate the at least one photodiode detector
device from the at least one light emitting diode device.
28. The instrument of claim 1, wherein the at least one waveguide
partially extends into the one or more sample wells.
29. The instrument of claim 1, wherein the at least one waveguide
includes one or more fiber optic bundles.
30. The instrument of claim 1, wherein the at least one waveguide
includes a joined armed which extends into at least one bifurcated
portion, and the bifurcated portion includes the at least one first
excitation fork portion and the at least one second emission fork
portion.
31. The instrument of claim 1, wherein the at least one light
emitting diode device is an integrated assembly of LEDs or a
compact group of light emitting diodes.
32. The instrument of claim 1, wherein the at least one light
emitting diode device is less than 1 cm on each side.
33. The instrument of claim 1, wherein the at least one photodiode
detector device is a photodiode pixel array or compact grouping of
photodiodes, such that the wavelengths of light received across
individual pixels or photodiodes are of known wavelengths
corresponding to one or more different fluorescent agents present
within the one or more sample tubes.
34. The instrument of claim 1, wherein the one or more sample tubes
are optically transparent along a bottom portion of the one or more
sample tubes.
35. The instrument of claim 1, wherein each of the at least one
light emitting diode device includes at least 4 light emitting
diode elements.
36. The instrument of claim 1, at least one converging lens is
present between the second end of the at least one second emission
fork portion and the at least one photodiode detector device.
37. The instrument of claim 1, wherein one or more emission filters
are configured to be optically aligned the at least one photodiode
array detector.
38. The instrument of claim 26, wherein the housing includes an
upper portion aligned with the sample holder, and a base portion
having a cavity therein through which the at least one waveguide is
passed.
39. The instrument of claim 1, wherein for each sample there is one
or more of the at least one light emitting diode device, one or
more of the at least one photodiode detector device, or both.
Description
FIELD OF THE INVENTION
[0001] The present invention relates generally to devices and
systems for facilitating polymerase chain reactions.
BACKGROUND OF THE INVENTION
[0002] A number of optical detection systems have been developed
for use in qualitative and quantitative nucleic acid measurements.
Many such systems involve the use of fluorescing agents
(fluorescent probes, markers, labels, or dyes) in which the
resulting signal intensities are generally proportional to the
reaction products of polymerase chain reaction (PCR)
amplification.
[0003] As an example, U.S. Pat. No. 5,928,907 describes a system
for facilitating real-time fluorescence-based measurements of
nucleic acid amplification products utilizing a lens co-axially
disposed with a fiber optic cable for focusing a single color
excitation beam into the volume of a sample. U.S. Pat. No.
6,144,448 describes a fluorescence detecting device including
direct fiber optic connections between a single light source,
container holder and single fluorescence detector.
[0004] U.S. Pat. No. 7,315,376 describes a sample holder provided
together with an optical manifold having an excitation source, a
photo receiver, or both, for each sample. U.S. Pat. No. 7,507,575
describes a data acquisition device and a detection device coupled
to the data acquisition device. The detection device includes a
plurality of removable optical modules and a rotating disk having a
plurality of process chambers having a plurality of species that
emit fluorescent light at different wavelengths. U.S. Pat. No.
8,137,616 describes a system for performing multi-color real time
PCR, comprising a flexible real time PCR instrument and a specific
composition or reaction for performing multiplex PCR.
[0005] There remains a need for an improved system and device for
facilitating polymerase chain reaction that allows for detection of
stationary samples, reduced sample read time and optionally
simultaneous reading of multiple light wavelengths, resulting in an
increase in the speed with which amplification and quantification
take place. There is a further need for instruments that include
multiple light sources and detectors that occupy minimal space and
require little or no ancillary instrumentation for facilitating
light provision fluorescence detection, or movement of samples to
read different samples or fluorescent wavelengths. There is a need
for instruments that do not rely on precise and/or complex
alignments of reflective components such as mirrors, enclosures,
beam splitters, dichrotic/dichroric filters, or microelectronic
mirrors for light routing. There is also a need for instruments
that facilitate PCR and detection without direct connection between
a sample holder and fiber optic cable.
SUMMARY OF THE INVENTION
[0006] The present teachings meet one or more of the above needs by
providing an instrument for performing polymerase chain reaction
with real-time detection, including a light source, detector,
waveguide, a filters that occupy minimal space and facilitate
detection of stationary samples, reduced sample read time, and
simultaneous reading of multiple light wavelengths.
[0007] The present teachings provide for a device comprising a
polymerase chain reaction instrument that includes a sample holder
configured to receive one or more sample tubes that each have at
least one portion that is generally optically transparent, and that
receives a biological sample having a nucleic acid to be amplified
and at least one fluorescing agent that interacts with the nucleic
acid during amplification and that emits light upon excitation by
light of a known wavelength. The instrument may further include at
least one light emitting diode device (device being an integrated
assembly of light emitting diodes or a compact group of light
emitting diodes) that is carried on at least one support substrate,
is in electrical communication with a power source, and is adapted
to emit light at a plurality of different wavelengths, optionally
through a lens. At least one photodiode detector device (the device
being an integrated assembly of photodiodes (e.g. photodiode
array), an individual photodiode or compact group of photodiodes)
may also be included such that the detector is adapted to issue
signals based upon intensity of light it receives. The instrument
may also include a light transmission assembly that includes at
least one multi-branched waveguide and at least one manifold (e.g.,
a fiber optics block) that is configured to support the waveguide
between the sample holder and both the at least one light emitting
diode device and the at least one photodiode detector device. The
waveguide may include a first fork portion and a second fork
portion. The waveguide may include at least one excitation fork
portion and at least one emission fork portion. The first fork
portion (e.g., at least one excitation fork portion) may extend
between the sample holder and the light emitting diode device for
transmitting light emitted from the light emitting diode device to
the sample contained in the sample holder to excite the fluorescing
agent. The second fork portion (e.g., at least one emission fork
portion) may extend between the sample holder and the photodiode
detector device for transmitting light emitted by the fluorescing
agent upon its excitation and having a first end that is proximate
the sample holder and a second end that is proximate the photodiode
detector device. The instrument may include at least one
single-band or multi-band bandpass filter such that the light
emitted from the at least one light emitting diode device is
filtered into at least one distinct wavelength band. The instrument
may also include a linear variable bandpass filter, a series of
bandpass filters, or a multi-band bandpass filter disposed between
the second end of the second fork portion and the photodiode
detector device and is adapted to filter the light emitted by the
fluorescing agent so that the wavelengths of light received across
the photodiode detector device are known.
[0008] The present teachings further provide for an instrument for
performing polymerase chain reaction with real-time detection
comprising a polymerase chain reaction instrument that includes a
sample holder configured to receive one or more sample tubes that
each have at least one portion that is generally optically
transparent, and that receives a biological sample having a nucleic
acid to be amplified and at least one fluorescing agent that
interacts with the nucleic acid during amplification and that emits
light upon excitation by light of a known wavelength, in which the
signal is generally proportional to the amount of nucleic acid
amplified. The instrument may further include a light emitting
diode device that is carried on at least one support substrate, is
in electrical communication with a power source, and is adapted to
emit light at a plurality of different wavelengths, optionally
through a common lens. At least one heat sink may be included, the
heat sink being carried on the support substrate for dissipating
heat from the at least one light emitting diode device. At least
one photodiode detector device may also be included which is
adapted to issue signals that are generally proportionally based
upon intensity of light it receives. The instrument may also
include a light transmission assembly that includes at least one
multi-branched waveguide and at least one manifold that is
configured to support the waveguide between the sample holder and
both the at least one light emitting diode device and the at least
one photodiode detector device. The waveguide may include a first
fork portion and a second fork portion. The waveguide may include
at least one excitation fork portion (e.g., the first fork portion)
and at least one emission fork portion (e.g., the second fork
portion). The first fork portion may extend between the sample
holder and the light emitting diode device for transmitting light
emitted from the light emitting diode device to the sample
contained in the sample holder to excite the fluorescing agent. The
second fork portion may extend between the sample holder and the
photodiode detector device for transmitting light emitted by the
fluorescing agent upon its excitation and having a first end that
is proximate the sample holder and a second end that is proximate
the photodiode detector device. The instrument may also include a
linear variable band pass filter, a series of bandpass filters, or
a multi-band bandpass filter disposed between the second end of the
second fork portion and the photodiode detector device and adapted
to filter the light emitted by the fluorescing agent so that the
wavelengths of light received across the photodiode detector device
are known.
[0009] The present teachings also provide for an instrument for
performing polymerase chain reaction with real-time detection
comprising a polymerase chain reaction instrument that includes a
sample holder configured to receive one or more sample tubes that
each have at least one portion that is generally optically
transparent, and that receives a biological sample having a nucleic
acid to be amplified and at least one fluorescing agent that
interacts with the nucleic acid during amplification and that emits
light upon excitation by light of a known wavelength. The
instrument may further include a light emitting diode device that
is carried on at least one support substrate, is in electrical
communication with a power source, and includes at least four
(preferably at least five) light emitting diodes each adapted to
emit light at a different wavelength relative to each other,
optionally through a single common lens or optic fiber fork. At
least one heat sink may be carried on the support substrate for
dissipating heat from the at least one light emitting diode device
and at least one photodiode detector device may be included and
adapted to issue signals that are generally proportionally based
upon intensity of light it receives and optionally including a
plurality of discrete pixels or photodiodes. A light transmission
assembly may also be included that is positioned below the sample
holder and that includes at least one multi-branched waveguide and
at least one manifold that includes a cavity and is configured with
flanges to mount to within the polymerase chain reaction instrument
to support the waveguide between the sample bolder and both the at
least one light emitting diode device and the at least one
photodiode detector device. The waveguide may include a first and
second fork portion. The waveguide may include at least one
excitation fork portion and at least one emission fork portion. The
first fork portion may extend through the cavity and between the
sample holder and the light emitting diode device for transmitting
light emitted from the light emitting diode device to the sample
contained in the sample holder to excite the fluorescing agent. The
second fork portion may extend through the cavity and between the
sample holder and the photodiode array for transmitting light
emitted by the fluorescing agent upon is excitation and having
first end that is proximate the sample holder and a second end that
is proximate the photodiode detector device. The waveguide may also
include a cover portion for the cavity of the manifold that
includes a port that is aligned with the light emitting diode
device and an opening for aligning the second end of the second
fork portion with the photodiode detector device. The instrument
may also include a linear variable bandpass filter that is disposed
between the second end of the second fork portion and the
photodiode array, wherein the linear variable filter includes a
bandpass filter coating that is intentionally wedged in one
direction, so that the peak wavelength transmitted through the
filter varies in a linear fashion in the direction of the wedge,
and wherein the linear variable filter is generally optically
aligned with predetermined discrete pixels of the photodiode array,
so that the wavelengths of light received by the discrete pixels of
the photodiode array are known upon detection of light by the
array. The instrument may also include a Series of bandpass filters
that is disposed between the second end of the second fork portion
and the photodiode array, wherein each bandpass filter of the
series is generally optically aligned with predetermined discrete
pixels or photodiodes of the photodiode detector device, so that
the wavelengths of light received by the discrete pixels or
photodiodes of the photodiode detector device are known upon
detection of light by the array.
[0010] As will be seen, the instrument described herein offers a
unique approach to providing a modular PCR device providing
relatively high-speed PCR amplification and detection by virtue of
the device's ability to provide reduced sample read time, and the
ability to quickly detect light at multiple wavelengths. The
instrument described herein may not rely upon reflective components
which are expensive or difficult to align for the routing of light.
The instrument described herein may not rely upon a direct
connection from the sample holder and a fiber optic cable.
DESCRIPTION OF THE DRAWINGS
[0011] FIG. 1A is a perspective view of an illustrative real-time
cycling module in accordance with the present teachings.
[0012] FIG. 1B is a view showing illustrative internal components
of the module shown in FIG. 1A.
[0013] FIG. 2 is an exploded view of the module shown at FIG.
1.
[0014] FIG. 3 is an exploded view of an illustrative optical
detection module in accordance with the present teachings.
[0015] FIG. 4A is a perspective view of an illustrative fiber
optics block.
[0016] FIG. 4B is a perspective view of the fiber optics block of
FIG. 4A shown with an illustrative fiber optics cap.
[0017] FIG. 5A is a perspective view of the fiber optics block of
FIG. 4A shown from beneath the block.
[0018] FIG. 5B is a perspective view of the fiber optics block of
FIG. 5A shown with an illustrative bottom alignment cover.
[0019] FIG. 6 is a perspective view of an illustrative fiber optics
cap in accordance with the present teachings.
[0020] FIG. 7 is a perspective view of an illustrative bottom
alignment cover in accordance with the present teachings.
[0021] FIG. 8 is a top-down view of the fiber optics block of FIG.
4A.
[0022] FIG. 9 is a bottom-up view of the fiber optics block of FIG.
4A.
[0023] FIG. 10 is perspective view of an illustrative RTD
guide.
[0024] FIG. 11 is a top-down view of an illustrative circuit board
in accordance with the present teachings.
[0025] FIG. 12 is a flow diagram showing an illustrative
relationship among the components of an instrument in accordance
with the present teachings.
[0026] FIG. 13 is a perspective view of an illustrative 4-module
instrument in accordance with the present teachings.
[0027] FIG. 14 is a perspective view of an illustrative filter
alignment holder in accordance with the present teachings.
[0028] FIG. 15 is a perspective view of an illustrative fiber optic
block in accordance with the present teachings.
[0029] FIG. 16 is a perspective view of an illustrative sample
block/fiber optic block module in accordance with the present
teachings.
[0030] FIG. 17A is perspective view of an illustrative tube and cap
in accordance with the present teachings.
[0031] FIG. 17B is perspective view of an illustrative tube having
an optically clear bottom portion in accordance with the present
teachings.
[0032] FIG. 18 is an exploded side profile view of an illustrative
fork portion in accordance with the present teachings.
[0033] FIG. 19 is an exploded perspective view of the fork portion
of FIG. 18.
[0034] FIG. 20 is an exploded side profile and perspective view of
an illustrative fork portion in accordance with the present
teachings.
[0035] FIG. 21 is a side profile view of an illustrative light path
of the fork portion of FIG. 18.
[0036] FIG. 22 is an exploded side profile and perspective view of
an illustrative fork portion in accordance with the present
teachings.
[0037] FIG. 23 is an exploded side profile and perspective view of
an illustrative fork portion in accordance with the present
teachings.
[0038] FIG. 24 is a bottom view of an illustrative sample tube and
optical fibers in accordance with the present teachings.
DETAILED DESCRIPTION
[0039] The explanations and illustrations presented herein are
intended to acquaint others skilled in the art with the invention,
its principles, and its practical application. Those skilled in the
art may adapt and apply the invention in its numerous forms, as may
be best suited to the requirements of a particular use.
Accordingly, the specific embodiments of the present invention as
set forth are not intended as being exhaustive or limiting of the
teachings. The scope of the teachings should, therefore, be
determined not with reference to the above description, but should
instead be determined with reference to the appended claims, along
with the full scope of equivalents to which such claims are
entitled. The disclosures of all articles and references, including
patent applications and publications, are incorporated by reference
for all purposes. Other combinations are also possible as will be
gleaned from the following claims, which are also hereby
incorporated by reference into this written description.
[0040] This application is related to and claims the benefit of the
filing dates of U.S. Provisional Application Nos. 61/681,879 filed
Aug. 10, 2012 and 61/752,494, filed Jan. 15, 2013. This application
is also related to U.S. application Ser. No. 13/484,963 filed May
31, 2012. The contents of the aforementioned applications are
hereby incorporated by reference for all purposes.
[0041] The present teachings pertain generally to an improved
device for performing high-speed real-time polymerase chain
reaction. The device includes one or more PCR modules, each PCR
module including one or more light sources, one or more detectors,
one or more waveguide devices and optical componentry for light
differentiation. Advantages of the instrument described herein
include reduced componentry which allows for interchangeability of
PCR modules and a reduced footprint. This includes the ability to
employ less hardware per sample. Further, minimal hardware is
required per sample such that the functionality of the components
described herein is maximized over a wider number of samples. As a
specific example, the instrument described herein may require only
one light source (or one light source component) for multiple
samples). Additional benefits provided in accordance with the
teachings herein include that the optical detection portion is
optionally free of moving parts (or moving samples) for increased
reliability and fast multiplex detection. In addition, the present
teachings provide for the emission and detection of multiple colors
for multiplex PCR, and for the ability to give each fluorescent
agent an intense specific light color that more closely matches the
fluorescent agent's peak light absorption wavelengths. Further,
detecting from the bottom of one or more samples as taught herein
may leave side walls of the sample tubes available for maximum heat
flow/thermal control and the top of the sample tubes available for
simplified sample access. The multiple module arrangement of the
present teachings also allows for on-demand instrument availability
and increased sample throughput. The inclusion of multiple samples
per module allows for each sample to be given a nearly identical
thermal profile to better perform statistical comparisons of
multiple samples.
[0042] The thermocycler instruments of the teachings herein follow
the basic principles of WO/2009/105499 and U.S. application Ser.
No. 12/918,594 (U.S. Publication No. 2011/0039305) and Ser. No.
13/484,963 in that a sample block (e.g., a sample holder) is
sandwiched between opposing thermoelectric devices. The teachings,
however, address a number of new features for thermocycler
instruments that successfully and unexpectedly improve efficiency
and operation of the instruments as compared with instruments that
do not employ such features. The teachings further provide for
thermocycler instruments that facilitate simultaneous amplification
and quantification of nucleic acids.
[0043] The nature of the sample block being sandwiched between
opposing thermoelectric devices indicates that samples located
within the sample block receive light from a light source from
either above or below the sample holder, given the difficulty with
transmitting light through the thermoelectric devices. As a further
result of the sandwich design, detection should preferably also
occur from above or beneath the sample holder. It is also possible
that the fiber optics may be integrated into the sample block in
which excitation and/or emission light is transmitted through the
side of the tube. It is also possible that apertures may be present
within the thermoelectric devices such that the optical pathway for
emission and/or detection occurs through these apertures.
[0044] The instrument thus includes a combination of components
selected and adapted for relatively rapid cycling and real time
quantification of nucleic acids. For example, the teachings herein
contemplate use of instruments within the teachings for performing
real-time nucleic acid amplification over a period less than about
40 minutes, less than about 30 minutes, less than about 20 minutes,
or even less than about 15 minutes. The teachings herein
contemplate that such amplification and quantification rates can be
successfully employed for sample sizes of greater than about 2
microliters, 10 microliters, 30 microliters, 50 microliters, or
even 70 microliters (e.g., a sample size of about 25 microliters).
Relatively large yields of amplified nucleic acids (e.g., at least
levels detectable by gel electrophoresis) are possible over a
relatively short period of time. The unexpected ability to perform
such rapid real-time amplification and quantification on relatively
large sample sizes is one of the advantageous aspects of the
present teachings. Aspects of the instrument also may be premised
upon the recognition that thermal inertia characteristics of
structures and materials used for thermocycler instruments can
impede the rate at which thermal cycling can take place as may
intrinsically occurring lags that occur due to electronic
processing capabilities of an instrument. Accordingly, the present
teachings also pertain, in various aspects, to unique approaches
addressing such obstacles.
[0045] The teachings herein envision the efficient operative
employment of at least one first thermal cycling element for
thermally cycling a sample in generally opposing relationship with
at least one second thermal cycling element for thermally cycling
the sample. Though other devices may be employed, the thermal
cycling element for thermally cycling the sample typically will be
one or more thermoelectric devices ("TEDs"). Thus, it is envisioned
that a first TED and a second TED may be in generally opposing
relation with one another. They may be generally identical and may
be controlled to operate substantially identically with each other.
A sample holder may be employed to carry a sample (e.g., a sample
enclosed or otherwise carried within a sample container, such as a
tube). The sample holder may be adapted to receive at least one
sample (e.g., a sample carried in a sample container such as a
tube) and to be disposed (e.g., in a sandwiching relationship)
between the thermal cycling elements (e.g., between the first TED
and the second TED). The sample holder may be adapted to receive a
plurality of samples. Further, the thermocycling instrument may
include a plurality of sample holders, each sample holder being
located in thermal conducting relation with one or more thermal
cycling elements. The thermal cycling elements may each include at
least one heat exchanger (e.g., a suitable heat sink) for
transferring heat relative from or to each of the cycling devices
(e.g., the first and second TEDs).
[0046] The sample holder may be formed within a sample block, which
may be metallic sample block (e.g. heat block). The sample block
may be a silver sample block. The heat block to house samples may
be manufactured from rolled silver stock that has the oval bores
formed by wire electrical discharge machining (EDM). An alternative
manufacturing process such as a casting process or potentially
splitting the block into two pieces for direct machining may also
be used. Additionally, a slight increase in sample block thickness
(e.g., an increase to about 3 mm) may improve temperature
uniformity among the bores that receive the samples while having
minimal impact on speed of the thermocycling.
[0047] As with other hardware components described herein, the
above components may be configured and positioned in a way to
afford efficient heat transfer to and from a sample. They may be
configured and positioned in a way to help potentially reduce
thermal inertia obstacles to efficient heating or cooling. They may
be configured and positioned in a way to achieve substantially
uniform heating or cooling rates to a plurality of samples that may
be carried within the sample holder. Thus, the first TED and second
TED may both operate to heat and/or cool one or more samples
simultaneously in an effort to achieve a more uniform heating
and/or cooling. They may be configured and positioned in a way to
substantially account for the thermal phenomena of the components
in executing temperature control.
[0048] To improve temperature control a fan may be included within
the instrument. The fan may be a variable speed fan. The
incorporation of a variable speed fan is advantageous in that it
reduces audible noise and may also provide improvement to
temperature uniformity at low fan speeds. Although, some PCR
protocols may be run with no fan. The fan may be powered by a
signal that is pulse width modulation (PWM) controlled. Thus, a fan
may be selected that can handle a PWM power signal, or additional
electronic circuitry may be added to modify a PWM signal into
steady DC voltages.
[0049] The teachings envision the use of stable temperature sensing
componentry. For example, the componentry may be such that two or
more sensors, which may include two or more sensors for each sample
block, monitor (e.g., simultaneously and/or continuously) at least
two temperature conditions, each originating in a location remotely
of each other within the thermocycling device. For example, one
sensor might sense a condition within the above-noted sample holder
that approximates the temperature to which the sample is being
subjected. That is, the temperature conditions are selected so that
they can be relied upon as being related to (e.g., generally
corresponding with in a direct manner) the temperature within the
sample holder, which may be indicative of the temperature of a
sample located within the sample holder. Another sensor might sense
a temperature condition of a component, such as a heat exchanger,
that provides useful information in accounting for the thermal
inertia and thermal interactions during heating, cooling, and
temperature holding. The componentry also is adapted to deliver
information (e.g., via electrical signaling) corresponding with one
or more sensed temperature conditions.
[0050] The teachings also contemplate a method (e.g., a
computer-implemented method) for operating a thermocycler (such as
the thermocyclers as described herein) for real-time amplifying and
quantifying of nucleic acid (e.g., DNA (deoxyribonucleic acid)) of
a sample (e.g., a patient sample, such as a human patient sample).
The method may include obtaining user input such as in the design
of a desired PCR protocol. The method may include a step of
displaying one or more user interfaces. Such user interfaces may be
configured so that a user is able to input operational instruction
protocol information for operating the thermocycler. Such
instruction information may be selected from one or any combination
of at least one temperature setting, number of cycles to be
performed, times for one or more cycles, hold times at one or more
temperatures, or the like. The method may include a step of
receiving user operational instruction protocol information
inputted by the user. The method may include a step of causing the
thermocycler to execute a protocol for nucleic acid amplification
and/or quantification on the basis of the operational instruction
protocol information inputted by the user. The method may include a
step of storing (e.g., in a suitable memory device in communication
with the instrument) operational instruction protocol information
inputted by the user. The method may include a step of displaying
for a user previously programmed operational instruction protocol
information so that the user can modify such information for
designing a protocol. The method may include a step of receiving
information about a temperature condition to which a sample is
being subjected and causing such information to be displayed to a
user substantially in real time. The method may include a step of
providing a user with an opportunity to start, stop and/or pause a
protocol during execution of such protocol on a sample. The method
may include a step of outputting data about an actual or proposed
protocol. The method may include one or any combination of other
steps of storing notes Inputted by a user, providing a preview of a
protocol before causing a thermocycler to execute the protocol, or
performing a diagnostic check to ascertain operability of a
thermocycler.
[0051] The method may include a step of receiving optical input
parameters from the user which includes one or more of the
following: the PCR cycles in which to perform an optical read, the
fluorescing which are being used for the optical detection, the
color wavebands to use to excite the fluorescing agent, the color
wavebands to use to detect the fluorescing agent, the sample
identification, the sample type (no sample, known standard, unknown
sample, positive control sample, negative control sample, or no DNA
template control sample), the DNA template quantity of known
standards and/or controls, and melting curve information including
temperature start, temperature stop, and melting curve resolution.
The method may include a step of storing the optical input
parameters. The method may include a step of retrieving stored
optical input parameters. The method may include a step of
displaying optical detection data which includes one or more of the
following: compatibility of user-selected fluorescing agents,
estimated quantification threshold (e.g. the fractional cycle
number at which the amplified DNA is detectable from the background
noise), estimated initial DNA copy number for unknown samples,
estimated melting temperature of the detected DNA. The method may
include a step of graphing the optical detection data which
includes one or more of the following: a graph of the optical
signal as a function of PCR cycle number, a graph of the optical
signal as a function of sample or sample-holder temperature, a
graph of the negative slope of the optical intensity with respect
to temperature as a function of temperature, a graph of the actual
and/or expected optical data as a function of wavelength. The
method may include a step of storing the optical data. The method
may include a step of retrieving stored optical data. The method
may include a step of applying the temperature and/or optical input
to one or more modules independently or simultaneously. The method
may include a step of displaying, storing, or retrieving stored
data from one or more modules. The method may include step of
obtaining temperature and optical input from a barcode scanner, 2D
barcode scanner, NFC (near field communications), or RFID (radio
frequency identification) from an appropriate test kit, assay, or
sample tube.
[0052] The teachings herein also contemplate a non-transitory
computer readable medium comprising program instructions for
performing the methods (or any of the steps) as described in the
herein. The teachings thus envision at least one computer software
or firmware program including code that provides instructions to
hardware for performing PCR which, when executed by a suitable
electronic processor or other computer processor, performs the
methods (or any of the steps) as described in the herein. The
teachings also contemplate a system for performing a PCR
amplification reaction the system comprising a device including a
memory storage medium for implementing the program instructions of
the non-transitory computer-readable medium. The memory storage
medium may be on a computer (e.g., a computer having a processor
with a processing speed of at least about 1.67 GHz, such as an
Inspiron Mini 1018, from Dell). The computer may be external and
attached to the instrument. computer may be internal to the
instrument (e.g. an industrial mini-ITX based computer with
extended life cycle such as a J&W ITX-IC2M1026S (available from
J&W, South San Francisco, Calif.) dual core atom mini-ITX
mainboard) with a display unit (e.g. a screen or a touch-screen)
internal to the instrument or a port for attaching an external
monitor. The computer may employ a Windows.RTM.-based operating
system, or some other like system. The system may include a
thermocycler in accordance with the present teachings, one or more
devices for collecting information about the temperature condition
of the sample holder, and an output device for displaying data
obtained or generated by the analyzing device. The output device
may be a display panel associated with the computer. Multiple
functions of the software may be caused to be performed by code on
a single non-transitory storage medium, or on multiple media. For
example, functions may reside on firmware associated with a
controller that is on-board the thermocycler instrument.
[0053] The instrument of the present teachings may require the use
of a specialized tube for facilitating qPCR (quantitative real time
polymerase chain reaction) that facilitates transfer of light. The
tube preferably allows for detecting the emission of light from
fluorescent dyes/probes within the tube. The amount of light
detected is generally proportional to the amount of formed PCR
product, resulting in simultaneous PCR-based amplification and
detection. Preferably, the tube (or at least a portion thereof) is
optically clear for high transfer of light to/from a reaction
mixture within the tube with at least about 50% transparency (and
preferably at least about 80% transparency) to the visible light
spectrum.
[0054] As an example, an optically clear resin may be used and
injection-molded to form the entire tube. An exemplary
polypropylene resin is a cyclic olefin copolymer resin from TOPAS
Advanced Polymers, sold under the trade name 5013S-04. Another
exemplary polypropylene resin is a clarified, high-melt random
copolymer from LyondellBasell Industries, sold under the trade name
Pro-fax RP448S. These resins exhibit high flowability to fill
thin-walled areas pf the tube while providing high
transparency.
[0055] As a further example, the tube may be optically transparent
only in portions of the tube in which the light excitation and
emission occurs. Both excitation and emission may be performed
throngh the bottom of the tube and thus only the bottom tip of the
tube need be optically clear. As such, a two-shot mold process may
be used to create a bottom portion comprised primarily of an
optically clear resin with the rest of the tube may comprise a
second, different resin that is not necessarily optically
clear.
[0056] An over-molding technique may also be used to construct an
optically clear portion of the tube. By way of example, an
optically clear bottom piece may be over-molded during the tube
fabrication process (see FIG. 17B). The optically clear piece may
be introduced into the mold cavity prior to injection of a
polymeric material. The optically clear portion may be flat to
minimize light reflection, light distortion, and light absorption
by the sample tube. The optically clear portion may be a lens
shaped plastic, glass, fiber optic cable, or the like. The
optically clear portion may also serve to stabilize the core-pin of
the injection molding process to minimize core pin deflection.
[0057] Alternatively, a secondany external operation may be
utilized to form an optically clear portion of the tube. By way of
example, the tube may be molded with an open end to which an
optically clear piece is then inserted. Fusion between the tube and
the optically clear piece may be achieved by thermal bonding,
adhesive bonding, mechanical fitment, or other means as known in
the art of plastics bonding and manufacturing.
[0058] One or more optically clear portions of the tube may take on
specific dimensions and curvatures (i.e. lens design) to achieve
optimal coupling (i.e. transmission, dispersion, and focusing of
light) among the sample fluid, the excitation means, and the
detection means. The optically clear portions may be comprised of
planar, concave, convex, meniscus, Fresnel, or other lens surfaces
as known in the art of optics. In a preferred embodiment, the shape
of the optical pathway of the bottom of the tube may be comprised
of two substantially parallel planar surfaces with a relatively
thin wall thickness. A high degree of polish of the optical pathway
surfaces is also advantageous to light transmission.
[0059] The one or more optically clear portions may be formed on
the bottom of the tube. Alternatively, the one or more optically
clear portions may be formed along the top of the tube. The top of
the tube (i.e. cap) may be optically clear in embodiments in which
excitation, emission, or both occur above sample fluid (see FIG.
17A). In one embodiment, the light source may be located above the
sample fluid while the detection means is located below the tube,
such that the tube may include more than one optically clear
portion. In another embodiment, both the light source and detection
means are located above the tube such that transmission of light
necessary to conduct real-time PCR occurs through the cap.
[0060] As mentioned above, a light source may be utilized within
the instrument. The light source may be located within the
instrument such that it provides light through one or more
optically clear portions of a tube in which a sample is located.
The light source may be located on a printed circuit board. The
printed circuit hoard may thus provide an electrical supply to the
light source. The light source may include one or more light
emitting diodes (LEDs). In the event that the instrument contains
more than one sample block, each sample block may include its own
light source. Each sample block may have multiple light sources,
with one or more light sources for each sample well or a shared
light source among wells (e.g. one light source optically connected
to two or more sample wells). Each light source may be carried on a
common substrate. Further, each light source may include a
plurality of distinct lights such that each distinct light provides
light at a different wavelength. As an example, each sample block
may include an array of LED lights, each array including distinct
lights at one, two, three, four, or more different wavelengths in
order to better match the peak optical absorption wavelengths of
various fluorescent agents. In this case, the LED light sources may
be grouped underneath a fiberoptic waveguide such that one or more
light sources enter the same fiber optic fork. Alternatively, the
LED's may be grouped together on the same common substrate (i.e. a
compact printed circuit board or assembly), but with each LED
positioned beneath its own fiber optic fork. A plurality of high
power LEDs (of wavelengths typically covering the 400 nm to 700 nm
visible light region) may be grouped together in an area less than
about 3 mm by 4 mm (an example of which is available from Philips
Lumileds Lighting Company under the designation Luxeon Z). One such
grouping may include four Luxeon Z LEDs with wavelength peaks of
approximately 477.5 nm, 522.5 nm, 585.5 nm, and 665.0 nm. A second
such grouping may include four Luxeon Z LEDs with avwavelength
peaks of approximately 447.5 nm, 494.0 nm, 537.5 nm, and 635.0 nm.
Two or more such groupings may be incorporated in each module with
each grouping having its own fork of the fiber optics waveguide and
optionally its own multi-band bandpass filter.
[0061] Alternatively the grouping may include seven Luxeon Z LEDs
which are staggered to form a hexagonal shape and include up to
seven colors with wavelength peaks selected from the following
list: 442.5 nm, 447.5 nm, 452.5 nm, 457.5 nm, 462.5 nm, 467.5 nm,
472.5 nm, 477.5 nm, 494 nm, 503 nm, 522.5 nm, 527.5 nm, 532.5 nm
537.5 nm, 585.5 nm, 588.5 nm, 591 nm, 593.5 nm, 615 nm, 625 nm, 635
nm, 655 nm, or 665 nm. A grouping of seven LEDs staggered to form a
hexagonal shape may include wavelength peaks of approximately 477.5
nm, 494 nm, 522.5 nm, 537.5 nm, 585.5 nm, 635 nm, and 665 nm. The
groupings of LEDs may have a lens to focus light through one or
more filters and/or into one or more fiber optic excitation forks.
The lens may be an array of individual lenses or it may be a single
unit with multiple integrated lense, one for each LEO.
Alternatively, each LED light source may include only 1 distinct
light adapted to emit a plurality of different wavelengths. In this
case, a plurality of LEDs (each of a different peak wavelength) may
be encapsulated behind a single lens within a single assembly (an
example of which is available from LED ENGIN, Inc., under the
designation LZ4-00MA00). Each compact grouping or single assembly
of LEDs may be considered as a light emitting diode device. As
alternatives to light emitting diodes, white light sources such as
halogen or tungsten bulbs or lamps, laser light sources, or other
excitation means may be employed.
[0062] the light source may be part of an assembly that includes a
carrier having a first surface and a generally opposing second
surface. The light emitting diode may be exposed via the first
surface. One or more electrical contacts (e.g., pads) may be
located on or as part of the second surface and be in electrical
communication with the diode. In this manner, the pads may be
applied to a substrate (e.g., by way of a soldering to a printed
circuit board). The upper surface may invlude one or more apertures
through which the light may be emitted from the LEDs. The upper
surface may include one or more conduits of a predetermined depth
(e.g. about 1 mm, 2 mm, 3 mm, 4 mm, 5 mm or higher) that may be
suitably adapted to connect in light transmission relationship with
a wave guide structure (e.g., a fiber optic structure). The
conduits may be elongated and include a longitudinal axis. They may
be generally cylindrical. They may be at least partially conical.
They may include a generally round, oval, triangular, rectangular
or other polygonal cross-sectional profile relative to the
longitudinal axis. They may have a wall structure defining a
passage in the conduit that has a taper (e.g., less than about 15,
10, or even 5.degree., though tapers of at least 20, 30 or
45.degree. are possible) relative to the longitudinal axis.
[0063] The light source will typically include an exposed end
through which light is emitted. For each light source of a
predetermined wavelength, the end may have an area that is smaller
than about 9 mm.sup.2, 6 mm.sup.2, or even 3 mm.sup.2. It may have
an area that is larger than about 0.5 mm.sup.2, 1 mm.sup.2, or even
2 mm.sup.2. The emitted beam may have an emission axis, and may
exhibit a generally linear, rectangular, oval, circular, or other
cross-sectional profile relative to the emission axis.
[0064] The light source may exhibit one or any combination of
performance characteristic as set forth in the LUXEON Z Datasheet
DS105 20120916, incorporated by reference herein (without
limitation, pages 3 through 9, page 14-20, and 24 through 27). The
light source may exhibit one or any combination of structural
characteristic as set forth in the LUXEON Z Datasheet DS105
20120916, incorporated by reference herein (without limitation,
pages 10 through 13 and 21 through 23).
[0065] The light source may be a relatively high power light source
which may provide for more sensitive detection capability. As an
example, the light source may be rated at 40 Watts or more,
although the light source may or may not be operated at the maximum
level. As a result of the high power of the light source, it may be
capable of dissipating heat. The light source may thus be in close
thermal communication with a heat sink, which may be located onto
the printed circuit board. The heat sink may be located beneath,
and/or around, the light source. The heat sink may assist in
dissipating heat from the light source.
[0066] An additional benefit of LEDs is that they use less power
than other types of light sources (e.g., compact fluorescent or
incandescent bulbs) per unit of light generated. LEDs also have
improved durability as compared to other light sources. In
addition, the use of LEDs as the light source allows for compact
packaging for insertion into small spaces within the instrument.
Preferably the packaging for the light source may be less than 3 cm
on each side, or less than 1 cm on each side, or even less than 0.8
cm on each side or a grouping of LEDs with the grouping being less
than 1 cm on each side, or even less than 4 mm on each side. As a
result, LEDs allow for effective output and performance from a
device that occupies minimal space. In one embodiment, the light
source can be located beneath the heat exchangers. In an
alternative embodiment, the light source may be located above the
sample block. In the event that the fiber optics are flexible, the
light source may be located anywhere depending upon the arrangement
of the samples and the nature of the tubes containing the samples.
The small packaging of the light source assists in maintaining the
small, lightweight and portable nature of the instrument.
[0067] The selected light source should be compact, compatible with
a fiber optics design, and sufficiently bright. In the event that
LEDs are selected as the light source, it may be beneficial for
multiple LED elements to be located into a single housing. For
example, a single housing may include at least 4, at least 5, at
least 8, or even at least 12 LED elements such as the LuxiGen
family of LEDs available from LED Engin, San Jose. Calif. Any LED
lens may be formed with a flat top for improved connection to any
fiber optic cable. Ultra-small LEDs may be utilized such as Luxeon
Z LEDs, Phillips Lumileds Lighting Company, San Jose, Calif. or
XLamp LEDs from Cree, Morrisville, N.C. These ultra-small LED's may
be compactly grouped together. A four-color LED grouping may be
utilized as the light source. A seven-color LED grouping in a
hexagonal shape may be utilized as the light source with seven
distinct colors. A seven-color LED grouping in a hexagonal shape
may be utilized as the light source with five distinct colors and
one or two colors repeated for additional light intensity of that
specific color and/or additional lifespan by switching from one LED
of a specific color to another LED of that same color. An
eight-color LED combination may be utilized as the light
source.
[0068] The instrument may also include a device for detecting a
reaction within a sample. The detector may include a photodiode
array which issues a signal proportionally based upon intensity of
light it receives. An example of a photodiode is the Taos TSL
1402R, available from AMS-TAOS USA Inc., Plano, Tex. The detector
may be located within less than about 10 mm, less than about 5 mm,
or even less than about 3 mm from an end of a waveguide to help
avoid light from becoming diffuse. The detector may be located in
an isolated contained chamber so that it is not exposed to any
other light source and is insulated from heat generated by the rest
of the instrument. The chamber may be formed as a surrounding wall
structure that substantially insulates the detector from other
light. The detector may be formed as an individual array for each
sample or alternatively may be a singl array subdivided into array
portions that are dedicated to individual samples. The detector may
be formed as arrays arranged in elongated thin strips so that
pixels of the arrays are aligned end to end. Each elongated strip
may include from about 25 to about 200 pixels (each being about 65
microns by 55 microns). The detector may be a two-dimensional array
of pixels such as with complementary metal-oxide-semiconductor
(CMOS) or charge-coupled device (CCD) detector circuitry.
Alternatively the photodiode array may consist of several larger
individual photodiode elements (about 1 mm.times.1 mm, or about 3
mm.times.3 mm) each with one pixel per detection color.
Aternatively, PIN (p-type, intrinsic and n-type semiconductor
regions) photodiodes may be employed and may be present with one
PIN photodiode per sample, multiple PIN photodiodes per sample, or
one PIN photodiode shared by multiple samples. An array of the PIN
photodiodes may exist for each sample in sitruations where each PIN
photodiode is paired with a bandpass filter of a specific
wavelength. For instances in which one PIN photodiode is used per
sample, a lens may be used which directs light from at least one
bandpass filter to the single PIN photodiode. For instances in
which one PIN photodiode is used by multiple samples, a lens may be
used which directs light from at least one sample to the PIN
photodiode.
[0069] Each array may monitor one, two, three, or more samples at a
time. Each array may be adapted for moving from sample to sample.
The arrays may be arranged to read more than one pixel at a time
(from more than one sample). The time between the readings may
affect sensitivity due to the entry of light. It may thus be
desirable to complete readings as quickly as possible (e.g., less
than about 0.5 milliseconds average per pixel per reading) to
maximize sensitivity. It may be desirable to complete readings for
each pixel less than 0.1 second, or even less than 0.01 seconds. A
sum of reads for each pixel may be used to result in a total read
value per specified integration time. It may be desirable to
complete the total reads of all samples for all dyes in less than
10 seconds, less than 5 seconds, or even less than 3 seconds to
maintain minimal run times of the instrument.
[0070] In another embodiment, the photodiode array may simply be a
grouping of individual photodiodes. In this case, unique bandpass
filters may be positioned above each photodiode such that the
signal from that photodiode is related to a specific fluorescent
agent. In yet another embodiment, a single photodiode (e.g. PIN
photodiode) is used for detection of all fluorescent agents. In
this case, different bandpass filters may be moved into position
above the photodiode (e.g. a filter wheel or shuttle) so that the
signal generated at a specific time corresponds to a fluorescent
agent. This allows for detection of multiple fluorescent agents by
cycling through the filters during a detection step. Alternatively,
a stationary multi-band bandpass filter may be employed above the
photodiode such that the light detected corresponds to a certain
fluorescent agent, dictated by the excitation wavelength provided
at that instance.
[0071] Alternatively, the detector may include at least one
spectrometer which may also require the use of a prism device or
optical diffraction grating to separate light according to
different wavelengths. The detector may also include at least one
charge-coupled device or other capacitor containing device or
photomultiplier tube.
[0072] The ability to excite one or more probes contained within a
sample for testing may be enhanced by employing one or more
features for controlling the light that is directed to the sample
holder from one or more light sources. For example, without
limitation, as to light from one or more light source, one or more
features may be employed to attenuate, intensify, modulate,
collimate, refract, reflect, diffract, or filter such light or any
combination of the foregoing.
[0073] Consistent with the foregoing, the ability to detect light
from one or more excited probes contained within a sample may be
enhanced by employing one or more features for controlling the
light that is emitted from the sample (or at least one probe
therein). For example, without limitation, as to light from a
sample, one or more features may be employed to attenuate,
intensify, modulate, collimate, refract, reflect, diffract, or
filter such light or any combination of the foregoing.
[0074] An approach that may be employed for enhancing transmission
of light for excitation of one or more probe, for detecting
fluorescence emitted by one more probe or both may involve the
selection of a suitable filter arrangement. One or a combination of
two or more filters may be employed for this purpose. Selection of
a filter for this purpose may be based upon one or more desired
attribute of the filter.
[0075] In the context of detecting light, it may be expected in
some instances that a filter is selected by which a significant
amount of light of one or more predetermined wavelengths is allowed
transmission through the filter for affording a larger amount of
detectable light for a detector. For example, it may be possible
that one or more absorptive filter is employed, such as a filter
with an optical density (OD) value of about 4, 3, 2, 1 or lower.
Successful results may be achieved by the use of one or more
filters having an OD value of greater than 4 (e.g., a value of OD
5, OD 6, or OD 7). The cumulative OD value of such filters may be
greaterthan 4 (e.g. a value of OD 5, OD 6, or OD7). The OD values
are based upon transmission values measured at a wavelength from
about 400 nm to about 800 nm in accordance with spectrometer
according to standard optical metrology transmission measurement
techniques (often a custom modified spectrometer is used to measure
large optical densities, over about OD 4, and to measure filters
with sharp transitions in optical density as a function of
wavelength).
[0076] The filters may be present on the LED waveguide fork, the
detection waveguide fork, or both. The filters may be separate
components or the filters may be deposited directly onto lenses,
LEDs, photodiode detector devices, and/or fiber optic
waveguides.
[0077] The filters may be neutral density filters. They may be
uncoated. They may be metallic coated. They may be made of optical
quality glass, UV-grade quartz or some other suitable material.
[0078] One or more interference filters may be employed for
selectively allowing transmission of light within one or more
predetermined range of wavelengths, while reflectin light of other
wavelengths. For example, one or more dichroic filters may be
employed. Examples of suitable dichroic filters may exhibit one or
more performance characteristics including transmitting light from
the LEDs at the excitation wavelength range(s), and reflecting
light at the fluorophore emission wavelength range(s) (or the
reverse of reflecting the excitation light and transmitting the
emissed light). An example of a suitable dichroic filter employed
herein is commercially available from Edmund Optics, Barrington,
N.J. under the designation #67-055.
[0079] One of more filters may be employed at one or locations
within a system. One or more filters may be employed between a
source of light and a waveguide (e.g., a fiber optic structure)
through which the light is transmitted. One or more filter may be
employed between a light emitting portion of the waveguide (e.g.,
fiber optic structure) and the sample (and/or holder within which
the sample is ontained). One or more filter may be employed between
the sample (and/or holder within which the sample is contained) and
any detector.
[0080] One or more components of the system may have a filter
assembled to it. One approach may be to select materials for the
sample holders of the system by which the material intrinsically
filters one or more predetermined wavelength or range of
wavelengths.
[0081] One example of a filter that may be employed herein is a
linear variable filter. For example, such a filter may be employed
in advance of a detector of the system. Another option that may be
employed alone or in combination with a linear variable filter may
be to employ one or more bandpass filters or other filter. Examples
of suitable bandpass filters may exhibit one or more performance
characteristics including a hard coating, at least 90% transmission
in the bandpass wavelength range, an optical density of at least
OD5 in the blocking wavelength ranges, a transmission band of
approximately 10 nm to 50 nm, and a sharp transition (less than
about 5 nm) between the transmitting wavelengths and the blocked
wavelengths. Example of a suitable bandpass filter employed herein
is commercially available from Edmund Optics, Barrington, N.J.
under the designation 67-013.
[0082] Any linear variable filter may be utilized for filtering
light such that only light having certain wavelengths can pass
through the filter at different filter locations. As a result, only
light of a known wavelength may pass through the filter and to the
detector (e.g., specific pixels of an array) so that the light that
is passing through is a predetermined known wavelength for which
only intensity needs to be measured for each pixel in the detector.
Examples of suitable linear variable filters may exhibit one or
more performance characteristics including a hard-coating,
separation of light to a spectral range from about 450 nm to about
800 nm, average transmission of over 40%, and an optical density of
at least OD3. Examples of suitable linear variable filters employed
herein are commercially available from Delta, Horsholm, Denmark
under the designation LF102155 or JDS Uniphase, Santa Rosa, Calif.
under the designation 30119150. The filter may be substantially
similar in size to the detector. The filter may be located onto a
support with the detector or may be located on a separate support
from the detector. The filter may be permanently adhered to the
detector with optically transparent adhesives so that there is a
precise and repeatable relationship between the wavelength and
pixel number. While typically the transmitted wavelengths will vary
linearly across the linear variable filter, other monotonic
functions (e.g. logarithmic) may be utilized.
[0083] As an alternative to the linear variable filter, a series of
discrete bandpass filters may be deployed. The series of bandpass
filters may include distinct filters grouped together or an
integrated assembly in which various portions of a substrate
represent different bandpass characteristics. The bandpass filters
may be lined in parallel so that the assembly aligns optically with
the detector pixels or photodiodes. In this respect, this
embodiment can be simply viewed as a linear variable filter with
discrete step-wise portions rather than continuously variable.
Alternatively, a multi-band bandpass filter may be used in
conjunction with the detector. In this case, the wavelength of
light transmitting through the multi-band bandpass filter to the
detector is related to the excitation light provided at that
instance based upon the excitation/emission behavior of the
fluorescent agent. The discrete bandpass or multi-band bandpass
filters may be arranged in a fixed position generally with one
filter per LED or photodiode detector device. The discrete bandpass
or multi-band bandpass filters may be arranged on a filter-wheel
which moves the excitation and/or detection filters between the LED
and fiber optics and/or between the fiber optics and the photodiode
detector device.
[0084] Another example of a filter system would be a aeries of
dichroric beamsplitters, dichroric filters, dichroric mirrors,
and/or dichroic prisms which reflect light of certain wavelength
ranges at an approximately 90.degree. angle to the incoming light
and the reflected colored light branches then pass through a series
of suitable bandpass filters located over a detector device. In
this latter example, the incoming beam of light is split into one
or more different colored light branches by passing through or
being reflected by the series of dichroric beamsplitters. The
series of bandpass filters further filter the colored light
branches into specific wavelength ranges. Each bandpass filter is
located over a known number of photodiode elements in a photodiode
array and/or individual photodiodes in a compact group of
photodiodes within the detector device. Thus, the intensity of
light of each colored light branch can be measured simultaneously
with no moving parts. An example of a suitable colored light branch
detection device is the OptoFlash Optical Engines from Newport
Corporation, Franklin, Mass. One or more optical fibers can be used
within the same OptoFlash, and thus multiple sample tubes can be
ansyzed sequentially by exciting each sample tube sequentially with
light. A custom OptoFlash may be used with filtered color light
branches with light wavelength ranges of approximately 510 nm to
547 nm; 555 nm to 565 nm; 565 nm to 575 nm; 575 nm to 600 nm; 608
nm to 655 nm; 665 nm to 691 nm; and 699 to 770 nm. Additional color
light branches could be added to the OptoFlash to detect additional
wavelength ranges or fewer color light branches. The color light
branch wavelengths could be adjusted to be more suited for
different fluorescing agents with the color light branch bandwidth
being used to control sensitivity and to control the total number
of different fluorescing agents that will be detected.
[0085] The employment of one or more suitable waveguide structures
may be employed as discussed herein. One particular approach is to
employ a fiber optic structure. Though it may be believed that the
selection and employment of a suitable fiber optic structure is
readily within the skill in the art, experience is believed to
prove the contrary. Without intending to be bound by theory, it is
believed that the selection of a suitable optical fiber structure
may not be readily predictable. By way of example, it is possible
that certain applications may seek to employ a fiber optic
structure having a relatively large numerical aperture value (e.g.,
greater than about 0.55, 0.65 or even 0.75). This may be a sensible
approach both for assuring a relatively large transmission of light
for excitation, a relatively large angle of light acceptance (e.g.,
at least about 33.degree.) or both. However, for sensitivities
desired for certain of the applications herein, such structure may
actually lead to less efficient performance in the way of light
transmission and/or detection. Thus, the teachings herein
contemplate the employment of fiber optic structures that have a
numerical aperture value that is less than about 0.52, 0.50, 0.45,
0.40 or smaller (e.g., to as low as about 0.5).
[0086] The structure may be configured so that the angle of light
acceptance may also be a value that is below about 32%, 30%, 25%,
20% or lower. It may be an angle of 5%, 10% or higher. The angle of
incidence is measured as the angle between the normal surface (of
the terminal end of the optical fibers) and the incident light
ray.
[0087] It will be recognized that numerical aperture values refer
generally to a maximum angle at which a particular fiber can accept
the light that will be transmitted through it. The numerical
aperture value of an optical fiber is thus correlated with the size
of a cone of fight that can be coupled into its core. As the
skilled artisan will appreciate, a value for numerical aperture can
be derived by calculating the sine of a half angle of acceptance
within a cone of light that enters a core of a fiber. An approach
to measure numerical aperture is illustrated in TIA Fiber Optic
Test Procedure FOTP-177 (Method Numerical Aperture Measurement of
Graded-Index Fiber.
[0088] The waveguide may be a bifurcated waveguide such that it
includes a first and second fork portion. The first fork portion
may extend between the sample holder and the light sourrce (e.g.,
an LED device) for transmitting light emitted from the light source
to the sample contained in the sample holder to excite a
fluorescing agent. The second fork portion may extend between the
sample holder and the detector (e.g., a photodiode detector device)
for transmitting light emitted by the fluorescing agent upon its
excitation and having a first end that is proximate the sample
holder and a second end that is proximate the detector. The
waveguide may be formed of a single structure or may be formed of
optical fiber bundles. The waveguide or waveguide fibers may be
formed of a polymeric or glass material. The waveguide or waveguide
fibers may be made of single-mode optical fibers or multi-mode
optical fibers, or any combination thereof. The waveguide may have
the optical filters (bandpass filters and/or linear variable
filters) or lenses directly deposited on the terminal ends.
[0089] The waveguide may be a multi-branched waveguide such that it
includes at least one excitation fork portion (e.g., a first fork
portion) and at least one emission fork portion (e.g., a second
fork portion). The waveguide may include at least two, at least
three, at least four, at least five, or more excitation fork
portions. The number of excitation fork portions may be the same as
the number of LED's present in the light emitting de device. The
excitation fork portion end proximate the end of a light source may
branch out to provide light to one, two, four, eight, or more
samples. The waveguide may include at least two, at least three, at
least four, at leave five, or more emission fork portions. The
number of emission fork portions may be the same as the number of
detector wavelength ranges. The at least one emission fork portion
proximate a sample may branch out to different detector portions.
The at least one emission fork portion proximate a detector or
detector portion may branch out to provide deteotion of at least
one, two, four, eight, or more samples. In embodiments in which the
excitation occurs from above the samples, the waveguide positioned
below the samples may be void of excitation fork portions with only
emission fork portions present.
[0090] The waveguide may be arranged so that a terminal end
interfaces with the detector and will be elongated to coincide with
the elongated structure of an array as discussed above. The
instrument may include a manifold assembly that connects with the
printed circuit board that carries the light source (e.g., the
LEDs), and includes passages. These passages may allow for
isolation of the individual light source assemblies and may be
adapted to receive the waveguide (e.g., fiber bundles).
[0091] The instrument may include a housing for receiving the
waveguide. The housing may include an upper portion that is adapted
to fit in between the heat exchangers and to be aligned with (and
located below) a sample holder. The waveguide may partially extend
into the wells of the sample holder for close coupling and
alignment of the waveguide to the sample tube. The housing may
include one or more projections for aiding in aligning the housing
within the instrument. The housing may also include one or more
mounting flanges to provide a surface for attaching to a cavity
within the instrument. The housing may further include a base
portion having a cavity defined therein through which one or both
fork portions of the bifurcated waveguide (e.g., fiber optic
bundles) are passed, and which can receive a resin for potting the
waveguide. The housing may also include one or more cover portions.
A bottom cover portion may be adapted to interface with the
detector and may be located above the printed circuit board and
light source located thereon. One or more ports may also be formed
along a surface of the housing so that the one or more ports align
with the light source. The light source may penetrate through the
ports or alternatively may remain adjacent to the ports without
penetrating the ports. There may be an optical filter (such as a
bandpass filter) between the light source and the penetrating
ports.
[0092] The detector may be adapted to receive light from a
plurality of sources. For example, the detector may receive (e.g.,
detect) light from a fluorescing sample and light reflected from
the light source. Multiple fluorescing agents with different
emission wavelengths may be present in the sample. As such, it may
be necessary for the detector to be capable of differentiating
different colors (e.g, light emanating from different sources and
fluorescing agents) so that the software can differentiate data
obtained from the fluorescing sample. As a result, it may be
beneficial to include a filter such as a bandpass filter.
Alternatively, a prism device or optical diffusion grating may be
utilized for prismatic separation of the light (which may require
detectors that will detect the difference between the light from
one or more fluorescing agents and the light from the light source
so that data from each can be separated).
[0093] As mentioned above, one possible approach is to employ a
plural band bandpass filter. A plural band (in other words,
multi-band) bandpass filter may be employed in conjunction with
either or both the light source or detector. The band amount can be
selected to correspond generally with the number of light sources
of different wavelengths used for excitation of a sample, or the
number of different detection wavelengths desired. For example, the
employment of an excitation quad-band bandpass filter (if a four
light source is employed) may be advantageous. Alternatively,
dual-band or tri-band bandpass filters may be partially employed to
minimize the number of com.sub.ponentsas compared to a design using
single band bandpass filters. Such a multi-band bandpass filter may
suitably be employed. Such a filter may be sized to be within a
predetermined size (e.g., covering an area that is only a portion
of the total area of the array that defines the detector). For
example, a detector may include an array of a predetermined number
of pixels adapted for detection. However, the filter may be sized
for allowing transmission of light to only a fraction of the pixels
(e.g., less than about 75%, less than about 50%, less than about
25%, less than about 10% or even less than about 5% of the pixels)
available for detection.
[0094] As also discussed above, the light source selected may
include groupings of two or more, preferably at least four, LEDs
for ease of providing equal light into a fiber optic cable and ease
of printed circuit board design. In addition, one or more light
source bandpass filters may be utilized. Preferably, multi-band
bandpass filters, more preferably quad band bandpass filters, may
be utilized. The multi-band bandpass filters may be hard-coated for
maximal resistance to heat and humidity. The multi-band bandpass
filters may be adapted to allow light in certain wavelength regions
to reach the PCR samples for fluorescent dye/probe excitation but
block wavelength regions where those fluorescent dyes/probes emit
light to maximize the signal-to-noise ratio in the detection
signal. For example, the multi-band bandpasss filters may be a
quad-band bandpass filter which is hard-coated to allow light with
at least 80% transmission (or even greater than 95% transmission)
in the 460 nm to 500 nm region, the 510 nm to 535 nm region, the
570 nm to 590 nm region, and the 640 nm to 690 nm region while
allowing less than 1% transmission, less than 0.1% transmission, or
even less than 0.01% transmission in the rest of the visible
wavelength spectrum. The optical density of that filter in the
transmission regions could be 0.25, 0.1, 0.05, 0.02, 0.01 or lower.
The optical density between the transmission regions could 3, 4, 5,
or even 6 or higher. A second hard-coated quad-band bandpass filter
may allow light with at least 80% transmission (or even greater
than 95% transmission) in the 405 nm to 460 nm region, the 485 nm
to 510 nm region, the 535 nm to 565 nm region, and the 610 nm to
650 nm region while allowing less than 1% transmission, less than
0.1% transmission, or even leas than 0.01% transmission in the rest
of the visible wavelength spectrum. The optical density of that
second filter in the transmission regions could be 0.25, 0.1, 0.05,
0.02, 0.01 or lower. The optical density between the transmission
regions could be 3, 4, 5, or even 6 or higher. It will be apparent
to those of skill in the art that slight variations (up to about 5
nm or even 10 nm) in wavelength cutoffs of the multi-bandpass
filters would still be acceptable for exciting florescent
dyes/probes or that any of the transmission regions its the above
quad-band filters could be swapped in any combination without any
harm to the performance of the optical detection system. Such
quad-band bandpaas filters can be custom manufactured by any number
of companies such as Omega Optical, Inc., Brattleboro, Vt.;
Evaporated Coatings, Inc, Willow Grove, Pa.; or Delta, Copenhagen,
Denmark.
[0095] Preferably, the instrument is capable of providing for at
least four excitation colors for each sample and is further capable
of detecting at least four emission colors from each sample (see
Table 1 for a short list of commonly used dyes/probes). As shown in
Table 1, only approximate peak wavelengths are listed, but the
reporter dyes/probes can be used outside that wavelength range,
albeit less efficiently. The most commonly used fluorescing agents
require blue (480 nm to 495 nm), green (520 nm to 550 nm), amber
(585 nm to 615 nm), and red (640 nm to 660 nm) excitation light. It
is expected that the real-time optical detection be capable of
producing light at or quite near those four wavelengths. A five or
six color instrument would be preferred.
TABLE-US-00001 TABLE 1 Table 1: Commonly used fluorescing agents,
their excitation wavelength peaks, and their emission wavelength
peaks. Generally, real-time PCR will function if the cycler can
emit and detect within .+-.10 nm to 20 nm of the peak.
Excitation/Absorption Emission/Detection Peak Fluorescing Agent
Peak (nm) (nm) AMCA 353 (violet) 442 (indigo) Cyan 500 450 (indigo)
500 (blue green) Fluorescein 483 to 495 (blue) 520 to 533 (green)
FAM 483 to 495 (blue) 520 to 533 (green) SYBR Green I/ 480 to 500
(blue) 520 to 530 (green) Rhodamine green Tet 521 (green) 536
(green) VIC/HEX/JOE 523 to 535 (green) 555 to 568 (green/green-
yellow) NED 546 (green) 575 (yellow) Cy3 550 (green-yellow) 570
(yellow) TAMRA 553 (green-yellow) 576 (yellow) Red 610 558 (yellow)
610 (orange-red) ROX/Texas Red 585 (yellow-orange) 605 (orange) Red
640 615 (orange-red) 640 (red) Cy5 649 (red) 670 (red) Cy7 743
(red) 767 (red) Licor IRDyes 651 to 778 668 to 794 (red - infrared)
(several) (red - infrared)
[0096] As another embodiment, the bandpass filters could be any
combination of single, dual-band, or quad-band bandpass filters
with at least 80% transmission in these range: 415 nm to 450 nm for
excitation of Atto 425, Alexa fluor 430, and similar fluorescing
agents with a corresponding detection bandpass filter with at least
80% transmission the 470 nm to 510 nm range for the appropriate
detection of those fluorescing agents; 460 nm to 495 nm for
excitation of FAM, SYBR Green I, and similar fluorescing agents
with a corresponding detection bandpass filter with at least 80%
transmission in the 515 nm to 548 nm range for the appropriate
detection of those fluorescing agents; 480 nm to 505 nm for
excitation of SYBR Green I, Rhodamine green Oregon Green 514, and
similar fluorescing agents with a corresponding detection bandpass
filter with at least 80% transmission in the 525 nm to 565 nm range
for the appropriate detection of those fluorescing agents: 505 nm
to 533 nm for excitation of JOE, VIC, HEX, and similar fluorescing
agents with a corresponding detection bandpass filter with at least
80% transmission in the 553 nm to 600 nm range for the appropriate
detection of those fluorescing agents; 530 nm to 555 nm for
excitation of NED, TAMRA, Cy3, Rhodamine Red, and similar
fluorescing agents with a corresponding detection bandpass filter
with at least 80% transmission in the 575 nm to 620 nm range for
the appropriate detection of those fluorescing agents; 568 nm to
589 nm for excitation of ROX, Texas Red, Red 610, and similar
fluorescing agents with a corresponding detection bandpass filter
with at least 80% transmission in the 600 nm to 660 nm range for
the appropriate detection of those fluorescing agents; 605 nm to
645 nm for excitation of Cy5 and similar fluorescing agents with a
corresponding detection bandpass filter with at least 80%
transmission in the 665 nm to 705 nm range for the appropriate
detection of those fluorescing agents; and 650 nm to 680 for
excitation of Cy5.5, Quasar 705, and similar fluorescing agents
with a corresponding detection bandpass filter with at least 80%
transmission in the 700 nm to 780 nm range for the appropriate
detection of those fluorescing agents.
[0097] Such detection filter may be sized to be within a
predermined size (e.g., covering an area that is only a portion of
the total area of the photodiode detector device that defines the
detector). For example, a detector device may include an array of a
predetermined number of pixels or individual photodiodes adapted
for detection. However, the filter may be sized for allowing
transmission of light to only a fraction of the pixels (e.g., leas
than about 75%, less than about 50%, less than about 25%, less than
about 10% or even less than about 5%) available for detection.
[0098] Another consideration that may prove beneficial in the
performance and operation of the systems herein is the location,
angular disposition, and/or spacing of any filter relative to any
light source, the sample (and/or holder), the detector, or any
combination thereof. For example, suppose that a filter includes
generally planar opposing surfaces, though substantial
perpendicularity may be possible. There may be an angular
disposition of the filter that is less than or greater than
perpendicular by at least about 5, 10, 20, 30, 45.degree. or more
relative to the principal emission axis from the light source.
[0099] One or more filters employed herein may be such that they
transmit at least a portion of the emitted visible light (e.g., at
least about 50%, 65%, 75% or even 90%), as measured using a
suitable spectrometer for optical metrology transmission
measurement. One or more filters may be selected to absorb all or
substantially all visible light.
[0100] It may be desirable for such filters, or one or more other
noise reduction filters used in combination therewith to be
selected so that wavelengths that translate as background noise are
reduced as compared with a system that omits any such filter. By
way of example, it is one object to substantially reduce or even
eliminate any significant contribution to background noise that may
result from infrared radiation arising from any light source used.
Desirably, one or more filters may be employed to substantially
block infrared radiation (e.g., to block transmission of infrared
radiation to a level that is less than about 50%, 60%, 70%, 80%, or
even of the total infrared radiation that seeks to be transmitted).
Thus, one possible approach may be to employ a filter that
transmits at least about 70%, 80% or 90% visible light, but absorbs
or otherwise blocks infrared radiation to a level that is less than
about 30%, 20% or even 10%.
[0101] Among the various filter types that may be employed herein
are those such as hot mirrors, heat absorbing glass, shortpass
filters, longpass filters, infrared cutoff filters, and wide
bandwidth bandpass filters.
[0102] Filters herein may have a first face, a generally opposing
(e.g., generally parallel) second face, and a periphery that
typically spans between the first and second face. It is possible
that one or more of any of the filters herein may be at least
partially encapsulated (e.g., about at least a portion of its
periphry) by a material that differs from the filter. One or more
of any of the filters may include a suitable filter alignment
holder. Such holder may be adapted to attach to one or more of the
other components of the system. For instance, the holder may be
sized and configured to receive one or more filters, and may also
include an attachment portion (e.g., as part of and/or adjoining a
peripheral portion of the holder) that includes suitable structure
for attaching the holder within the system. For example, the holder
may be such that it can be positioned between a light source and a
sample holder, between a sample holder and a detector, or both. A
depiction of one example of a filter alignment holder is shown in
FIG. 14. The material of the filter alignment holder may be
suitable for withstanding the temperature fluctuations to which it
may be subjected during operation, such as for avoiding thermal
distortion to it, any filter it holds, or both. One approach is to
employ a material that has a generally anti-reflective outer
surface for avoiding stray emissions. For example, the outer
surface to which any light may be directed may be black. Other
components within the system (e.g., the one or more boards upon
which the circuits are printed) may also be coated or selected to
be relatively light absorptive (e.g., they may be generally opaque,
such as a black material).
[0103] The filter alignment holder may be coupled with the light
source. For example, the light source may be supported upon, and/or
integrated with one or more circuit boards. One or more filter
alignment holder may be coupled with such one or more of such
circuit boards. Such coupling may be a permanent coupling that
would effectively require destruction of one of the components for
detachment. Such coupling may be temporary or removable. For
example, one approach may be to employ one or more of an adhesive,
a fastener (e.g., a mechanical fastener such as a push pin
fastener, a threaded nut assembly, a pin, a clamp or otherwise), a
weld (e.g., a stake weld) or any combination of the above. For
example, one approach may be to employ a gasket, a layer of
adhesive that has a certain amount of compliance and will withstand
compression and thermal cycling without distortion, or both. Any
filter alignment holder, or combination of filter holders may also
have a thickness dimension that is selected to adjust the angle of
excitation light that enters the fiber optics and the amount of
emission light that reaches the detectors. An example of a suitable
material for a filter alignment holder includes thermoplastic or
thermoset polymeric containing materials. They may be filled and/or
reinforced (e.g., with glass fibers) to help foster dimensional
stability during cycling. The filter alignment holder may be made
of a material with high thermal mass such that it bel maintain the
temperature of the LEDs and detectors at a constant temperature. It
may also be desirable to help isolate any metallic materials of the
holders from any adjoining circuit boards to help reduce the
possibility of electrical interference or short circuits. The
filter alignment holder may be assembled in a manner that it
includes respective filters for performing the respective functions
of filtering light transmitted to a sample, and filtering light
emitted by the sample. The filter alignment holder may also include
one or more other filter portions that filter background light.
[0104] One approach is to employ a filter alignment holder that
includes a different thickness for a transmission portion that
transmits light to the sample as compared with the thickness of the
holder sample emission portion through which light is emitted to
the detector. The transmission portion, for instance desirably will
be thick enough to allow light to enter at a relatively small angle
of incidence from the light source (e.g., below the angle of
incidence of a bandpass filter, which is about 5.degree.). The
holder sample emission portion desirably will be relatively thin
(e.g., less than about 90%, 75% or even 20% of the thickness of the
sample emission portion). The width of the incident area of light
emitted from an emission optical fiber is a function of the
distance between the terminal end of the fiber and the detector.
Since the detector elements are fixed in size (such as about 55
.mu.m by 65 .mu.m), the further the terminal end of optical fiber
is located from the detector, the less light that will reach the
detector. The optimal thickness of the holder sample emission
portion is thus determined by the width of the emission optical
fiber bundle and the width of the detector elements. The optimal
thickness is also limited by the thickness of the detection filter
(such as a linear variable filter or a set of bandpass filters)
which may be 1 mm, 2 mm, or even 3 mm thick. One preferred design
may have the detection filter directly deposited onto the terminal
ends of the optical fibers and thus the filter thickness is
negligible. Alternatively, the light source circuitry and the light
detection circuitry could be placed on separate circuit boards and
the relevant transmission and emission filter holder sections could
be optically isolated from each other as a single unit or as
separate filter alignment holder components. In this manner, it is
believed possible to help reduce the amount of light from the light
source that reaches any detector without first exciting a sample to
achieve sample emission.
[0105] The ininstrument may include lenses that are present within
the optical componentry. More specifically, a lens may be present
between the various optical components to improve the efficiency of
the excitation and emission means. A lens or lens assembly may be
present between the light emitting diode and the excitation
bandpass filter, such that the spreading light is converged into
substantially parallel beams passing through the filter. An
additional converging len (e.g., biconvex) may be present between
the excitation filter and the waveguide to focus these resulting
beams into the waveguide. Such lenses allow for more efficient use
of the LED light and homogenize the light entering into the fiber
optic waveguide for improved sample excitation. Further, a similar
lens arrangement may be employed on the detector side. Light
exiting the emission fork portion that is becoming diffuse due to
angular incidence may be focused and optimally directed through a
detection bandpass filter by a converging lens present
there-between. Another converging lens may be present between the
detection bandpass filter and photodiode to further focus the light
passing through the detection bandpass filter onto the photodiode
so that a high efficiency of signal detection is achieved. A lens
may also be present between the sample tube and the terminal end of
the waveguide proximate thereto. A lens may be integrated into any
of the other components, such as attached to the bandpass filter.
The instrument may be void of a lens between any of the optical
components.
[0106] It may also be desirable in the invention to include means
for addressing background noise phenomena. A certain level of
background noise is commensurate with detector reading and leads to
a baseline signal offset which may typically be subtracted during
data processing. Due to the temperature dependency and other
factors associated with the optical components, signal noise and
baseline drift may be experienced during the execution of a
real-time protocol. In this sense, it is advantageous to include
means for accounting for baseline noise and drift. The use of a
reference dye is one such aspect for normalizing signal reads at
each cycle. Notwithstanding, it is also contemplated that a
separate detector or simply some pixels of each photo-diode array
serve as a reference from which any baseline drift may be further
corrected.
[0107] The teachings herein include componentry enabling for
high-speed real time polymerase chain reaction in a mobile,
relatively compact instrument. The instrument includes one or more
components adapted for transmitting light emitted from a light
source (e.g., a light emitting diode device) to one or more samples
located in a sample holder. The instrument includes one or more
components adapted for transmitting light emitted from at least one
fluorescing agent to one or more detectors. A filter (e.g., a
linear variable filter) may filter any light emitted by fluorescing
material within the one or more samples prior to reaching the
detector. A filter (e.g. quad band-pass filter) may filter the
light emitted from the light source prior to reaching the
sample.
[0108] As shown for example in FIGS. 1A and 1B, the instrument may
include an instrument component portion 10 for housing components
including fiber optic and electric componentry 16. The fiber optic
and electric components may be located within the instrument below
the thermal cycling assembly 12. As shown in FIG. 1A, one or more
panels (which may form a sheath) 14 may be included for enclosing
the components and for keeping proper airflow to maintain proper
component temperature. FIG. 1B shows the components within the
instrument with the panels 14 enclosing the components made
transparent to expose the fiber optic waveguide and electric
componentry 16. One or more electrical components are mounted to a
printed circuit board 18.
[0109] FIG. 2 shows an exploded view of the instrument component
portion 10. A plurality of panels 14 is shown for enclosing
components therein. The thermocycling assembly 12 is shown above a
fiber optics module 20, which is shown above the electronics 24,
which together comprise the fiber optic and electrical components
16. The electronics are shown mounted to a platform 18, which may
include a printed circuit board (PCB). A fan 22 that is generally
located at the back of the instrument component portion 10 is also
shown.
[0110] FIG. 3 shows an exploded view illustration of the internal
fiber optic and electrical components of the fiber optics module
20. A sample holder 26 is shown for locating within the
thermocycling assembly 12 (not shown). A resistance temperature
detector (RTD) guide 28 is also shown which travels through a fiber
optics block 34 (see FIG. 15 for an additional view of the fiber
optics block). A fiber optic cap 30 may be located over and/or onto
the fiber optic block 34. A waveguide including one or more fiber
optics 32 are located within the fiber optics block 34. The fiber
optics 32 may be formed as bifurcated fiber optics, such that a
first fork 32a locates over a light source, and a second fork 32b
locates over a detector. The first and second fork converge with
one another to form a joined arm 32c which is rotated about
90.degree. from the direction of the first and second arm and
extends upward toward one or more samples. A bottom cover 36 is
located in contact with a bottom edge of the fiber optic block 34.
One or more detection filters 38 may be located below the bottom
cover and aligned with one or more photodiode arrays 44. One or
more light source bandpass filters 40 may be located below the
bottom cover and aligned with one or more light sources 46. The one
or more detection filters 38 and one or more light source bandpass
filters 40 may be located onto a filter alignment holder 42 (see
FIG. 14 for an additional view of the filter alignment holder). The
filter alignment holder 42 may be located in contact with an optics
PCB 48, which may include one or more detectors 44 that correspond
to the one or more detection filters 38 and one or more light
sources 46 that correspond to or more light source bandpass filters
40.
[0111] FIGS. 4A and 4B depict an example fiber optics block 34,
shown from a top-down view of the fiber optics block. FIG. 4A shows
the fiber optics block prior to locating the fiber optics cap onto
the block, while FIG. 4B shows the fiber optics cap 30 located onto
the block. The fiber optics block is shown including a plurality of
recesses 50 for receiving the fiber optics 32 (not shown) and then
receiving the fiber optics cap 30 (as shown in detail at FIG. 6).
FIGS. 5A and 5B show the fiber optics block 34 as viewed from
beneath the block. The RTD guide 28 is shown extending into the
bottom of the block. FIG. 5A shows the block prior to addition of
the bottom cover, whereas the bottom cover 36 is shown located onto
the block in FIG. 5B. The bottom cover 36 (as shown in detail in
FIG. 7) may include an opening 52 for receiving and/or being
substantially aligned with the RTD guide (as shown in detail in
FIG. 10).
[0112] FIG. 8 shows an additional top-down view of an example fiber
optics block 34, while FIG. 9 shows an additional bottom-up view of
the fiber optics block. The views include the plurality of recesses
50 for aligning with and receiving the fiber optics cap 30. The
resulting gap formed between the block 34 and the cap 30 forms an
opening for the fiber optics 32 to align directly under each sample
in the sample holder 26. One or more gaps may be formed between the
block 34 and the cap 30. Each gap is an opening for the fiber
optics 32 to align directly under each sample in the sample holder
26. An opening 56 may be formed in the block for receiving the RTD
guide. The opening 56 may be located in a substantially centralized
location along the block 34. The block may further include a
plurality of openings 54 adapted for attaching the block to a
surface within the instrument. The block 34 may be potted with a
resin or similar material to permanently keep the assembled block
together, to protect the fiber optics 32, and to keep the fiber
optics stationary.
[0113] The RTD guide 28 is shown in further detail at FIG. 10. The
RTD guide preferably includes one or more tapered ends 58 for
entering into one or more openings within the fiber optics block.
The RTD guide is hollow to allow an RTD (not shown) to pass through
the block 34 and measure the temperature of the sample holder
26.
[0114] As discussed with reference to FIG. 3, a printed circuit
board (PCB) 48 is included within the instrument, an example of
which is shown at FIG. 11. The PCB includes one or more detectors
44, the number of detectors times the number of sample regions per
detector corresponding with the number of PCR samples per module.
For example, the four detectors 44 shown each have two sample
regions per detector corresponding to eight samples. The PCB
further includes one more light sources 46. In the illustrative
embodiment, each light source 46 contains four different wavelength
LEDs. For illustrative purposes, the PCB is shown having two
surfaces 60 to which light sources have not been attached.
[0115] In the illustrative figures, each light emitting diode
device provides light to two samples and each detector has two
sample regions (i.e. one for each sample). Other numerical
strategies are contemplated. For example, each light emitting diode
device may provide light to even more samples, such as four or even
eight samples. On the other hand, each sample could have its own
light emitting diode device. In this instance it would be possible
for a detector with only one sample region to be shared by multiple
samples by sequential timing of the light emitting diode devices.
Given the short read times required for each sample, a sequential
sample read strategy may have insignificant impact on total read
time. In the extreme, each sample may have dedicated light sources
and detectors. However, communal strategies would reduce the total
number of components required and thus the required space and
overall cost of the instrument.
[0116] In one embodiment, for each sample there is one light
emitting diode device and one photodiode detector device. In
another embodiment, for every two samples there is exactly one
light emitting diode device and two photodiode detector devices.
Alternatively, for every two samples there are exactly two light
emitting diode devices and one photodiode detector device. In yet
another embodiment, for every four samples there is one light
emitting diode device and four photodiode detector devices.
Alternatively, for every four samples there are four light emitting
diode devices and one photodiode detector device. In yet another
embodiment, for every eight samples there is one light emitting
diode device and eight photodiode detector devices. Alternatively,
for every eight samples there are eight light emitting diode
devices and one photodiode detector device. In the instances where
an unbalanced number of light emitting diode devices and photodiode
detector devices employed, the optical reading process may be
executed in such a way that the signal from each sample can be
isolated. By way of illustration, for a shared photodiode detector
device the light emitting diode devices are energized at different
times (sample 1 measured, then sample 2, etc.). in a preferred
embodiment, there are individual photodiode detector devices for
each sample with shared light emitting diode devices such that
multiple samples may be read simultaneously.
[0117] Another embodiment of the invention may include a step of
locating the light emitting diode device above the sample holder.
Excitation of the sample may be provided through transmission of
light through the cap and may include the multiple band pass filter
and additional fiber optic cables to transmit the light to the
sample. In this instance, the light transmission assembly below the
sample holder would be comprised of waveguides for transmission of
light emitted by the fluorescing agent to the detector.
[0118] A flow-chart depicting connectivity of the instrument
described herein with an illustrative four thermocycling modules
shown at FIG. 12. The system architecture diagram 62 shows the
central computer 66 as controlling the user interface 64. PCR
protocols 68 (including temperature and optics settings), PCR data
70 (including temperature and optics data), and the communications
board 74. The PCR data 70 is also in communication with data
analysis software 72 which provide for usable data storage and
statistical analysis resulting from the PCR protocols. The central
computer 66 further optionally receives power from a DC power
supply 76 if the computer is internal to the instrument, otherwise
the computer has its own DC power supply. DC power supply 76
receives power from a filtered AC power source 78. The
communications board 74 is in direct two-way communication with
each PCR module (depicted in this example as 80a, 80b, 80c, and
80d). Each PCR module also receives power from the DC power supply
76. Each PCR module provides communications to a thermoelectric
cooler (TEC) device 82a, 82b, 82c, 82d; a light source 84a, 84b,
84c, 84d; and a fan device 86a, 86b, 86c, 86d. Each PCR module
receives communication from one or more temperature sensors 90a,
90b, 90c, 90d. Each PCR module is in two-way communication with one
or more light detectors 88a, 88b, 88c, 88d.
[0119] Each module may be mostly self-contained. Each module may be
independently controllable and may perform real-time PCR on up to
2, up to 8, up to 12, or even up to 20 samples. The module includes
all necessary electronics and optics (controller board, H-bridge,
sensors, thermal protection, LEDs, optical detection hardware, etc)
with the exception of the power supply and user interface. Each
module may be contained in a sheath (e.g., plurality of panels) 14
for optimum airflow to keep the samples uniform in temperature. The
airflow may also go past all sensitive electronics, detectors, and
light sources, keeping them cool. The sheath 14 may also serve as a
protective barrier separating the hot components, electrified
circuits, and static sensitive components from the user and
external elements. The module may have one 2-wire connector for
power, and one 2-wire connector for communication with the
user-interface electronics. Alternatively the module may have one
4-wire connector which handles both power and communication. This
minimal wiring keeps the modules easy to install, maintain,
replace, calibrate, and allows for the modules to be easily placed
within an instrument box or as external add-ons to existing
equipment. The wiring connections 94 may extend out the side of the
module as shown in FIG. 1A, or may extend out of the bottom of the
module. The wiring connections may be plugs and receptacles or pins
and matching pin terminals for easy module installation and
removal. The modules may be fully independent, individually
calibrated, may be swapped for easy repair/maintenance, may be
produced in an instrument with 1, 2, 3, 4, or more modules, and are
generally small and portable. The modules may be pre-programmed so
that no user interface software or computer is required (ideal for
medical applications and ease of use). The modules may be
programmed by a barcode scanner, 2D barcode scanner, NFC (near
field communications), or RFID (radio frequency identification)
from an appropriate test kit, assay, or sample tube.
[0120] FIG. 13 shows an example instrument including four separate
PCR modules 92, each module including a sample holder and each
sample holder having its own fiber optic componentry. FIG. 14 shows
an exemplary filter alignment holder 42 showing additional detail
for shape and arrangement of openings within the filter holder for
receiving filter components. FIG. 15 shows an additional
perspective of the fiber optics block 34. FIG. 16 shows a sample
block 12 and connected fiber optic and electrical components 16
below.
[0121] FIG. 18 shows a side view of an embodiment of the first
excitation fork portion. A light emitting diode device 110 shines
light through a LED lens array 108. The LED lens array 108 focuses
the light emitted from the individual elements of the light
emitting diode device 110 through bandpass filters located in the
excitation filter holder 106. The filtered light continues to the
excitation fiber lens 104 which focuses all of the filtered light
beams to the fiber optic bundle 102. The fiber optic bundle 102
contains at least one optical fiber 100 in a compact staggered
arrangement to minimize the amount of light lost to unusable space
between the optical fibers 100. The optical fiber 100 transmits the
filtered light to at least one sample tube (not shown) and may be
flexible or bent into a permanent configuration to allow for
precise alignment with the sample tube. The light emitting diode
device 110 may be integrated assembly of light emitting diodes or
the light emitting diode device 110 may be a compact group of
individual light emitting diodes located on a substrate such as a
printed circuit board, with an arrangement such that the light
emitting diodes require an area which is less than 3 cm per side,
or less than 1 cm per side, or even less than about 4 mm per side.
The group of light emitting diode elements may have at least one
color, at least 4 colors, at least 5 colors, or at 7 colors. The
light emitting diode elements may be repeated such that more than
one element has the same color in the light emitting diode device
110 to increase intensity of that color and/or to increase the
overall life-span of using that color. The LED lens array 108 could
be a single integrated component as shown in FIG. 18, or a compact
arrangement of individual lenses. The lens arrangement in the LED
lens array 108 would match the pattern of light emitting diodes in
the light emitting diode device.
[0122] In one embodiment shown in FIG. 18, the lenses are staggered
in the LED lens array 108. In another embodiment the LED lens array
is in a rectangular grid arrangement (as example of which is
available from Edmund Optics, Barrington, N.J. under the
designation #64-486). The excitation filter holder 106 may be a
stationary device that holds individual bandpass filters. There may
be one bandpass filter for each LED element in the light emitting
diode device 110 as shown in FIG. 19. In another embodiment, one or
more multi-band bandpass filter may filter light from more than one
LED element in the light emitting diode device 110. The excitation
filter holder 106 may be a moving filter wheel that holds bandpass
or multi-band bandpass filters as shown in FIG. 20. The excitation
fiber lens 104 may be a single converging lens designed to transmit
light from all of the LED elements to the fiber optic bundle 102.
In another embodiment the excitation fiber lens may be an array of
individual lenses. The optical fibers 100 may be designed with a
relatively large numercial aperture (0.55 or greater) to maximize
the light that is transmitted to the samples. The optical fibers
100 may be plastic or they may be glass such as borosilicate
selected to have high light transmission in the about 400 nm to
about 700 nm range. The optical fibers 100 may have a diameter of
about 0.1 mm, 0.25 mm, 0.5 mm, or even 1.0 mm. The optical fibers
100 may all go to a single sample tube or the optical fibers may be
split to go to more than one sample tube. The optical fibers may go
to the top of the sample tube so that the light can be transmitted
through the optically clear cap of the sample tube. The optical
fibers may go to the bottom of the sample tube so that the light
can be transmitted through the optically clear bottom portion of
the sample tube. The grouping of the light emitting diode device
110, LED lens array 108, excitation filter holder 106, excitation
fiber lens 104, and optionally one end of the fiber optic bundle
102 may be enclosed in a filter alignment holder (not shown). The
filter alignment holder blocks light from entering or escaping the
first excitation fork portion other than through the optic fibers
100; holds the excitation fiber lens 104, filter holder 106, and
LED lens array 108 in proper alignment with the light emitting
diode device 110 and the fiber optic bundle 102; and can withstand
and potentially dissipate heat generated from the light emitting
diode device 110.
[0123] FIG. 19 shows a perspective view of one preferred embodiment
of the first excitation fork portion. There are seven light
emitting diodes located in a staggered arrangement on the light
emitting diode device 110. Each light emitting diode element is
approximately 1 mm.times.1 mm such that the entire hexagonal
grouping of light emitting diode elements occupies a space of less
than about 4 mm.times.4 mm. The LED lens array 108 is a single
optically clear array which is staggered such that each lens is
approximately centered over the top of the individual light
emitting diode elements of the light emitting diode device 110. The
excitation filter holder 106 contains seven bandpass filters with
an optical density of less than 1, less than 0.1, or even less than
0.01 in the desired wavelength ranges and an optical density of
greater than 4, greater than 5, or even greater than 6 in the
undesired wavelength ranges. There are up to seven different
bandpass filters to match the up to seven different light emitting
diode elements. A single excitation fiber lens 104 focuses the
seven filtered light paths to a grouping of 32 staggered optical
fibers 100 of 0.33 mm diameter and a 0.55 numerical aperture which
are tightly grouped in the fiber optic bundle 102. The grouping of
32 staggered optical fibers may be split to transmit light through
32 optical fibers to one sample, 16 optical fibers each to two
samples, eight optical fibers each to four samples, or four optical
fibers each to eight samples. Another embodiment may use 16 optical
fibers with each sample receiving light from 16, 8, 4, or 2 optical
fibers respectively depending on the number of samples. Another
embodiment may use 64 optical fibers with each sample receiving
light from 64, 32, 16, or 8 optical fibers respectively.
[0124] FIG. 20 shows a side view and perspective view of another
preferred embodiment of the first excitation fork portion. There
are seven light emitting diodes located in a staggered arrangement
on the light emitting diode device 110. Each light emitting diode
element is approximately 1 mm .times.1 mm such that the entire
hexagonal grouping of light emitting diode elements occupies a
space of less than 4 mm.times.4 mm. The LED lens array 108 is a
single optically clear array which is staggered such that each lens
is approximately centered over the top of the individual light
emitting diode elements of the light emitting diode device 110. The
excitation filter holder 106 is comprised of an excitation filter
wheel 112 which contains approximately seven bandpass filters 116
with an optical density of less than 1, less than 0.1, or even less
than 0.01 in the desired wavelength ranges and an optical density
of greater than 4, greater than 5, or even greater than 6 in the
undesired wavelength ranges and a motor 114 which turns the filter
wheel. There are seven different bandpass filters 116 to match the
different light emitting diode elements. A single excitation fiber
lens 104 focuses the seven filtered light paths to a grouping of
optical fibers 100 in the fiber optic bundle 102. In another
embodiment, there may be fewer than seven bandpass filters if one
or more of the light emitting diode element is repeated to emit
approximately the same color in the light emitting diode device
110. In another embodiment, there may be more than seven bandpass
filters if it is desirable to use more than one waveband from one
or more of the light emitting diode elements to fine-tune the
filtered light.
[0125] FIG. 21 is a representative drawing of the light path
through the embodiment of FIG. 18 and FIG. 19. Light from the
emitting diode 110 spreads away from the light emitting diode
element and through the LED to lens space 118. The LED to lens
space 118 is small (less than 3 mm, less than 2 mm, or even less
than 1 mm) such that the bulk of the light from a single light
emitting diode element goes to a single desired lens in the LED
lens array 108. Light focused through the LED lens array 108 passes
through the lens array to excitation filter holder space 120. Light
may focus in a crossing pattern through the excitation filter
holder 106 as shown in FIG. 21 or the light may be approximately
collinear and perpendicular to the light emitting diode device 110.
The filtered light passes through the excitation filter to
excitation fiber lens space 122 and then is focused by the
excitation fiber lens 104 to pass through the excitation fiber lens
to fiber optic bundle space 124. The distances of the spaces 118,
120, 122, and 124 are chosen to maximize the amount of light that
reaches the optical fibers 100 at a light angle that the optical
fibers can accept depending on the numerical aperture of the
optical fibers and the specific lens designs. The total distance
from the light emitting diode device 110 to the fiber optic bundle
102 may be less than 1 cm, less than 5 cm, or even less than 10
cm.
[0126] FIG. 22 shows an embodiment of the second detection fork
portion. Detection optical fibers 126 collect light from the sample
tubes and transmit that light to the detection fiber to filter lens
128. In FIG. 22, one representative light path 142 is shown. The
detection fiber to filter lens 128 could be an array of individual
lenses or an integrated lens array. The detection fiber to filter
lens 128 focuses the light from the detection optical fibers 126
into an approximately collinear path that is approximately
perpendicular to the detection filter holder 130 and the photodiode
detector device 134. Detection filter holder 130 is comprised of a
motor 138 that rotates the filter wheel 136 and various detection
bandpass filters 140. Light is filtered by the detection band as
filters 140, is focused by filter to detector lens 132, and is
detected by photodiode detector device 134. The components are
arranged in FIG. 22 such that each detection fiber 126 has one
detection to filter lens 128, one detection bandpass filter 140,
one filter to detector lens 132, and one photodiode detector 34.
However, any other configurations also may be utilized. More than
one detection fiber 126 could share an optical path through the
lenses, filters, and to the detector. A bandpass filter 140 could
be large enough to be shared by multiple light paths to reduce the
number of components required. The detection fiber to filter lens
128 and/or filter to detector lens 132 could be individual lenses
or an integrated array of lenses. The photodiode detector device
134 could be an integrated device with an array of photodiode
elements or an array of separate photodiode detectors. The bandpass
filters 140 could be a single wavelength band or could be
multi-band bandpass filters to minimize the number of components
and reduce the number of filter wheel rotations that are necessary.
The number of bandpass or multi-band bandpass filters 140
determines the number of colors that could be detected which may
allow for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more different colors
to be detected. The bandpass filters could be arranged such that
all photodiode detectors in the photodiode detector device 134
receive the same light wavelength simultaneously, or they could be
arranged such that each photodiode in the photodiode detector
device receives different wavelengths of light.
[0127] One or both of the detection fiber to filter lens 128 and/or
filter to detector lens 132 could be removed if the detection area
of the photodiode detection device 134 is large enough to accept
most or all of the light spread from the detection optical fibers
126. Minimizing the distance between the detection optical fibers
128 and the photodiode detection device 134 will assist in
minimizing that light spread. For example a distance of 10 mm, 5
mm, or 3 mm or less is desirable. In FIG. 22 the components (fiber
optics, lenses, bandpass filters, and photodiode detectors) are
arranged in two rows of four. However, many other configurations
exist. The shape of the grouping could be one single row of eight,
a curved row, or other grouping such as a round or square ngement.
Multiple detection fibers 126 could share the same lenses, filters,
and photodiode to increase the light sensitivity. The detection
filter wheel 136 could be distinct and separate from the excitation
filter wheel 112 or they could be the same filter wheel which
shares the same motor 114/138. This combination of filter wheels
112 and 136 minimizes the number of components and ensures
simultaneous timing of the excitation and detection filters. The
entire second detection fork portion is enclosed in a detection
filter alignment holder (not shown). The detection filter alignment
holder blocks light from the surroundings, especially any light
that may escape from the first excitation fork portion. All or part
of detection filter alignment holder may act as a thermal insulator
such that the photodiode detection device 134 will not be impacted
by higher temperatures generated in the instrument. All of part of
the detection filter alignment holder may act as a thermal
conductor to remove heat generated by the photodiode detection
device 134.
[0128] FIG. 23 shows another embodiment of the second detection
fork portion. In this case the filter to detector lens 132 is large
enough to be shared by all light paths from all detection fibers
126. The large filter to detector lens 132 focuses light onto a
single photodiode detection device 134. This arrangement allows for
a reduction in the number of components and assurance that the
photodiode detection device sensitivity is the same for all light
paths. The large filter to detector lens 132 could be a single
converging filter as shown in FIG. 23 or a lens array of individual
lenses which focuses each detection light path onto the same
photodiode detection device 134.
[0129] FIG. 24 shows the bottom of a sample tube. This sample tube
has optically clear bottom portion which has a low optical density
of less than 1, less than 0.1, or even less than 0.01 to light in
the about 450 nm to about 750 nm wavelength range. The tube bottom
150 is comprised of a flat tube portion 146 and an angled/curved
tube portion 148. The light can transfer to/from the sample within
the tube and to/from optical fibers underneath the tube through the
flat tube portion 146 with minimal light reflection, light
distortion, and light absorption due to the flat, thin, and
parallel inner/outer surfaces of the sample tube bottom. Optical
fibers 142 carry excitation light from the first excitation fork
portion of the optical manifold 100, within fiber optic bundle 102,
and transmit that light into the sample tube. Two potential
configurations of the optical fibers 142 are shown in FIG. 24. In
the top image of FIG. 24, there are four excitation optical fibers
142, two on either side of the flat tube portion 146; in the bottom
image of FIG. 24 there are eight excitation optical fibers 142,
four on either side of the flat tube portion 146. The optical
fibers are shown to be of maximal diameter in each configuration to
fit within the flat tube portion 146 in order to maximize the
amount of light that is transferred per excitation optical fiber.
The excitation optical fibers 142 have a diameter of about 0.33 mm
and about 0.25 mm respectively in FIG. 24. There may be other
configurations in which there are additional, but smaller,
excitation optical fibers 142 to increase the surface area which is
covered by the excitation optical fibers 142 and therefore increase
amount of light that can be transferred. The optical fibers also
extend into the angled/curved tube portion 148; however, there is
diminished light transmission in those regions. A large diameter
emission optical fiber 144 is centered underneath the flat tube
portion 146. The large diameter and placement of the emission
optical fiber 144 allows for maximum surface area and therefore
maximum amount of fluorophore emission light to be passed through a
single fiber. The diameter may be about 0.5 mm, about 0.75 mm,
about 1.0 mm, oe even about 1.25 mm. In another configuration,
there may be more than one emissionoptical fiber 144 with diameters
which are smaller in order to remain within or mostly within the
flat tube portion 146. For example, there may be four emission
optical fibers 144 which are about 0.5 mm in diameter and placed
within the center of the flat tube portion 146. The emission
optical fiber 144 may be round as shown in FIG. 24 or it may be a
molded optically transparent plastic with a more rectangular shape
which acts as a light pipe. The emission optical fiber may be
optically transparent to light with an optical density of less than
1, less than 0.1, or even less than 0.01 in the about 450 nm to
about 750 nm wavelenth range.
[0130] As to all of the foregoing general teachings, as used
herein, unless otherwise stated, the teachings envision that any
member of a genus (list) may be excluded from the genus; and/or any
member of a Markush grouping may be excluded from the grouping.
[0131] Unless otherwise stated, any numerical values recited herein
include all values from the lower value to the upper value in
increments of one unit provided that there is a separation of at
least 2 units between any lower value and higher value. As an
example, if it is stated that the amount of a component, a
property, or a value of a process variable such as, for example,
temperature, pressure, time and the like is, for example, from 1 to
90, preferably from 20 to 80, more preferably from 30 to 70, it is
intended that intermediate range values such as (for example, 15 to
85, 22 to 68, 43 to 51, 30 to 32 etc.) are within the teachings of
this specification. Likewise, individual intermediate values ere
also within the present teachings. For values which are less than
one, one unit is considered to be 0.0001, 0.001, 0.01 or 0.1 as
appropriate. These are only examples of what is specifically
intended and all possible combinations of numerical values between
the lowest value and the highest value enumerated are to be
considered to be expressly stated in this application in a similar
manner. As can be seen, the teaching of amounts expressed as "parts
by weight" herein also contemplates the same ranges expressed in
terms of percent by weight. Thus, an expression in the Detailed
Description of the Invention of a range in terms of at "`x` parts
by weight of the resulting polymeric blend composition" also
contemplates a teaching of ranges of same recited amount of "x" in
percent by weight of the resulting polymeric blend
composition."
[0132] Unless otherwise stated, all ranges include both endpoints
and all numbers between the endpoints. The use of "about" or
"approximately" in connection with a range applies to both ends of
the range. Thus, "about 20 to 30" is intended to cover "about 20 to
about 30", inclusive of at least the specified endpoints.
Concentrations of ingredients identified in Tables herein may vary
.+-.10%, or even 20% or more and remain within the teachings,.
[0133] The disclosures of all articles and references, including
patent applications and publications, are incorporated by reference
for all purposes. The term "consisting essentially of" to describe
a combination shall include the elements, ingredients, components
or steps identified, and such other elements ingredients,
components or steps that do not materially affect the basic and
novel characteristics of the combination. The use of the terms
"comprising" or "including" to describe combinations of elements,
ingredients, components or steps herein also contemplates
embodiments that consist essentially of, or even consist of
elements, ingredients, components or steps. Plural elements,
ingredients, components or steps can be provided by a single
integrated element, ingredient, component or step. Alternatively, a
single integrated element, ingredient, component or step might be
divided into separate plural elements, ingredients, components or
steps. The disclosure of "a" or "one" to describe an element,
ingredient, component or step is not intended to foreclose
additional elements, ingredients, components or steps.
[0134] It is understood that the above description is intended to
be illustrative and not restrictive. Many embodiments as well as
many applications besides the examples provided will be apparent to
those of skill in the art upon reading the above description. The
scope of the invention should, therefore, be determined not with
reference to the above description, but should instead be
determined with reference to the appended claims, along with the
full scope of equivalents to which such claims are entitled. The
disclosures of all articles and references, including patent
applications and publications, are incorporated by reference for
all purposes. The omission in the following claims of any aspect of
subject matter that is disclosed herein is not a disclaimer of such
subject matter, nor should it be regarded that the inventors did
not consider such subject matter to be part of the disclosed
inventive subject matter.
* * * * *