U.S. patent application number 10/602469 was filed with the patent office on 2004-05-06 for scanning system with calibrated detection and method.
Invention is credited to Dorsel, Andreas N., Staton, Kenneth L..
Application Number | 20040084612 10/602469 |
Document ID | / |
Family ID | 25399553 |
Filed Date | 2004-05-06 |
United States Patent
Application |
20040084612 |
Kind Code |
A1 |
Staton, Kenneth L. ; et
al. |
May 6, 2004 |
SCANNING SYSTEM WITH CALIBRATED DETECTION AND METHOD
Abstract
A self-calibrating scanning system and method are used in the
analysis of biomolecules on a microarray. The self-calibrating
scanning system comprises an excitation light source, an optical
portion, a detection portion and a calibration portion that
includes a calibration apparatus and compensation portion. The
calibration apparatus comprises a light source having a highly
reproducible or calibrated light based on a preselected or
reference light level. The calibration apparatus emits the
calibrated light that is measured by the detection portion of the
scanning equipment. If the detection components are stable, the
components will measure a constant output value for the calibrated
light over time. As a detection component changes with time, the
output value will change for the same calibrated light. The method
comprises the steps of initially calibrating the detection portion
of the scanning system and subsequently calibrating the detection
portion to compensate for sensitivity changes.
Inventors: |
Staton, Kenneth L.; (San
Carlos, CA) ; Dorsel, Andreas N.; (Menlo Park,
CA) |
Correspondence
Address: |
AGILENT TECHNOLOGIES, INC.
Legal Department, DL429
Intellectual Property Administration
P.O. Box 7599
Loveland
CO
80537-0599
US
|
Family ID: |
25399553 |
Appl. No.: |
10/602469 |
Filed: |
June 23, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10602469 |
Jun 23, 2003 |
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09892209 |
Jun 25, 2001 |
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6583424 |
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Current U.S.
Class: |
250/252.1 |
Current CPC
Class: |
G01N 21/6428 20130101;
G01N 21/6452 20130101; G01N 21/274 20130101; G01N 21/6458
20130101 |
Class at
Publication: |
250/252.1 |
International
Class: |
G01N 021/64; G01D
018/00 |
Claims
What is claimed is:
1. A self-calibrating scanning system for scanning a microarray of
biomolecules comprising: an excitation light source that produces
an excitation light; an optics portion that directs the excitation
light from the excitation light source to the microarray of
biomolecules; a detection portion that produces an output signal
responsive to an emission detected from a label on the microarray
being scanned with the excitation light; and a calibration portion
that calibrates sensitivity of the detection portion, the
calibration portion comprising: a calibration apparatus that
produces a calibrated light at a reference light level that is
detected by the detection portion; and a compensation portion that
compensates for changes in the sensitivity of the detection
portion, or which saves an indication of sensitivity in a memory in
association with data read from the array in response to
illumination with excitation light.
2. The self-calibrating scanning system of claim 1, wherein the
calibration apparatus comprises a calibration light source that
consistently reproduces the calibrated light.
3. The self-calibrating scanning system of claim 1, wherein the
compensation portion comprises a reference value corresponding to
an initial output value from the detection portion responsive to
the reference light level.
4. The self-calibrating scanning system of claim 2, wherein the
calibration apparatus further comprises a calibration detector and
a control in a closed loop to provide reproducibility of the
calibrated light from the calibration light source.
5. The self-calibrating scanning system of claim 1, further
comprising an analysis portion that comprises one or more of a
computer, a processor and memory to collect and analyze the output
signal from the detection portion and to produce information about
the labeled biomolecule.
6. The self-calibrating scanning system of claim 5, wherein the
compensation portion uses a respective one or more of the computer,
the processor and the memory of the analysis portion to provide an
indication and a magnitude of the change in sensitivity for use
with the information about the labeled biomolecule.
7. The self-calibrating scanning system of claim 3, wherein the
compensation portion further comprises one or more of a computer, a
processor and memory to optionally provide an indication and a
magnitude of the change in sensitivity.
8. The self-calibrating scanning system of claim 7, wherein the
compensation portion further comprises a digital to analog
converter to adjust the detection portion when there is a change in
sensitivity.
9. The self-calibrating scanning system of claim 3, wherein the
compensation portion further comprises a digital to analog
converter to adjust the detection portion when an output value from
the detection portion responsive to the calibrated light differs
from the reference value.
9. The self-calibrating scanning system of claim 3, wherein the
compensation portion indicates if an output value from the
detection portion responsive to the calibrated light differs from
the reference value and saves a magnitude of the difference for
reference.
10. The self-calibrating scanning system of claim 7, wherein the
reference value is stored in the memory, and wherein the change in
sensitivity is indicated by a difference between the reference
value and an output value from the detection portion responsive to
the calibrated light.
11. The self-calibrating scanning system of claim 1, wherein the
excitation light source comprises one of a laser or other light
source that produces the collimated light, and the detection
portion comprises a photomultiplier tube detector, and the system
further comprising an optional analysis portion that comprises a
microprocessor.
12. The system of claim 1, wherein the calibration portion is
integral to the scanning system.
13. The system of claim 1, wherein the calibration apparatus is
integral to the scanning system.
14. The system of claim 1, wherein the calibration portion further
comprises one or more of an optical component and a filter, wherein
the optical component efficiently distributes the calibrated light
to a detector in the detection portion, and the filter attenuates
signal noise from reaching the detection portion.
15. The system of claim 1, wherein the calibration portion further
comprises a filter to modify the calibrated light to correspond to
the emission from the scanned label on the microarray.
16. The system of claim 1, wherein the detection portion comprises
multiple channels having a photomultiplier tube in each channel,
and wherein the calibration portion further comprises a filter, and
wherein the calibration apparatus and the filter provide different
calibrated light levels from the calibration portion to the
multiple channels of the detection portion.
17. The system of claim 1, wherein the calibration apparatus
comprises a plurality of calibration light sources, with different
ones of the calibration light sources emitting a different
calibrated light at a different reference light level that
corresponds to an emission in a different spectral range from a
scanned label on the microarray of biomolecules, and wherein the
detection portion comprises a photomultiplier tube detector to
detect the emissions in the different spectral ranges.
18. The system of claim 1, wherein the detection portion comprises
a plurality of different color channels to detect emissions in a
plurality of different color spectral ranges, each different color
channel comprising a photomultiplier tube detector, and wherein the
calibration portion comprises a plurality of calibration
apparatuses, at least one different calibration apparatus for each
different color channel, such that the photomultiplier tube
detector in each color channel is calibrated with one corresponding
color calibrated light.
19. The system of claim 4, wherein the calibrated light source is
selected from a lamp with a filter, a solid state emitter, or a
light emitting diode, the calibration detector is selected from a
photodiode or phototransistor, the control is a control amplifier,
and the closed loop is provided by a regulator or
servomechanism.
20. A method of calibrating an scanning system used for scanning an
array of biomolecules that has an excitation light source that
produces a stable collimated light, an optics portion, and a
detection portion comprising the steps of: initially calibrating
the detection portion with a reference light level, the detection
portion producing an initial output signal in response to the
initial calibration that is stored for reference; and subsequently
calibrating the detection portion with a calibration apparatus that
produces a calibrated light at the reference light level, the
detection portion producing a subsequent output signal in response
to the subsequent calibration that is analyzed for calibration, or
saving an indication of sensitivity in a memory in association with
data read from the array in response to illumination with
excitation light.
21. The method of claim 20, wherein the step of initially
calibrating comprises the steps of: initially generating a fixed
signal corresponding to the reference light level with the
calibration apparatus; and measuring the output signal from the
detection portion in response to the initial fixed signal.
22. The method of claim 21, wherein the steps of initially
generating and measuring are repeated one or more times, the output
signal from the detection portion is recorded each time, and a mean
value for the initial output signal is calculated from the recorded
output signals and is stored as a reference value.
23. The method of claim 20, wherein the step of subsequently
calibrating comprises the steps of: subsequently generating the
calibrated light with the calibration apparatus; measuring the
output signal from the detection portion in response to the
subsequently generated calibrated light to compare the subsequent
output signal to the initial output signal for changes; and
compensating for any changes in the subsequent output signal.
24. The method of claim 23, wherein the step of compensating
comprises adjusting the detection portion until the subsequent
output signal corresponds to the initial output signal.
25. The method of claim 23, wherein the step of compensating
comprises providing sensitivity change data for analysis.
26. The method of claim 23, wherein the steps of subsequently
generating and measuring are repeated one or more times, the
subsequent output signal from the detection portion is recorded
each time, and a mean value for the subsequent output signal is
calculated from the recorded output signals before the respective
output signals are compared.
27. The method of claim 24, wherein the step of adjusting comprises
adjusting voltage of the detection portion.
28. The method of claim 24, wherein the step of adjusting comprises
adjusting a scale factor of the detection portion.
29. The method of claim 24, wherein the step of adjusting comprises
adjusting the gain of the detection portion.
30. The method of claim 20, further comprising the step of:
repeating the step of subsequently calibrating periodically.
31. The method of claim 30, wherein the steps of subsequently
calibrating and repeating occur automatically at predetermined
times.
32. The method of claim 20, wherein the step of subsequently
calibrating occurs after a predetermined time.
34. The method of claim 20, wherein the step of initially
calibrating and the step of subsequently calibrating are performed
at the same location.
35. The method of claim 20, wherein the step of initially
calibrating is performed at a first location and the step of
subsequently calibrating is performed at a second location remote
from the first location.
36. The method of claim 35, wherein the step of subsequently
calibrating is initiated from the first location.
37. The method of claim 20, further comprising the step of scanning
an array of labeled biomolecules to obtain data on the array,
wherein the step of subsequently calibrating one or both of
precedes or follows the step of scanning, and wherein any change in
detection sensitivity is correlated with the array data in the step
of subsequently calibrating.
38. The method of claim 25, further comprising the step of scanning
an array of labeled biomolecules to obtain data on the array,
wherein the step of providing comprises displaying whether a
sensitivity change was measured.
39. The method of claim 38, wherein the step of providing further
comprises correlating the sensitivity change data with the array
data during analysis to correct the array data for any sensitivity
changes.
40. In a scanning system for scanning a microarray of labeled
biomolecules that has an excitation light source that produces a
stable collimated light, an optics portion, and a detection
portion, the improvement comprising: a calibration portion for
calibrating sensitivity of the detection portion, the calibration
portion comprising: a calibration apparatus that produces a
calibrated light at a preselected light level that is detected by
the detection portion; and a compensation portion that measures an
output value from the detection portion responsive to the
calibrated light, compares the output value to a reference value to
determine whether the output value is different from the reference
value, and compensates for any differences.
41. The system of claim 40, wherein the compensation portion
compensates by adjusting the detection portion when a difference in
values is determined so as to make the difference equal or approach
zero.
42. The system of claim 40, wherein the calibration portion
monitors the sensitivity of the detection portion periodically.
43. The system of claim 40, wherein the compensation portion
compensates by providing a magnitude of difference between the
output value and the reference value to an array read file for
analysis.
44. The system of claim 43, wherein the compensation portion
further compensates by displaying whether a difference was
determined.
45. The system of claim 40, wherein the calibration portion is
integral with the scanning system.
46. The system of claim 40, wherein the calibration apparatus is
integral with the scanning system.
47. The system of claim 40, wherein the calibration apparatus
comprises: a calibration light source that consistently reproduces
the calibrated light; and optionally further comprises: a
calibration detector that measures a signal from the calibration
light source corresponding to the calibrated light; and a control
connected between the calibration light source and the calibration
detector that can adjust the calibration light source in a closed
loop when needed, such that the calibration light source
consistently reproduces the calibrated light at the preselected
light level.
48. The system of claim 40, further comprising an analysis portion,
wherein all or part of the compensation portion is incorporated
into the analysis portion.
Description
TECHNICAL FIELD
[0001] This invention relates to calibration of detection systems
for non-elastically scattered light. In particular, the invention
relates to the calibration of scanners for detection of
biomolecules on microarrays.
BACKGROUND ART
[0002] Microarrays of biomolecules, such as DNA, RNA, cDNA,
polynucleotides, oligonucleotides, proteins, and the like, are
state-of-the-art biological tools used in the investigation and
evaluation of biological processes, including gene expression and
mutation for analytical, diagnostic, and therapeutic purposes.
Microarrays typically comprise a plurality of polymers, e.g.,
oligomers, synthesized or deposited on a substrate in an array
pattern of features. The support-bound polymers are typically
called "probes", which function to bind or hybridize with a sample
of polymer material under test, i.e., a moiety in a mobile phase
(typically fluid), called a "target" in hybridization experiments.
However, some investigators also use the reverse definitions,
referring to the surface-bound polymers as targets and the solution
sample of polymer as probes. Further, some investigators bind the
target sample under test to the microarray substrate and put the
polymer probes in solution for hybridization. Either of the
"target" or "probes" may be the one that is to be evaluated by the
other (thus, either one could be an unknown mixture of polymers to
be evaluated by binding with the other). All of these iterations
are within the scope of this discussion herein. The plurality of
probes and/or targets in each location in the array is known in the
art as a "feature". A feature is defined as a locus onto which a
large number of probes and/or targets all having the same monomer
sequence are immobilized. In use, the array surface is contacted
with one or more targets under conditions that promote specific,
high-affinity binding of the target to one or more of the probes.
The targets are typically labeled with an optically detectable
label, such as a fluorescent tag, dye or fluorophore, so that the
targets are detectable with scanning equipment after a
hybridization assay. DNA array technology, for example, offers the
potential of using a multitude (hundreds of thousands) of different
oligonucleotides to analyze changing mRNA populations.
[0003] Typical scanning equipment used for biomolecular analysis,
such as scanning fluorometers, comprise an excitation light source,
an optical system for directing light to and from a sample being
scanned, a detection system and optionally an analysis system. To
analyze a microchip after a hybridization assay, the scanner scans
a light from its excitation light source across the microchip. The
light excites the optically detectable labels on the hybridized
biomolecules. The excited labels in turn emit light at one or more
particular wavelengths. The emitted light from the biomolecules is
detected and measured by the detection system and the measurements
are analyzed by analysis equipment to determine the results of the
assay. In competitive hybridization assays, more than one label may
be used, each of which emit light having a characteristic emission
spectrum, which may be narrow or broad, to distinguish the
biomolecules on the microchip. The light emitted by each different
label must be separately detected by the scanning equipment for
analysis. State-of-the-art scanners are equipped with a detection
system having multiple channels for detecting emissions at
different wavelengths, for example. The detection systems having
multiple channels are designed to detect signals from a combination
of dyes or dyes having broad emission spectra that are used in
labeling. Parameters such as the intensity, the wavelength, and the
location of the emitted light on the microchip provide important
information about the target material being assayed. Therefore,
accurate measurement of these parameters is essential to providing
accurate information about the target material.
[0004] The detection systems used in scanning equipment comprise
one or more detector components, such as photomultiplier tubes
(PMTs). PMTs are known to age and to also deteriorate as a function
of signals and overloads previously received.
[0005] An approach to improving the accuracy of a fluorometer used
for scanning flow cells is to determine the relative fluorescence
intensity or index (RFI) for a bulk sample in the flow cell.
Gifford et al., U.S. Pat. Nos. 4,750,837 and 4,802,768, discuss and
illustrate approaches for compensating for variations in excitation
light using reference signals or reference paths, and the
advantages and disadvantages of these approaches, and further,
disclose a reference system that accounts for variations in signal
levels from light sources and detection components that affect the
RFI. A computation is made on measurements taken on the detection
components and light sources, which indicates the relative
concentration of the target being assayed using the flow cell. The
computation is intended to cancel out the variations in the light
sources and the detectors. The system described by Gifford et al.
provides only a relative measurement of the target concentration in
a bulk sample using flow cells. Therefore, there is little or no
consistency between fluorometer systems taught by Gifford et
al.
[0006] Thus, it would be advantageous to have a scanning system for
scanning microarrays of biomolecules on microchips that is
self-calibrating in that the sensitivity changes in the detection
components are compensated for. Further, it would be advantageous
to have a scanning system that could provide absolute target
concentration measurement results where the results are
reproducible from scanner to scanner. Still further, it would be
advantageous if such self-calibration could be integrated into the
scanner and the calibration be performed automatically.
SUMMARY OF THE INVENTION
[0007] The present invention provides a novel self-calibrating
scanning system and method of calibrating which are useful for
scanning microarrays of biomolecules on microchips. Since the
present system is a scanning system that scans microarrays of
minute quantities of biomolecules, a laser or other stable
collimated light source is typically used as the excitation light
source. The laser is characteristically very stable, such that the
need to account for variations in excitation light on the system is
essentially eliminated. The self-calibrating scanner and method
compensate, and may also monitor, for changes in the component
whose sensitivity will most likely to drift or vary with time and
use, i.e., the detection components. Further, for scanning systems
with multichannel detection components, the calibration portion of
the invention can be made fairly redundant without much extra
effort, if any. The self-calibrating scanner is particularly useful
in scanning fluorometry of arrays. The self-calibrating scanner
provides calibration capability of the specific sensitivities/scale
factors in the detection color channels.
[0008] In one aspect of the invention, the self-calibrating
scanning system comprises an excitation light source that produces
an excitation light, an optics portion, a detection portion, and a
calibration portion. The optics portion directs the excitation
light from the excitation light source to a microarray of labeled
biomolecules on a microchip that is under test. The detection
portion comprises a detector that detects or measures emissions
from labels on the microarray that are excited by the excitation
light and produces an output signal responsive to the detected
emissions. The calibration portion comprises a calibration
apparatus and a compensation portion. The calibration apparatus
comprises a calibration light source and optionally a calibration
detector for ensuring a constant or calibrated light level from the
calibration light source via a closed feedback control loop. The
compensation portion comprises components to perform one or more of
data collection, data storage, data comparison, data communication,
and adjustment to the scanning system to compensate for any
changes.
[0009] The calibration apparatus provides a calibrated light to the
detection portion of the scanner. The detection portion measures
the calibrated light and provides a corresponding output. The
compensation portion measures or collects the output from the
detection portion corresponding to the calibrated light and may
compare the output to a stored reference value. If the output is
different from the stored reference value, i.e., there is a change
in detection sensitivity, the compensation portion compensates for
the sensitivity change, either by adjusting the detection portion
or providing sensitivity data for analysis. Such provided
sensitivity data may be stored in a memory (for example, in
association with data read from the array in response to excitation
light). Any sensitivity data herein may be an indication of any
change in sensitivity, so that such differences can be used in the
processing of read data from an array to substantially compensate
for the sensitivity changes, for example, which occurred between
scanning different arrays. Alternatively, the sensitivity data may
simply be an indication that sensitivity did not change, for
example that between the scanning of arrays sensitivity remained
constant, allowing a user to confidently compare results from
arrays scanned at different times (or from different machines if
any or no change in sensitivity with regard to a reference value is
provided, or an absolute sensitivity value provided). The
calibration portion can provide periodic calibration checks of the
detection portion. The calibration portion may be a discrete unit
or integral to the scanning system. The scanning system optionally
further comprises an analysis portion. Alternatively, the scanning
system may be otherwise associated with analysis equipment. The
analysis portion comprises one or more of data collection, storage
and analysis equipment components. The analysis portion receives
the output signals from the detection portion and provides array
data, such as the concentration of target in each location on the
microarray. The analysis portion may further receive the
sensitivity change data from the compensation portion, so that the
sensitivity change data can be correlated with the array data.
[0010] The self-calibrating scanner of the invention compensates
for sensitivity changes in the detection portion of the system to
provide an absolute amount or concentration of target material on
the microchip, not a relative amount, as in Gifford et al. (cited
supra). Advantageously, the same microchip can be analyzed on other
self-calibrating scanners of the present invention for the target
concentration on the same microchip and the results will be
substantially the same. In contrast, the system described by
Gifford et al. essentially would not work for scanning minute
quantities on arrays, and further, provides only relative target
concentration values for bulk samples in a flow cell. Therefore, it
is unlikely that any two or more systems described Gifford et al.
will provide the same result for the same bulk sample/flow cell.
The present invention does not determine target concentration on a
relative scale. Advantageously, the present invention provides
absolute results that are reproducible from one self-calibrating
scanning system to another self-calibrating scanning system of the
invention.
[0011] In another aspect of the invention, a method of calibrating
a scanning system is provided. The method comprises the step of
initially calibrating the detection portion of the scanner. The
step of initially calibrating comprises the steps of generating a
fixed signal (corresponding to the calibrated light level mentioned
above) and measuring an output signal from the detection portion of
the scanner in response to the fixed signal. The step of measuring
may be repeated one or more times. The measurements are recorded
and the mean value is calculated and stored as one reference value.
The calibration apparatus and compensation portion described above
may be used in the step of initially calibrating.
[0012] An additional aspect of the present invention may include
simply retrieving from a memory stored sensitivity data and read
data from an array, and correcting the read data based on the
stored sensitivity data. Alternatively, another aspect may involve
retrieving stored sensitivity data for respective different arrays
(or different readings of the same array) and retrieving respective
sensitivity data and, when the sensitivity data indicate no change
in sensitivity, then comparing results from the different arrays
(or different readings) or, when the sensitivity data indicates
differences in sensitivity when the respective array readings were
taken, then first correcting the read data from the different
arrays (or different readings of the same array) then comparing the
read results from them.
[0013] The method further comprises the step of subsequently
calibrating the detection portion of the scanning system. The step
of subsequently calibrating comprises the steps of separately
generating another fixed signal that corresponds to the fixed
signal mentioned above, using the calibration portion, as described
above, measuring the corresponding output signal from the detection
portion and comparing the corresponding output signal to the
reference value, and compensating for any changes in sensitivity of
the detection portion with respect to array data collected during a
scan. The step of compensating comprises one or both of adjusting
the detection portion of the scanning system to achieve a
corresponding detection portion output signal with minimum
deviation from the stored reference value, or providing detection
sensitivity change data for analysis, so as to substantially
compensate for any sensitivity changes for a scanned array. The
step of subsequently calibrating may be repeated periodically and
may be automatically or manually initiated. Moreover,
implementation of the method of calibrating a scanning system in
accordance with the invention can be automatic or manual. The
present method helps to maintain throughput while reducing
variations in detection sensitivity over time, such that the
scanning system provides a substantially consistent accuracy
level.
BRIEF DESCRIPTION OF THE DRAWINGS
[0014] The various features and advantages of the present invention
may be more readily understood with reference to the following
detailed description taken in conjunction with the accompanying
drawings, where like reference numerals designate like structural
elements, and in which:
[0015] FIG. 1 illustrates a block diagram of a scanning system in
accordance with the present invention.
[0016] FIG. 2 illustrates a block diagram of the calibration
portion of the scanning system of FIG. 1.
[0017] FIG. 3 illustrates a flow chart of a method of calibrating
the scanning system of FIG. 1.
MODES FOR CARRYING OUT THE INVENTION
[0018] Typical "biopolymer" array construction and different
scanning methods and apparatus are described in detail in, for
example, U.S. patent application Ser. No. 09/846,125, filed Apr.
30, 1991 and entitled "Reading Multi-Featured Arrays" by inventors
Delenstarr et al., and the references cited therein which are
incorporated herein by reference.
[0019] A "processor" in the present application references any
combination of hardware or software which can control components as
required to execute recited steps and includes, for example, a
general purpose digital microprocessor suitably programmed (for
example, from a computer readable medium carrying necessary program
code or by communication from a remote location) to perform all of
the steps required of it, or any hardware or software combination
which will perform those or equivalent steps. A "memory" is any
suitable device in which data can be stored and retrieved, such as
magnetic, optical, or solid state storage devices (including
magnetic or optical disks or tape or RAM, or any other suitable
device, either fixed or portable).
[0020] It is common practice to scan a microarray more than once
during analysis, especially when fluorescent labels are used, and
the light levels measured during the subsequent scans are typically
compared. Therefore, in scanning hybridized samples, one skilled in
the art wants to make sure that the sensitivity of the detection
system components do not change unnoticed over time. If more than
one fluorescent dye is used (e.g. in scanning gene expression chips
using competitive hybridization) this becomes even more desirable.
When changes in sensitivity in detection components occur
unnoticed, the unknown difference in sensitivity changes for each
different fluorescent dye results in apparent changes in the
measured ratio of the different dye signals to be compared, thus
possibly introducing systematic errors. As mentioned above, often
the detector(s) used in fluorescent scanning are photomultiplier
tubes (PMTs) that are known to age and to also deteriorate as a
function of signals and overloads previously received.
[0021] A self-calibrating scanning system 100 for scanning arrays
according to the invention is illustrated in FIG. 1. The scanning
system 100 comprises a stable excitation light source 110, an
optical portion 120 for directing collimated excitation light to a
microarray of labeled biomolecule samples under test, a detection
portion 130 for receiving light from the labeled test sample and
converting the received light into a corresponding output signal,
which can be analyzed to produce data about the array. The scanning
system 100 optionally further comprises an analysis portion 140 for
collecting and analyzing the output signal data from the detection
portion 130. The optional analysis portion 140 is illustrated
within a dashed-line box for that reason. The scanning system 100
further comprises a novel calibration portion 150, which interfaces
with the detection portion 130 of the scanning system and
optionally interfaces with the optional analysis portion 140. The
present invention works particularly well with fluorescence
scanners or scanning fluorometers.
[0022] The stable excitation light source 110 is either a laser or
other collimated light source, which advantageously provides a
substantially stable and consistent light intensity or power and
controllable light beam during a scan. Further, the light
intensity, power and beam are compatible with that necessary to
excite the minute quantities of labels on the minute quantities of
the biomolecules of the microarray without damaging them, while the
collimated excitation light is scanned one or more times across the
microchip array.
[0023] The optical portion 120 comprises an electro optic modulator
(EOM) to modulate the light from the excitation light source and
one or more mirrors, lenses and/or filters necessary to direct the
collimated excitation light from the excitation light source 110 to
the microarray sample. Further, the optical portion 120 can
comprise one or more mirrors, lenses and/or filters necessary to
direct the emissions from the excited labels on the microarray to
the detection portion 130 of the scanning system.
[0024] The detection portion 130 comprises one or more detectors,
such as a photomultiplier tube (PMT), to detect the emissions from
the excited labels on the biomolecules. A PMT has the ability to
detect the fluorescence emissions of interest in minute amounts or
intensity levels. The detection portion 130 may comprise a
multichannel detection scheme 130' (not illustrated), wherein each
channel is designed to detect a different wavelength .lambda. range
of the emission spectrum of interest and/or to provide redundancy
to the detection capability of the detection portion 130. There is
a PMT, or other detector, for each detection channel. The detector
in each channel is adjusted to detect a particular emission range.
Multichannel schemes 130' are particularly useful for separately
detecting different labels (i.e., labels with different emission
spectra), such as the well-known CY3 and CY5 fluorescence labels,
which emit in the red/green color spectral ranges. While a PMT is
suitable for detecting minute intensity levels for the invention,
the PMT is notoriously subject to variations in its sensitivity due
to at least environmental conditions (e.g., temperature) and age
(e.g., time and usage). Without calibration, these sensitivity
variations will affect the accuracy of the conventional scanning
system in detecting the minute amounts of target material that were
assayed with the biomolecules on the microarray. Therefore, the
scanning system 100 with a self-calibrating capability of the
invention is particularly advantageous for overcoming the
conventional problems with scanning system accuracy.
[0025] The optional analysis portion 140 comprises one or more of
data collection, storage, calculation and comparison capabilities,
for example, to provide array data such as the absolute
concentration or amount of a target sample in the microarray of
biomolecules after a scan. The analysis portion 140 can provide the
specific amount of a target at each feature location on the
microarray. The analysis results provide valuable information about
the target sample under test. The analysis portion 140 comprises a
computer, such as a microprocessor, to perform the above
capabilities. By `optional` it is meant that the analysis portion
140 is not a necessary component for the operation of the scanning
system 100 of the invention. The analysis portion 140 provides the
additional capabilities described above to the inventive scanning
system 100. Depending on the embodiment, the analysis portion 140
may be a separate component but provided by the system 100 provider
or manufacturer, or may be a separate component and provided by a
third party or the user of the system 100, and in both cases
connected for communication to the scanning system 100, or the
analysis portion 140 may be included, such as being integral to or
interfaced with the basic inventive system 100 to provide the
additional capabilities. Moreover, in one embodiment of the
scanning system 100, one or more of the excitation light source
110, the optical portion 120, the detection portion 130 and the
optional analysis portion 140 may be similar to that of a
conventional scanning system. Any and all of these embodiments are
within the scope of the invention.
[0026] According to the invention, the scanning system 100 further
comprises a calibration portion 150 comprising a calibration
apparatus 160 and a compensation portion 180 further illustrated in
FIG. 3. The calibration portion 150 essentially calibrates the
detector portion 130. In one embodiment, the calibration portion
150 checks the sensitivity of the detection portion 130 for
variations in its detector(s) and adjusts the PMT detector(s) to
remove or compensate for the variation and maintain the accuracy of
the scanning system 100. The calibration portion 150 adjusts the
detection portion 130 to compensate for changes, so as to maintain
the same dynamic range of detection for the scanning system 100. By
"compensate" it is meant either at least in part maintaining the
sensitivity to within a predetermined tolerance, which is
preferably about zero. In other words, the calibration portion 150
ensures that a given signal of particular value emitted from the
scanned array causes the same output signal to be generated from
the detection portion 130 (within the predetermined tolerance) by,
for example, changing amplifier gain or detector sensitivity (e.g.
PMT voltage).
[0027] Alternatively, the calibration portion 150 can "compensate"
for any changes in detection portion 130 sensitivity by making
available the sensitivity data to correlate with array data after a
scan. For example, the sensitivity data may be provided to the
optional analysis portion 140, such that any sensitivity changes
are taken into account during array analysis. For example, the
sensitivity data from the calibration portion 150 can be stored for
later access by, or added to, the array read data file. In this
way, the analysis data is essentially compensated to account for
the changes in the sensitivity of the detector portion 130.
[0028] Referring to FIG. 3, the calibration apparatus 160 comprises
a calibration light source, and optionally may further comprise a
calibration detector and a control to keep the calibration light
source calibrated. The calibration light source may be any
controllable light source, such as a lamp with filters (e.g., an
incandescent lamp or an arc lamp, with e.g., an interference filter
or a colored-glass filter), a LED or other solid-state emitter, for
example, possibly with additional filters. By "controllable" light
source, it is meant that the light source is highly reproducible
(i.e., the light level is repeatable with little or no variation).
The calibration light source emits a calibrated light at an output
of the calibration apparatus 160. A signal associated with the
calibrated light level may be detected by the optional calibration
detector.
[0029] The calibration detector may be any stable detector, such as
a photodiode or phototransistor, possibly with an integrated
preamplifier, or a PIN diode, for example. By "stable" detector, it
is meant that the detector is more stable in its sensitivity over
time and temperature than a conventional PMT. The calibration
detector measures the associated signal emitted by the calibration
light source and produces an output signal corresponding to the
measured associated signal that is received by the optional
control, such as a control amplifier, for example.
[0030] The optional control comprises reference input value that
corresponds to a preselected or reference light level and compares
output signal received from the calibration detector to the
reference input value. The reference light level should be big or
high enough to be easily detected with good signal-to-noise ratio
(SNR) and small or low enough to not saturate the detection signal
path. By "good" SNR it is meant that the SNR is high enough to
allow rapid measurement with an accuracy high enough to only
contribute a minor fraction to the limit of the stability one is
trying to achieve.
[0031] The reference light level is a light level (i.e., power or
intensity) expected from the fluorescent tags or labels on the
biomolecules of a microarray during a scan that will be detected by
the detection portion 130 of a scanning system 100. There may be
more than one reference light levels used to cover the spectral
range of the tags that may be used with a microarray. Using the
reference light levels as the calibrated light levels of the
calibrated light from the calibrated light source ensures that the
detection portion 130 is most sensitive in the desired spectral
range of interest.
[0032] If necessary, the control adjusts the calibration light
source to produce the calibrated light at the output of the
calibration apparatus 160 at a fixed or constant level equal to the
reference level (i.e., corresponding to the fixed signal mentioned
below). The control electronically compares the output signal from
the calibration detector to the reference input value and adjusts
the current through the light source to increase or decrease its
signal, as needed, for the two values to be the same. The
calibration apparatus 160 produces a highly reproducible calibrated
light that, in one embodiment, is provided in a closed loop control
(i.e., such that the area over which the power is distributed is
constant). The closed loop control may use a regulator or a
servomechanism. The calibration apparatus 160 may be an
off-the-shelf unit, for example an IPL 10630 Series Self Monitoring
Emitter manufactured by Integrated Photomatrix, Ltd., England. The
calibration apparatus 160 may be a stand-alone unit, or preferably
is integrated into the scanning system 100.
[0033] The calibration apparatus 160 periodically provides the
calibrated light at its output to the detection portion 130 of the
scanning system 100, either manually or automatically. The
detection portion 130 detects the calibrated light and generates an
output signal in response to the calibrated light. The responsive
output signal from the detection portion 130 can be monitored for
changes in sensitivity to the calibrated light. The compensation
portion 180 measures the output signals from the detection portion
130 that are responsive to the calibrated light.
[0034] The compensation portion 180 comprises one or more of signal
data collection, calculation, storage and comparison and adjustment
capabilities. In one embodiment, the compensation portion 180 has
the ability to adjust the system 100, in particular the detection
portion 130, using a digital to analog converter, for example. In
another embodiment, the compensation portion 180 can be
accomplished with the analysis portion 140 and the compensation
portion 180 further comprises the digital to analog converter for
the adjustment capability not found in a conventional analysis
portion of a microarray scanner. In other embodiments, the
compensation portion 180 provides the above-mentioned capabilities
either redundantly to the analysis portion 140 or in part shared
with the analysis portion 140. In these embodiments, the
compensation portion 180 may further comprise one or more of
memory, a processor or computer. The compensation portion 180
collects the output signal data from the detection portion 130 that
is responsive to the calibrated light and stores the signal data.
Further, the compensation portion 180 has stored therein a
reference value or initial output signal provided upon initial
calibration of the system 100, described further below, and/or
provided during a previous calibration. The compensation portion
180 compares the reference or initial value to the responsive
output signal for changes in sensitivity.
[0035] In one embodiment of the compensation portion 180, if a
change is noted, the compensation portion 180 adjusts the detection
portion 130 so that the output signal equals the reference value to
compensate for the change. The compensation portion 180 may adjust
the PMT voltage, for example, to adjust the system gain and
compensate for the variation that was detected by the calibration
portion 150. Advantageously, the compensation portion 180 can store
the adjustments made during a calibration to simplify future
settings, as described further below. In another embodiment, the
compensation portion 180 stores measurements and notes measurement
changes in the memory that is associated with file data gathered on
the array being evaluated by the scanning system 100. In this
embodiment, the compensation portion 180 would provide a message
that indicated whether a change was noted or not and the magnitude
of the change, so that the detected change can be compensated for
in scanned array data.
[0036] The calibration portion 150 according to the invention,
provides a closed loop control of the detection portion 130 of the
scanning system 100. The calibration portion 150 provides for
initial calibration of the system 100, preferably at the factory,
and a subsequent calibration of the system, preferably in the
field, one or both of which may be manual or automatic, as are
further described below with respect to the method of the present
invention. The calibration portion 150, or at least the calibration
apparatus 160 thereof, is integrated into the scanning system 100
of the invention in the preferred embodiment. Further,
advantageously a conventional scanning system may be adapted to use
the calibration portion 150 with only minor modifications to the
conventional system.
[0037] The calibration portion 150 may further comprise optics
and/or filters. Optics may be employed to distribute the calibrated
light from one calibrated light source of the calibration apparatus
160 to multiple detectors in the detection portion 130 of the
scanning system 100. Further, optics, such as a light guide, a
mirror, a scattering screen or a relay lens, for example, may be
employed to make delivery of the calibrated light from the
calibrated light source to the detectors more efficient. Filters
may be used to suppress unwanted radiation, and/or to attenuate
overly strong signals, and/or to have the spectrum from the
calibrated light source more closely correspond to that of the tags
or labels to be detected on the microarray under test.
[0038] The calibration portion 150 of the present invention is
versatile and adaptable to different multichannel schemes 130' in
the scanning system 100. For example, in one embodiment of the
calibration portion 150, the controllable light source of the
calibration apparatus 160 may comprise a single lamp that is used
with more than one different filters, such that the calibration
apparatus 160 could be used to provide more than one different
levels of the calibrated light from the calibration portion 150 for
calibration of multiple detectors of the detection portion 130 of a
multichannel system 130'. Advantageously, a single calibration
light source used to calibrate all detectors in the detection
multichannels reduces cost. In another embodiment, the calibration
portion 150 may comprise a calibration apparatus 160 with either a
single calibration light source to calibrate the response of a
single detector or multiple calibration light source(s) to
calibrate the response of multiple detector(s) in the detection
portion 130, 130' of the scanning system 100.
[0039] Alternatively, the calibration portion 150 may comprise more
than one calibration apparatuses 160 for the same purpose. Further,
where the calibration apparatus 160 comprises multiple calibration
light sources, the multiple light sources may be used to calibrate
the response of one detector in the detection portion 130 of the
scanning system 100, where one detector is used in multiple
spectral ranges. This is particularly advantageous when a single
calibration light source in the calibration apparatus 160 is unable
to calibrate the multiple spectral ranges. In the preferred
embodiment, the calibration portion 150 comprises a calibration
apparatus 160 comprising one light source per `color` detection
channel of the multichannel detection portion 130', where the
detector in each respective color channel is calibrated using one
color-corresponding (i.e., spectrum- or wavelength-corresponding)
light source.
[0040] Where the detection portion 130 comprises one detector used
for detecting different colors, e.g., in consecutive scans with the
self-calibrating scanner 100, the calibration portion 150 may
comprise one or more calibration apparatuses 160, each with one or
several calibration light sources equal to the number of different
colors to be detected, such that there is at least one calibration
light source that corresponds to a particular color. In this
embodiment of the calibration portion 150, one compensation portion
180 can be used monitor and adjust the detector portion 130 to
compensate for spectrally differential sensitivity changes.
However, where the cost of device complexity outweighs the cost of
redundancy, more than one compensation portion 180 may be used and
still be within the scope of the invention.
[0041] Further, in the embodiment where one or more calibration
apparatuses 160, each having one or several calibration light
sources of different colors, is used in the calibration portion
150, it is not only possible to use each of the calibration light
sources to remeasure a respective `corresponding` detector of the
detector portion 130, 130', but it may also be possible to make
measurements with one or more of the calibration light sources on
one, a few, or each detector of the detection portion 130, 130',
thus making the calibration redundant in one calibration step.
[0042] Preferably, the scanning system 100 is first calibrated at
the factory to take into account, e.g., variations from unit to
unit in alignment and transmission of the optics portion 120. When
the scanning system 100 is manufactured, a desired system scale
factor is determined for the detection portion 130. The system
scale factor is defined as signal counts per photons detected at
fixed excitation power. The calibration portion 150 only needs to
track the changes of the component most likely to change the
sensitivity (scale factor) later, which advantageously, is expected
to be only the detector(s) in the present scanning system 100. The
calibration portion 150 is used to make sure that the contribution
of the detector(s) to the system scale factor remains constant
(i.e., detector variations are minimized, but not necessarily
zero).
[0043] A method 200 of calibrating the scanning system 100 includes
both an initial calibration of the detection portion 130 when the
scanning system 100 is first manufactured, and also subsequent
calibration of the detection portion 130 when the scanning system
100 is in the field. The method 200 essentially compensates for
detector sensitivity changes by measuring the output signal from
the detection portion 130 responsive to an initial calibration, and
in one embodiment, adjusting the system gain during a subsequent
calibration, such that the output signal from the detection portion
remains substantially the same. In another embodiment, instead of
physically adjusting the system 100, the method 200 compensates by
storing sensitivity change data for use with the scanned array file
data, so that accurate information about target samples can be
ascertained.
[0044] The method 200 of calibrating is illustrated in block
diagram in FIG. 2. The method 200 comprises the step of initially
calibrating 201 the detection portion 130 of the self-calibrating
scanning system 100. After the system 100 is manufactured, but
before its first use by a user, the initial calibration 201 is
performed. In a preferred embodiment, the step of initially
calibrating 201 is performed at the factory where the system 100 is
manufactured. However, the initial calibration step 201 can be
performed at the site of use (i.e., the user's facility). The step
of initially calibrating 201 comprises the step of generating 203 a
fixed signal (corresponding to the calibrated or preselected light
level mentioned above) with the calibration apparatus 160 of the
calibration portion 150 of the scanning system 100. Alternatively,
the fixed signal may be provided by some other source that
reproducible produces the same fixed signal. The step of initially
calibrating 201 further comprises the step of measuring 205 an
initial output signal from the detection portion 130 in response to
the fixed signal with the compensation portion 180. Again
alternatively, another measurement component other than the
compensation portion 180 may be used to take the measurements. The
measurements are made one or more times, and preferably are
repeated as needed to obtain sufficient SNR. The measurements are
recorded and the mean signal value (hereinafter `initial output
signal` or `reference value`) is calculated and stored in the
compensation portion 180 of the scanning system 100.
[0045] It is this stored initial output signal value that is the
standard or reference for the subsequent calibration of the
scanning system 100 in the field. Preferably, every scanning system
100 of the invention that is initially calibrated 201 in accordance
with the invention will perform substantially the same to the same
fixed signal. Advantageously, a user can expect consistency between
scanning systems 100 of the invention and reproducibility of the
microarray scanning results.
[0046] The method 200 further comprises the step of subsequently
calibrating 210 the detection portion 130 of the scanning system
100. The step of subsequently calibrating 210 comprises the steps
of separately and subsequently generating 211 another fixed signal
that corresponds to the first mentioned fixed signal from the
calibration portion 150; measuring 213 the output signal from the
detection portion 130 that is responsive to the subsequently
generated 211 fixed signal; and compensating 215 for any change
between the initial output signal and the subsequent output signal.
In one embodiment, the step of compensating 215 comprises
adjusting, if necessary, system gain to have a resulting output
signal deviate as little as possible from the stored initial output
signal. The system gain is adjusted by adjusting the detector(s)
voltage in the detection portion 130, 130', or with a digital
potentiometer, for example. In another embodiment, the step of
compensating 215 comprises providing data corresponding to the
sensitivity change for analysis. The step of providing comprises
storing the sensitivity change data in a file in a memory that is
made available to an array read data file that contains data
collected on a scanned array. Further, the step of providing the
sensitivity change data may comprise displaying whether a
sensitivity change was detected during a calibration that can be
correlated to particular array scans. The array data can be
corrected, if necessary, to compensate for the sensitivity changes
either manually or automatically, using the compensation portion
180 and/or the analysis portion 140.
[0047] The step of subsequently calibrating 210 is performed in the
field and may be repeated 217 periodically. Preferably, the first
subsequent calibration 210 is performed prior to a first scan of an
actual microarray under test in the field. In one embodiment, the
step of subsequently calibrating 210 can occur automatically at a
predetermined time, such as the first scan mentioned above. The
subsequent calibrations 210 may be repeated 217 manually or
automatically at certain predefined or predetermined time
intervals, such as once a day or once a week, for example. Other
examples include repeating 217 the step of subsequently calibrating
210 prior to performing the first scan of each different microarray
under test; and each time the power to the scanning system 100 is
turned from OFF to ON, or more or less frequently. How often the
subsequent calibration step 210 is repeated 217 may depend on a
trade-off between system performance level and instrument
throughput. Therefore, whether the step of subsequently calibrating
210 is repeated 217 and the frequency of the repetitions 217 are
not intended to limit the scope of the invention. What is important
is that the method 200 of the invention advantageously can repeat
217 the step of subsequently calibrating 210 in the field, either
manually or automatically.
[0048] The method 200 of calibrating the scanning system 100 in
accordance with the invention compensates for variations in the
detector sensitivity over time, so that the measurements taken
during a scan of a microarray under test are more accurate and
reliable. Moreover, the method 200 is readily automated, for
example with a computer or microprocessor in the compensation
portion 180 or in the optional analysis portion 140, such that the
scanning system 100 provides a substantially consistent accuracy
level. Still further, the method 200 provides monitoring and actual
calibration or adjustment capabilities, which advantageously
provides the user with absolute measurements results of the
microarray under test. The absolute measurement results are also
advantageously reproducible from one scanning system 100 to another
in accordance with the invention.
[0049] As mentioned above, the initial calibration step 201 may be
performed at the same location as the subsequently calibration step
210 is performed, or preferably, may be performed at a first
location remote from a second location where the subsequent
calibration step 210 is performed. Further, the subsequent
calibration step 210 may be initiated from a third location remote
from the second location of the self-calibrating scanning system
100. Still further, the third location may be the same or remote
from the first location where the initial calibration was
performed. The results of the initial calibration may be included
in the calibration portion 150 of the self-calibration scanning
system 100 when shipped to the user, or otherwise be readily
available at the time of the subsequent calibration step 210 at the
second location. The initial calibration results, or information
relating to the calibration results, can be forwarded (such as by
communication) to the self-calibrating scanning system 100 at the
second location. And the subsequent calibration results, or related
information, can be forwarded to the first or third location or
another remote location and be within the scope of the
invention.
[0050] A location is "remote" if it is at least a different
location, including but not limited to, a different room in a
building, a different building, a different city, different state
or different country, or if the location is at least one, at least
ten, or at least one hundred miles apart, for example.
"Communicating" information means transmitting the data
representing that information as electrical signals over a suitable
communication channel (for example, a private or public network).
"Forwarding" information refers to any means of getting that
information from one location to the next, whether by physically
transporting that information or otherwise (where that is possible)
and includes, at least in the case of data, physically transporting
a medium carrying the data or communicating the data. Moreover, as
used herein, the term "user" includes for example, a purchaser of
the system 100, an operator of the system 100, or an agent of the
user, purchaser, or operator, wherein an agent includes for
example, a parent or subsidiary organization, an employee or
officer of the user, purchaser or operator, or of any of their
parent or subsidiary organizations, a customer, a subcontractor,
vendor, an independent contractor of any of the aforementioned, or
the like.
[0051] Thus, there have been described a novel self-calibrating
scanning system 100 and method 200 of calibrating the scanning
system 100. It should be understood that the above-described
embodiments are merely illustrative of the some of the many
specific embodiments that represent the principles of the present
invention. Clearly, those skilled in the art can readily devise
numerous other arrangements without departing from the scope of the
present invention.
* * * * *