U.S. patent application number 09/839629 was filed with the patent office on 2002-10-24 for system and method for testing a biological sample.
This patent application is currently assigned to Sequenom, Inc.. Invention is credited to BHAKTA, KISHORCHANDRA, Opalsky, David, Yip, Ping.
Application Number | 20020155587 09/839629 |
Document ID | / |
Family ID | 25280251 |
Filed Date | 2002-10-24 |
United States Patent
Application |
20020155587 |
Kind Code |
A1 |
Opalsky, David ; et
al. |
October 24, 2002 |
System and method for testing a biological sample
Abstract
The method for testing a biological sample operates on a testing
system. The testing system generally comprises an instrument that
is configured to acquire data from a biological sample and a
processor. In performing the method for testing, the instrument
acquires data from the biological sample, and the processor
compares the acquired data to predefined data criteria. Responsive
to comparing the acquired data to the data criteria, the instrument
may be adjusted, and another data set acquired. In one disclosed
example of the testing system, a mass spectrometer acquires data
from a biological sample. The acquired data is compared to
predefined spectrum criteria. Responsive to the comparison, the
mass spectrometer may be directed to resample the biological sample
or proceed to another sample.
Inventors: |
Opalsky, David; (La Jolla,
CA) ; Yip, Ping; (San Diego, CA) ; BHAKTA,
KISHORCHANDRA; (San Diego, CA) |
Correspondence
Address: |
HELLER EHRMAN WHITE & MCAULIFFE LLP
4250 EXECUTIVE SQ
7TH FLOOR
LA JOLLA
CA
92037
US
|
Assignee: |
Sequenom, Inc.
|
Family ID: |
25280251 |
Appl. No.: |
09/839629 |
Filed: |
April 20, 2001 |
Current U.S.
Class: |
435/287.2 ;
702/19 |
Current CPC
Class: |
G16B 50/00 20190201;
G16B 50/20 20190201; G16B 20/00 20190201; G16B 20/20 20190201 |
Class at
Publication: |
435/287.2 ;
702/19 |
International
Class: |
G06F 019/00; G01N
033/48; G01N 033/50; C12M 001/34 |
Claims
What is claimed is:
1. A system for performing a biological assay, comprising: an
instrument configured to acquire biological data from a biological
sample; and a processor that communicates with the instrument, such
that the processor directs the instrument to acquire data
indicative of the biological sample, establishes a data spectrum
criteria, generates data parameters using the acquired data,
compares the data parameters to the spectrum criteria, adjusts the
instrument responsive to evaluating the data, and directs the
instrument to acquire other data for the biological assay.
2. The system according to claim 1 wherein the processor further
performs the step of receiving an assay design.
3. The system according to claim 1 further including a database in
communication with the processor, wherein the database holds assay
information.
4. The system according to claim 3 wherein the processor further
performs the steps of: receiving a portion of the assay information
from the database; and using the received portion of the assay
information to adjust the instrument.
5. The system according to claim 1 where the instrument is
configured as a mass spectrometer.
6. The system according to claim 1 where the processor is
configured as a computer device coupled to the instrument.
7. The system according to claim 1 where the processor is
configured as a computer device in the instrument.
8. The system according to claim 1 wherein the step of generating
the data parameters includes generating a data parameter indicative
of standard deviation.
9. The system according to claim 1 wherein the processor generates
the data parameters by generating a data parameter indicative of
statistical probability.
10. The system according to claim 1 wherein the processor generates
the data parameters by generating a data parameter indicative of
allele probability.
11. A system for testing a biological sample, comprising: an
instrument configured to acquire biological data from the
biological sample; a processor communicating to the instrument, the
processor performing steps comprising: directing the instrument to
acquire data indicative of the biological sample; evaluating the
acquired data; adjusting automatically the instrument responsive to
evaluating the data; and directing the instrument to acquire other
data indicative of the biological sample.
12. The system for testing a biological sample according to claim
11 wherein the processor further performs the steps comprising:
establishing a spectral criteria; and evaluating the acquired data
using the spectral criteria.
13. A system for performing a diagnostic assay using a set of
biological samples, comprising: an instrument configured to acquire
biological data from the biological samples; a processor
communicating to the instrument, the processor performing the steps
comprising: directing the instrument to acquire data indicative of
one of the biological samples in the set; evaluating the acquired
data; determining if the acquired data supports a diagnostic
conclusion; and directing the instrument to acquire data indicative
of a next one of the biological samples in the set responsive to
the determining step.
14. A system for performing a diagnostic assay using a set of
biological samples, the system comprising: a workstation that
communicates with an instrument that is configured to acquire
biological data from successive biological samples in the set, and
that controls the instrument to acquire data indicative of each
successive biological sample, determines if the instrument should
be adjusted in response to evaluating the acquired data from a set,
and directs the instrument to acquire other data indicative of the
biological sample responsive to the determination; and a database
server that stores the acquired data from the biological
samples.
15. The system according to claim 14, wherein the workstation
evaluates the acquired data, determines if the acquired data
supports a diagnostic conclusion, and directs the instrument to
acquire data indicative of a next one of the biological samples in
the set, responsive to the determination.
16. The system according to claim 14, wherein the workstation
includes an assay design controller that acquires assay design
specifications from the database server.
17. The system according to claim 14, wherein the workstation
includes an alignment controller that automatically aligns a laser
of the instrument on one of the biological samples and controls
movement of the sample in the instrument so as to receive
biological data from the instrument.
18. The system according to claim 17, wherein the workstation
includes a data controller that receives a data signal from the
alignment controller and makes the determination of directing the
instrument to acquire other data indicative of the biological
sample, in response to the determination.
19. The system according to claim 14, wherein the workstation is
constructed integrally with the instrument.
20. A method of performing a diagnostic assay using a set of
biological samples, the method comprising: directing an instrument
to acquire data indicative of one of the biological samples in the
set; evaluating the acquired data; determining if the acquired data
supports a diagnostic conclusion; and directing the instrument to
acquire data indicative of a next one of the biological samples in
the set responsive to the determination.
21. The method according to claim 20, further comprising:
establishing a data spectrum criteria; generating data parameters
using the acquired data; comparing the data parameters to the
spectrum criteria, and adjusting the instrument responsive to
evaluating the data.
22. The method according to claim 21, wherein generating the data
parameters includes generating a data parameter indicative of
standard deviation.
23. The method according to claim 21, wherein generating the data
parameters includes generating a data parameter indicative of
statistical probability.
24. The method according to claim 21, wherein generating the data
parameters includes generating a data parameter indicative of
allele probability.
25. The method according to claim 21, further including receiving
an assay design.
26. The method according to claim 21, further including storing the
acquired data from the biological samples of the set in a database
server.
27. The method according to claim 26, further including: receiving
a portion of the assay information from the database server; and
using the received portion of the assay information to adjust the
instrument.
Description
TECHNICAL FIELD
[0001] The field of the present invention is testing methods for
biological samples. In a particularly disclosed example, a system
having a processor is used to implement the disclosed testing
method.
BACKGROUND
[0002] Instruments, such as the mass spectrometer, are now
routinely used to assist in identifying components of a biological
sample. In particular, the MALDI time-of-flight (TOF) mass
spectrometer has proven particularly useful in making biological
determinations, such as genotyping or identifying single nucleotide
polymorphisms.
[0003] The MALDI TOF mass spectrometer generally operates by
directing an energy beam at a target spot on a biological sample.
The energy beam disintegrates the biological material at the target
spot, with the disintegrated component material being hurled toward
a measurement module. The lighter component material arrives at the
measurement module before the heavier component material. The
measurement module captures the component material, and generates a
data set indicative of the mass of the component material sensed.
Typically, the data set is generated as a two dimensional spectrum,
with the x-axis representing a mass number, and the y-axis
representing a quantity number.
[0004] The data, which is often presented as a data spectrum,
typically has peaks positioned on a generally exponentially
decaying baseline. Each peak should ideally represent the presence
of a component of the biological sample. Unfortunately, due to
chemical and mechanical limitations, the data spectrum is replete
with noise, so an accurate determination of biological components
is challenging. Indeed, it takes an experienced operator to
accurately read and interpret a data spectrum. However, the efforts
of even the best trained human operator can suffer from
inaccuracies and errors. Since the results derived from the data
spectrum are often used in health care decisions, mistakes can be
devastating. Therefore, operators are trained to make a
determination only when certain of the result. In such a manner, a
great number of tests result in no-calls, where the operator cannot
clearly identify a data result.
[0005] Accordingly, the use of mass spectrometers risks an
unacceptably large number of inaccurate calls if the operator is
applying a rather loose standard to the data spectrum.
Alternatively, the use of mass spectrometers becomes highly
inefficient if the operator discards a large number of tests due to
an inability to confidently make a call.
[0006] To assist the operator in making calls, the mass
spectrometer may provide a level of data filtering. Typically, the
data filtering attenuates a set magnitude of noise, thereby more
conspicuously exposing valid peaks. However, such a filtering
technique may actually mask important valid peaks, resulting in an
incorrect analysis.
[0007] Modern trends in biotechnology are taxing the capabilities
of instruments such as mass spectrometers and their operators. For
example, mass spectrometers are now being used to identify single
nucleotide polymorphisms (SNPs). However, SNPs may produce only
slight peaks on the data spectrum, which are easily missed by an
operator or buried in background noise. Further, mass spectrometers
are also now being used for multiplexing, where multiple gene
reactions may be present in a single sample. In such a manner, the
resulting peaks may be smaller, more difficult to identify, and
there may be more combinations of false readings. With such a
complicated data spectrum, it is becoming more difficult for an
operator to confidently determine if a valid peak exists for a
particular genetic component.
[0008] The mass spectrometer, therefore, provides a data spectrum
that is difficult for an operator to interpret. Even under the best
of conditions, the operator is likely to either make
identifications where the call should not have been made, or is
likely to discard good acquired data because of perceived
ambiguity. Accordingly, there exists a need for a more efficient
and accurate method and system for identifying a biological
sample.
SUMMARY OF THE INVENTION
[0009] It is therefore an object of the present invention to
provide a testing system and method that overcomes the deficiencies
in the prior art. It is also an object of the present invention to
provide for efficient and accurate biological identification.
[0010] The method for testing a biological sample in accordance
with the invention utilizes a testing system. The testing system
generally comprises a processor and an instrument that is
configured to acquire data from a biological sample. In performing
the testing method, the instrument acquires data from the
biological sample, and the processor compares the acquired data to
predefined data criteria. Responsive to comparing the acquired data
to the data criteria, the instrument may be adjusted, and another
data set acquired. In one disclosed example of the testing system,
a mass spectrometer acquires data from a biological sample. The
acquired data is compared to predefined spectrum criteria.
Responsive to the comparison, the mass spectrometer may be directed
to resample the biological sample or proceed to another sample.
[0011] Advantageously, the disclosed method and system for testing
a biological sample provides automated control of a mass
spectrometer. More particularly, the new testing method enables a
highly accurate determination of a biological sample with minimal
manual intervention. Accordingly, biological samples may be
identified and diagnostic tests performed with a degree of
precision, speed, and accuracy not available from known testing
systems.
BRIEF DESCRIPTION OF THE DRAWINGS
[0012] FIG. 1 is a block diagram of a testing system in accordance
with the present invention;
[0013] FIG. 2 is a flowchart of a testing process in accordance
with the present invention;
[0014] FIG. 3 is a flowchart of a testing process in accordance
with the present invention that illustrates automated control of a
testing instrument;
[0015] FIG. 4 is a flowchart of a testing process in accordance
with the present invention that illustrates over-sampling a
biological sample;
[0016] FIG. 5 is a flowchart of a testing process in accordance
with the present invention that illustrates acquiring data from
multiple samples to establish the presence of a biological
relationship; and
[0017] FIG. 6 is an illustration of a computer display showing
results from a testing system in accordance with the present
invention.
DETAILED DESCRIPTION
[0018] Referring now to FIG. 1, an example testing system 10 for
testing abilogical sample is illustrated. Generally, the testing
system 10 contains a real time (RT) workstation 12 which includes a
series of controllers that retrieve assay design parameters from
the database server 13 and directs the acquisition and processing
of data indicative of the biological sample from the mass
spectrometer 14. The processed data or genotyping results are then
downloaded into a directory in the database server 13.
[0019] With the testing system 10 generally disclosed, individual
components will now be described. The testing system 10 has a RT
workstation 12 that may be, for example, a computer system having
storage and computational components, including one or more
controllers. In a preferred embodiment, the RT workstation is made
up of one controller 30 which acquires assay design specifications
from the database server 13, includes another controller 31 which
automatically aligns the laser on the chip using an image system,
controls the motor movement of the assay substrate at the mass
spectrometer, and acquires the data signal directly from the mass
spectrometer, and includes another controller 32 that communicates
with the controller 31 by receiving a data signal and providing
instruction for additional data acquisition. Additional data
acquisition may be dependent on the quality of the data previously
obtained. The data is preferably stored on a local hard drive of
the RT workstation 12 until the results from all the samples are
compiled. The compiled data is stored in a directory in the
database server 13. The RT workstation 12 preferably has a display
16 for visually communicating test results and status information.
In a preferred embodiment, the RT workstation 12 is a computer,
such as an IBM compatible personal computer system, communicating
with the mass spectrometer using a known communication standard,
such as a parallel or serial interface. It will be appreciated that
the workstation and controllers may be alternatively embodied. For
example, the RT workstation 12 may be integral to the mass
spectrometer 14 or another system component, or the workstation and
controller 12 may be placed at a remote location from the mass
spectrometer. In such a manner the network topography, such as a
wide area network or a local area network, would provide a
communication path between the mass spectrometer 14 and the RT
workstation 12. Although the RT workstation 12 is preferably a
standalone computer device, it will be appreciated that one or more
of the controllers may be, for example, a microprocessor or other
programmable circuit device capable of performing a programmed
process.
[0020] The mass spectrometer 14 is preferably a MALDI
Time-of-Flight (TOF) instrument. Such a device is more fully
described in co-pending U.S. patent application Ser. No.
09/663,968, filed Sep. 19, 2000 and entitled, "SNP Detection
Method", and U.S. patent application Ser. No. 09/285,481, filed
Apr. 5, 1999 and entitled, "Automated Process Line", both of which
are incorporated herein by reference in their entirety. The mass
spectrometer 14 is configured with an interface to communicate with
the workstation controller 12. The interface preferably conforms to
a known data communication standard, for ease of connection.
Although a single interface may enable the controller 12 to both
receive data from the mass spectrometer 14 and send instructions to
the mass spectrometer 14, two or more separate interfaces may be
used. Although the preferred test system 10 incorporates a MALDI
TOF mass spectrometer, it will be appreciated that other types of
analytical instruments may be used.
[0021] The testing system 10 may provide the database server 13
with one or more databases, such as database 18, database 19,
database 20, database 21 and database 22 stored in direct access
storage devices. It will be appreciated that other forms of data
storage may be used. However, a structured database provides a
convenient format for storing and retrieving data. In a preferred
embodiment one of the databases, such as database 18, stores assay
design information, a database 19 stores genotyping profiles, a
database 20 stores allelotyping profiles, database 21 stores sample
identification information, while the other database 22 stores test
results for later analysis. It will be appreciated that fewer or
more databases may be used to store assay and test information. The
database server 13 may also contain one or more controllers such as
controller 23 and controller 24. In a preferred embodiment the
controller 23 monitors the data acquisition of the individual
samples on the assay substrate or chip. Once the data is received
from all samples in the assay, the data monitoring controller 23
downloads all or part of the assay information and stores the
information in a directory in the test results database 22. The
controller 24 imports the data into a directory in the results
database 22.
[0022] The RT workstation 12 has sufficient processing ability to
extract assay design information from the assay design database 18,
and to convert the assay design information into a format for
providing specific directions to the mass spectrometer 14. For
example, the controller may access the database 18 and request a
specific assay design. The specific assay may be set up to provide
a microtiter plate with hundreds, or even thousands, of samples on
each plate. The test may require that samples be tested in a
specific order, and based upon the result from previous tests, the
order may be adjusted, or some samples may even be eliminated from
the assay. The RT workstation receives the assay design information
and converts the assay design information into commands for the
mass spectrometer 14. Upon starting the assay, the RT workstation
12 sends initialization commands to the mass spectrometer 14
consistent with the assay design.
[0023] Extracting an assay design from a database and generating
mass spectrometer commands may be a time consuming and processor
intensive operation. It would be particularly undesirable for the
extraction process to interfere with the more real-time control of
the mass spectrometer. Accordingly, it is preferred that the RT
workstation 12 perform a database extraction process, and database
storage functions, as background tasks, or at a time when such
tasks will not materially interfere with the more real-time control
of the mass spectrometer 14. As used herein, real-time control
refers to the ability of the RT workstation 12 to receive data from
the mass spectrometer 14, process the data, and provide command
direction to the mass spectrometer in an automated and efficient
manner.
[0024] The RT workstation 12 defines physical map of the biological
samples on the assay plate or chip by manual input of the
information by the operator or an automated scanning system such as
a bar code reader.
[0025] A mass spectrometer 14 receives the biological sample for
analysis and generates an electrical data signal representative of
genotype information associated with the sample tested under
direction from the real time workstation 12. The instrument is
initialized when it is provided with specific data acquisition
parameters, either manually or in a default mode. The acquisition
parameters may include the number of laser shots per spot, the
maximum number of raster per sample, and voltage, delay time,
calibration constants and other parameters that will be well-known
to those skilled in the art. The mass spectrometer is initialized
according to test assay parameters, and acquires data indicative of
the biological samples. More particularly, the data acquired by the
mass spectrometer is typically in the form of an electronic data
spectrum. The electronic data spectrum can be retrieved by the RT
workstation.
[0026] Biological samples are analyzed when the RT workstation 12
directs the automatic alignment of the mass spectrometer laser on
assay surface or chip using an imaging system and controls movement
of the laser from sample to sample and assay surface to assay
surface when multiple assay surfaces or chips are held in a
multi-component holder.
[0027] Biological or genotyping information is acquired directly
from the mass spectrometer 14 by the RT workstation 12. The signal
is converted into amass data spectrum by the RT workstation 12
where a genotype is determined. If the sample genotype cannot be
called, the RT workstation 12 will recognize the situation and may
direct an adjustment to the mass spectrometer 14. For example, if
the acquired spectrum has an unacceptably high signal to noise
ratio, the workstation controller 12 may direct the mass
spectrometer 14 to test the same sample again, but may adjust the
mass spectrometer 14 to direct its beam at a different spot on the
sample, or may select alternative power settings or measurement
filters. In another example, the controller 12 may direct the mass
spectrometer 14 to take a series of data sets from the same sample
until the standard deviation in the aggregate results achieves a
desired degree of certainty. It should be understood that, even
though the same sample may be tested multiple times, each test will
be taken from a unique spot on the sample.
[0028] Referring now to FIG. 2, a method of testing a biological
sample is shown. The method of testing first predefines spectrum
criteria that predicts the presence of a biological relationship in
block 21. The predefined spectrum criteria will vary depending on
the assay being run. For example, the spectrum criteria may be set
to assure a minimum allelic ratio is exceeded. In this regard, the
spectrum criteria may be set to reject acquired data where the
allelic ratio is below a threshold, such as 5%. In another example,
the presence of specific markers may be required to validate
acquired data. In another example, the spectrum criteria may
require that a peak exceed a signal to noise figure before
accepting the acquired data as valid. Further, statistical methods
may be applied to the acquired data, or sets of acquired data, to
determine if a particular peak is statistically signification.
Using such a statistical method may dramatically increase the
accuracy of calling the composition of a biological sample. U.S.
application Ser. No. 09/663,968 filed Sep. 19, 2000 teaches a
specific example of a statistical method as applied to acquired
spectrum data. It will be appreciated that the spectrum criteria
can be defined in numerous ways consistent with the teaching of
this application.
[0029] With the spectrum criteria predefined, block 22 shows that
the assay design is defined, and then preferably stored in a
database for use in controlling the instrument. In a preferred
embodiment, the instrument is a MALDI TOF mass spectrometer. It
will be appreciated that other instruments may be substituted. The
defined assay design is used to generate the initial settings for
the instrument, and then is further used to direct the instrument
during the assay test.
[0030] Biological samples are then positioned in block 23 for test
in the instrument. The samples are positioned preferably on a
holder such as a microtiter plate. It will be appreciated that
other types of holders, such as test tubes or chips, may be
substituted for a microtiter plate holder. Although it is more
convenient to place all samples for one assay on a single holder,
samples for a single assay may be placed on multiple holders.
[0031] The holder is positioned in the instrument, as indicated in
block 24. The holder may be manually positioned, or may be
positioned under robotic control. If the holder is robotically
controlled, then information extracted from the assay design may be
used to direct the robotic control to place the proper holder in
the instrument. If manually positioned, a visual display may be
used to assist the human operator in identifying and verifying the
proper holder.
[0032] Blocks 25-28 represent the real time control of the
instrument and will be described further below. This real time
control enables the automated and efficient operation of the
instrument, and provides accuracies and repeatabilities in test
results that are not available in known systems.
[0033] In block 25, the instrument acquires a data set from a
biological sample. In a preferred embodiment, the acquired data is
in the form of an acquired data spectrum. In the exemplary system
described in the '968 Application, the data set is generated by
first finding height of each peak, then extrapolating noise
profile, and finding noise of each peak, next calculating signal to
noise ration, and finding residual error, and calculating and
adjusting signal to noise ratio, and developing a probability
profile, and determining peak probabilities, and determining
allelic penalty, and adjusting peak probability by allelic penalty,
and calculating genotype probabilities, and testing ratio of
genotype probabilities.
[0034] The acquired data is evaluated in block 26. In a preferred
embodiment, the acquired data is compared against the spectrum
criteria previously defined. As described above, this comparison
can be, for example, a comparison of peak strength, peak position,
markers, s/n ratio, allelic ratio, or a statistical calculation.
Further, the comparison may be multi-dimensional, for example,
requiring first that a particular marker be located and then
testing that an appropriate signal to noise ratio exists. It will
also be appreciated that the comparison step may use data from
multiple acquired data sets, for example, to calculate the standard
deviation for the group. Accordingly, the comparison will compare
the standard deviation in the group of data sets to determine if
the results should be derived from the newly acquired data.
[0035] Responsive to the comparison, the workstation controller
adjusts the instrument in block 27. For example, if the signal to
noise ratio was too low in a first data set, the instrument may be
adjusted to test the same sample, but at a different spot on the
sample. By moving to a new target spot, new data may be acquired
for the same sample. In testing the new spot, it is quite possible
that different or better analytical results may be found. Thus,
taking a reading at a second spot may enable making an analytical
call on a sample when it was not possible with only a single spot
test. Further, testing additional spots on an individual sample may
permit the calculation of aggregate results with a lower error rate
than relying solely on a single test spot. By automating the
evaluation of the acquired data and control of the instrument, the
overall assay test can be manipulated to provide a requisite level
of accuracy and tolerance. Accordingly, the maximum number of
samples can be accurately called for a particular assay, but yet
time and system resources are not wasted by testing more spots than
necessary.
[0036] After the instrument is adjusted and set to acquire a next
data set, the method returns to block 25 to acquire the next data
set. As described above, the next data set may be for the same
sample, or the instrument may have been adjusted to the next
sample. After testing is completed, processing moves to block
28.
[0037] Block 28 shows that the results from the acquired data are
analyzed to determine the presence of an object biological
relationship. For example, the assay may be attempting to locate
particular single nucleotide polymorphisms (SNPs), or may be allele
typing, or may be genotyping. Irrespective of the particular
biological relationship searched for, the relative success of the
search may be used by the FIG. 2 testing method in directing
further data acquisitions. For example, if in a multiple sample
assay, the biological relationship is ruled out after only the
first sample, then the method can be directed to skip testing the
rest of the samples in the assay and move on. In another example,
if after testing multiple samples for a particular assay the
results are still ambiguous, block 28 can be used to determine if
the ambiguity can be removed by increasing the certainty of the
results for a particular sample. If so, the test can be directed by
the workstation to automatically take additional data acquisitions
and attempt to salvage the assay. Without such an automated and
intelligent process, the assay would be rejected. Accordingly, the
FIG. 2 testing method provides a higher level of calls, and a
higher level of call certainty than with known testing methods.
[0038] Referring now to FIG. 3, another method of testing a
biological sample is shown. The FIG. 3 testing method 40 generally
has a control loop 42, an initialization loop 41, and a results
loop 43. The control loop 42 is responsible for acquiring data
sets, comparing the data sets to predefined spectrum criteria, and
adjusting the instrument responsive to the evaluation of the
acquired data. In this regard, the control loop must operate
efficiently enough to permit the timely operation of the overall
test system. Therefore, certain of the setup and storage functions
have been off-loaded to the background loops 41 and 43. It will be
appreciated that more or less functionality may be placed in the
background loops to accommodate different response times needed in
the control loop 42.
[0039] The initialization loop 41 is a background loop that permits
storage of assay design and plate information in block 44.
Preferably, the assay design and plate information is stored in a
database form. Preferably, the database of assay design and plate
information may be used by multiple test systems, and may be
accessed remotely. In such a manner a remote researcher may define
an assay in a single database, and that newly defined assay may be
operated on multiple test systems.
[0040] Since extracting and converting the assay information into
control information is a time consuming process, the extraction
process is performed in block 45. Of course, it will be appreciated
that as typical computer workstation computational powers increase,
it may be desirable to have the extraction process made a part of
the control loop 42. Since the extracting step is preferably a
background step, the extraction process may be performed for a next
assay while the control loop 42 is actively performing an assay.
Thus, when the control loop has finished an assay, the extracted
information from block 45 may be sent to block 51 to start the
control loop 42 for a next assay.
[0041] The information from block 45 is received in block 51, where
the information is used to initialize the instrument. In a
preferred embodiment, the instrument is a MALDI TOF mass
spectrometer. The initialization commands may include identifying
the first sample to test, the proper power settings, and the
desired filtering for the data.
[0042] A sample is selected for test in block 52, and data is
acquired from the test sample in block 53. The acquired data may be
sufficiently processed to determine target characteristics for the
acquired data. For example, if signal to noise ratio is an
important indication of test quality, then a signal to noise ratio
may be calculated for the acquired data. More particularly, the
acquired data will be processed to facilitate comparison with
predefined spectrum criteria.
[0043] The predefined spectrum criteria, as previously discussed,
define the analytical characteristics for good data. In block 54,
the acquired data is compared to the predefined spectrum criteria.
If the acquired data is good, a "YES" outcome at block 54, then the
acquired data is further processed in block 57 to extract
biological information, and the data is formatted and displayed in
block 58. However, if the acquired data is not good, a "NO" outcome
at block 54, then block 55 asks if the maximum number of spots have
been shot for this sample. For example, a typical mass spectrometer
can take a maximum of about 15 to 20 shots on any given sample. To
assure the integrity of the test, it may be advisable to set the
maximum to a safe number, such as 10. The sample is not further
processed if the maximum shots have been exceeded. Thus, if less
than 10 spots have been shot, a "NO" outcome at block 55, then the
instrument is adjusted to a new spot in block 56, and data is
acquired on the new spot in block 53. In block 54, the newly
acquired data is compared to the spectrum criteria. Alternatively,
block 54 can use aggregated data from multiple test spots to
determine if the aggregated data is good.
[0044] Once a sample has been judged good or bad, then block 59
asks if there are more samples in the assay. If so, a "YES" outcome
at block 59, then the instrument is adjusted in block 61 to shoot
the next sample. If all the samples have been tested, a "NO"
outcome at block 59, then the control loop 42 resets and a next
assay is initiated.
[0045] When the control loop 42 is complete, then the results from
the assay are passed to the background results loop 43. The results
loop 43 may perform additional post processing on the data in block
63, which may include a manual review of the results. The data and
results may then be stored in block 65. Preferably, the data and
results are stored in a database that is accessible from remote
locations so a remote researcher or other test operators may review
the results.
[0046] Referring now to FIG. 4, another testing method 70 is
illustrated. The testing method 70 allows an assay designer to
establish a minimum standard for each biological sample in block
71. More particularly, the testing method 70 is directed to
increasing the confidence in the results from each sample. As
discussed above, a typical mass spectrometer can take a data set
from multiple spots on a single biological sample. The testing
method 70 enables the test to dramatically increase the confidence
for each sample, while minimizing the number of testing samples
that must be acquired.
[0047] In the testing method 70, a biological sample is selected in
block 72, and a data set is acquired in block 73. In block 74, the
acquired data is evaluated against the data criteria set for the
sample. For example, the data criteria may expect a signal to noise
ratio to exceed a floor value. In this regard, each data set
acquired for a particular sample is compared against the data
criteria. Alternatively, data collected from multiple shots in the
same sample may be used in the comparison. For example, the data
criteria may require that the standard deviation between spots on
the same sample not exceed a particular value. Thus the comparison
step could include determining the standard deviation for all spots
in the single sample to determine if confidence is sufficiently
high to call the sample. It will be appreciated that the comparison
step may entail a wide range of analytical and algorithmic
calculations, either on individual data sets or aggregates of data
sets.
[0048] Importantly, the testing method 70 permits setting the data
criteria in a manner that minimizes the number of data
acquisitions. For example, the data criteria could be accept a
sample when a single data set has a signal to noise ratio meeting
one level, or meeting a lower level for aggregate data sets. Thus,
a single strong reading would be sufficiently robust, and multiple
shots would not be needed on that sample. In a similar manner, the
comparison could be set to accept sample data if the standard
deviation between two successive shots is less than 5%, or accept
the data if the standard deviation is less than 7% for 3 shots, or
less than 10% for 4 or more shots. Such flexible data criteria
permit the assay designer to set a high degree of confidence with a
minimum of data readings. Accordingly, the test system 70 operates
at high degree of efficiency and accuracy as compared to known
systems.
[0049] Once the data criteria have been met, a "YES" outcome at
block 75, the results are stored in block 76, preferably in a
database, and the instrument adjusted to move to the next sample in
block 77. Accordingly, a new sample is selected in block 72.
[0050] If the data criteria have not yet been met, a "NO" outcome
at block 75, then block 78 asks if there are any remaining spots on
the sample. If unshot spots exist, a "NO" outcome at block 78, the
instrument is adjusted in block 79 to acquire data from a new spot,
and the data is acquired in block 73. If the data criteria are not
met, and there are no unshot spots, a "YES" outcome at block 78,
then that particular sample is rejected, and the test moves on to a
new sample.
[0051] Referring now to FIG. 5, a diagnostic testing method 100 is
disclosed. The diagnostic testing method is directed to finding a
relationship among a set of samples that proves a particular
biological relationship exists. For example, certain clinical
diagnostics may look at multiple samples from an individual before
identifying that the individual is at risk for a particular
disease. The diagnostic testing method enables such a clinical
diagnosis at a level of certainty and a level of efficiency not
available in known systems.
[0052] The diagnostic testing method 100 receives an assay design
and relationship criteria at block 101. The relationship criteria
define the range of values and certainties where a relationship can
be identified. In a preferred embodiment, the relationship is the
likelihood that a particular individual will contact a particular
disease. Due to the seriousness of the identification, it is
crucial that such an identification be made only under the most
confident conditions. Accordingly, known systems have required
redundancies and over-testing to build confidence sufficient to
make such a drastic announcement regarding an individual's
health.
[0053] In block 102, a set of samples is identified for testing for
the relationship. As there are likely several, even tens of samples
to test, it is also likely that the set of samples may be present
on multiple holders. Thus the testing method 100 should account for
instructing an operator or a robot to deliver and load different
holders as needed.
[0054] A particular sample is selected from the set in block 103,
and data acquired from the sample in block 104. The acquired data
is evaluated against the relationship criteria in block 105. In a
preferred embodiment, testing system 100 incorporates aspects of
previously discussed testing system 70 to increase the confidence
that the results from an individual sample are robust. The
previously discussed method of over-sampling a single biological
sample can dramatically increase the confidence in the data from a
single sample.
[0055] In block 106, the acquired data is evaluated to determine if
it supports the object relationship. If the data does not support
the object relationship, a "NO" outcome, then it is reported that
the relationship does not exist in the set in block 111, and the
test moves on to the next set of samples in block 110. Due to the
high degree of confidence in sample results, it is possible for the
testing method 100 to reject the entire sample and move to the next
set. Accordingly, the testing method 100 may operate
efficiently.
[0056] If block 106 finds that the data does support the
relationship, a "YES" outcome, then block 107 asks if the data
acquired thus far conclusively proves the relationship exists. If
enough data has been collected, and the relationship proved, a
"YES" outcome at block 107, then block 112 reports that the
relationship exists, and the test moves on to the next set of
samples. Thus, the testing method 100 only takes the necessary
number of data acquisitions to call a diagnosis, enabling efficient
operation.
[0057] If block 107 finds that the collected data does not prove
the biological relationship, a "NO" outcome, then block 108 asks if
there are any more samples to be tested in the sample set. If no
more samples exist, a "NO" outcome at block 108, then block 113
reports that the relationship could not be proved, and the test
moves on to the next sample set. If there are more samples to be
tested, then the instrument is adjusted to the next sample in block
109, and data acquired from the new sample in block 104.
[0058] FIG. 6 shows an example user display 130 for a test system.
The user display 130 is preferably presented on a computer monitor
connected to an IBM compatible computer system. In a preferred
embodiment, the user display 130 is presented using a
Microsoft.RTM. Windows.RTM. compatible display program.
[0059] The user display 130 has a spectrum window 132 for
displaying a data spectrum of the most recently acquired data set.
The spectrum window 132 enables an operator to watch, in near
real-time, the data being collected by the instrument. If multiple
spots are shot for a particular sample, each successive data
spectrum may be displayed in a different color so variations
between spots is easily identified.
[0060] The user display also has a holder representation 134. The
holder representation of FIG. 6 shows individual sample wells in a
microtiter plate. For example, a well representation shows the
wells in a physical microtiter plate holder. As each well is
tested, the well representation turns a different color base on
whether the sample was accepted or rejected. A results display 138
shows assay data and a results quality display 140 shows run data
for data sets. Accordingly, as the test progresses, an operator may
identify certain systemic problems. For example, if all wells in a
particular column fail, then there may be a problem with the
syringe used to fill that particular column.
[0061] The user interface 130 also has a sample view 136 which
shows a live image of the sample currently being tested. With this
view, an operator may visually identify spots that have been used
within a particular sample. Also, the operator may be able to
identify certain systemic problems, such as a too small sample
being deposited into certain wells.
* * * * *