Quality assurance for high-throughput bioassay methods

• US 7,333,895 B2
• Filed: 07/28/2003
• Issued: 02/19/2008
• Est. Priority Date: 07/29/2002
• Status: Expired due to Fees

• Current Assignee: Vermillion, Inc.
• Original Assignee: Correlogic Systems, Inc. (Aspira Women's Health, Inc.)
• Inventors: Coleman, Timothy A., Levine, Peter J., Hitt, Ben A.
• Primary Examiner(s): Clow; Lori A.
• Application Number:
  US10/628,135
• Publication Number:
  US 20040058372A1
• Time in Patent Office: 1,667 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

The invention relates to a method of quality assurance/quality control for high-throughput bioassay processes. The method permits monitoring of an entire system for obtaining spectral data from biological samples. Generally, the method includes generating a bioassay process model, comparing a test sample against the bioassay process model. The bioassay process model may be based on the position of a centroid in n-dimensional space. The comparing may include comparing the location of a centroid associated with the test model against the centroid associated with the control model to determine the distance between the two centroids. By generating a trend plot of the distance between the centroid associated with the test sample and the centroid associated with the control model, overall system performance may be monitored over time.

Claims

1. A method of evaluating the results from a bioassay process, the method comprising:

preparing a mixture of molecules;

dividing the mixture of molecules into a plurality of aliquots;

preserving the plurality of aliquots;

retrieving a first aliquot, the first aliquot being a control aliquot;

obtaining data from the control aliquot using the bioassay process, the data including values for n features, which collectively define a control centroid in an n-dimensional space;

subsequently retrieving a second aliquot, the second aliquot being a test aliquot;

obtaining data from the test aliquot using the bioassay process, the data including values for the n features, which collectively define a test centroid in the n-dimensional space; and

determining whether the displacement in the n-dimensional space of the test centroid exceeds a predetermined distance from the control centroid as an indication of whether the bioassay has generated unreliable results.

2. The method of claim 1, wherein the obtaining data from the control aliquot using the bioassay process includes using an electrospray process.

3. The method of claim 1, wherein the obtaining data from the control aliquot using the bioassay process includes using a biochip.

4. The method of claim 1, wherein the obtaining data from the control aliquot includes:

selecting a subset of n features from a plurality of features associated with the control aliquot.

5. The method of claim 1, wherein each feature is a mass-to-charge ratio and the value of each feature is a magnitude.

6. The method of claim 1, wherein the retrieving a first aliquot includes retrieving two or more aliquots.

7. A method of evaluating the results from a bioassay process, comprising:

retrieving a test aliquot of a preserved molecular mixture;

analyzing data from the test aliquot using a bioassay process;

comparing a test set of features of the test aliquot with a control set of features based on a control aliquot from the preserved molecular mixture, the control set of features defining a control centroid in an n-dimensional space, the test set of features defining a test centroid in the n-dimensional space, the test set of features of the retrieved mixture being the same as the control set of features; and

determining whether the position of the test centroid is greater than a predetermined displacement from the control centroid as an indication of whether the bioassay has generated unreliable results.

8. The method of claim 7, wherein said features are mass-to-charge ratios and wherein said comparing includes comparing magnitudes of each of the test set of mass-to-charge ratios with the magnitudes of the control set of mass-to-charge ratios.

9. The method of claim 7, wherein the analyzing data from the test aliquot using a bioassay process includes analyzing data from the test aliquot using an electrospray process.

10. The method of claim 7, wherein the analyzing data from the test aliquot using a bioassay process includes analyzing data from the test aliquot using a biochip.

11. The method of claim 7, wherein the predetermined displacement is two standard deviations.

12. A method for evaluating the results from a bioassay that generates spectral data, comprising:

providing a location in an n-dimensional space of a control centroid associated with control spectral data generated from a first aliquot of a prepared mixture of molecules;

generating test spectral data from a second aliquot of the mixture;

computing a location in the n-dimensional space of a test centroid associated with the test spectral data;

comparing the test centroid to the control centroid to determine the displacement in n-dimensional space of the test centroid from the control centroid; and

determining whether the test centroid is greater than a predetermined displacement from the control centroid as an indication of whether the bioassay has generated unreliable results.

13. The method of claim 12, wherein the mixture of molecules includes a mixture of isolated peptides.

14. The method of claim 12, wherein the mixture of molecules includes molecules that are water soluble and have a molecular weight greater than 400.

15. The method of claim 12, wherein the bioassay includes an electrospray process.

16. The method of claim 12, wherein the bioassay includes a biochip-based process.

17. The method of claim 12, wherein the determining whether the test centroid is within a predetermined distance includes one of:

determining that the bioassay process is functioning properly when the test centroid is within or is equal to the predetermined distance from the control centroid, and determining that the bioassay process is not functioning properly when the test centroid is beyond the predetermined distance from the control centroid.

18. The method of claim 12, wherein each of the features is a mass-to-charge ratio.

19. The method of claim 12, wherein the mixture of molecules is a biological sample.

20. The method of claim 12, wherein the spectral data are generated by a mass spectrometer.

21. The method of claim 12, further comprising repeating the generating test spectral data and computing a location for multiple aliquots of the mixture of molecules over time to monitor performance of the bioassay.

22. The method of claim 12, wherein the mixture of molecules is selected from the group consisting of naturally-occurring and non-naturally-occurring molecules.

23. A method for evaluating the results from a bioassay that generates spectral data, comprising:

providing a location in an n-dimensional space of a control centroid associated with control spectral data generated from a first aliquot of a prepared mixture of molecules;

providing a location in an n-dimensional space of a test centroid associated with test spectral data generated from a second aliquot of the prepared mixture of molecules;

comparing the test centroid to the control centroid to determine the displacement in n-dimensional space of the test centroid from the control centroid; and

determining whether the displacement in n-dimensional space of the test centroid exceeds a predetermined distance from the control centroid, wherein the determining whether the displacement in n-dimensional space of the test centroid exceeds a predetermined distance from the control centroid includes one of;

indicating to a user that the bioassay process is functioning properly when the test centroid is within or is equal to the predetermined distance from the control centroid, and indicating to a user that the bioassay process is not functioning properly when the test centroid is beyond the predetermined distance from the control centroid.