System and method for temperature gradient capillary electrophoresis

• US 20050064400A1
• Filed: 11/05/2002
• Published: 03/24/2005
• Est. Priority Date: 10/18/2001
• Status: Abandoned Application

• Current Assignee: Spectrumedix LLC
• Original Assignee: Spectrumedix LLC
• Inventors: Li, Qingbo, Guo, Zhiyong, Liu, Zhaowei
• Application Number:
  US10/287,808
• Publication Number:
  US 20050064400A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2565/125 Electrophoretic separation

Abstract

The present invention relates to a method for determining the presence of a mutation in a first sample comprising first polynucleotides. The reference sample comprises reference polynucleotides. The first sample and a reference sample are subjected to electrophoresis in the presence of at least one intercalating dye. During electrophoresis the temperature of the first sample and the reference sample is changed by an amount sufficient to change an electrophoretic mobility of at least one of the first or reference polynucleotides. Fluorescence intensity data are obtained. The fluorescence intensity data are indicative of the presence of the first and reference polynucleotides. The data are processed to determine the presence of mutation in the first polynucleotides.

Claims

1. A system for determining the presence of a mutation in at least one sample polynucleotide, comprising:

a processor configured to at least;

receive (1) at least a first set of sample electrophoresis data indicative of a temperature gradient electrophoresis (TGE) separation of at least one sample polynucleotide, and (2) at least a first set of reference electrophoresis data indicative of a TGE separation of at least one reference polynucleotide; and

process at least a subset of the first set of sample electrophoresis data and at least a subset of the first set of reference electrophoresis data to prepare a set of result data corresponding to the first set of sample electrophoresis data, wherein the set of result data includes data indicative of whether a sample polynucleotide of the first set of sample electrophoresis data includes a mutation.

2. The system of claim 1, wherein the system further includes a display and the processor is configured to display result data corresponding to the first set of sample electrophoresis data.

3. The system of claim 2, wherein the displayed result data includes at least one indicium of whether a sample polynucleotide of the first set of sample electrophoresis data includes a mutation.

4. The system of claim 3, wherein displayed result data corresponding to the first set of sample electrophoresis data includes an indicium of whether the first set of sample electrophoresis data includes more than one sample polynucleotide.

5. The system of claim 4, wherein displayed result data corresponding to the first set of sample electrophoresis data includes an indicium corresponding to each sample polynucleotide of the first set of sample electrophoresis data, each indicium being indicative of whether a respective one of the sample polynucleotides includes a mutation.

6. The system of claim 3, wherein the processor is configured to at least:

receive at least a second set of sample electrophoresis data;

process at least a subset of the second set of sample electrophoresis data to prepare a set of result data corresponding to the second set of sample electrophoresis data; and

display result data corresponding to the second set of sample electrophoresis data, the displayed result data including an indicium of whether a sample polynucleotide of the second set of sample electrophoresis data includes a mutation.

7. The system of claim 1, wherein the processor is configured to at least:

receive at least a second set of reference electrophoresis data;

receive user input defining members of a first group of sets of sample electrophoresis data for processing with respect to the first set of reference electrophoresis data, the first group of sets including the first set of sample electrophoresis data;

receive user input defining members of a second group of sets of sample electrophoresis for processing with respect to the second set of reference electrophoresis data;

process at least a subset of each member of the first group and at least a subset of the first set of reference electrophoresis data to prepare respective sets of result data corresponding to members of the first group; and

process at least a subset of each member of the second group and at least a subset of the second set of reference electrophoresis data to prepare respective sets of result data corresponding to members of the second group.

8. The system of claim 7, wherein the system includes a display and the processor is configured to simultaneously display result data corresponding to members of the first and second groups of sets of sample electrophoresis data.

9. The system of claim 8, wherein the displayed result data includes plurality of indicia, each of the indicia indicative of whether a sample polynucleotide of a respective one of the sets of sample electrophoresis data includes a mutation.

10. The system of claim 1, wherein the processor is configured to normalize at least one subset of the first set of sample electrophoresis data and the subset of the first reference electrophoresis data.

11. The system of claim 1, wherein the processor is configured to receive user input indicative of a size of the subset of the first set of sample electrophoresis data and a size of the subset of the first set of reference electrophoresis data and to process the subsets of electrophoresis data to prepare the result data corresponding to the first set of sample electrophoresis data.

12. The system of claim 1, further comprising a capillary array electrophoresis system configured to obtain sample electrophoresis data and reference electrophoresis data.

13. The system of claim 1, wherein the processor is configured to write the result data to a storage medium.

14. A computer-readable medium comprising executable software code, the code for determining the presence of a mutation in at least one sample polynucleotide, comprising:

code to receive (1) at least a first set of sample electrophoresis data indicative of a temperature gradient electrophoresis (TGE) separation of at least one sample polynucleotide, and (2) at least a first set of reference electrophoresis data indicative of a TGE separation of at least one reference polynucleotide; and

code to process at least a subset of the first set of sample electrophoresis data and at least a subset of the first set of reference electrophoresis data to prepare a set of result data corresponding to the first set of sample electrophoresis data, wherein the set of result data includes data indicative of whether a sample polynucleotide of the first set of sample electrophoresis data includes a mutation.

15. The computer-readable medium comprising executable software code of claim 14, wherein the code includes code to display result data corresponding to the first set of sample electrophoresis data.

16. The computer-readable medium comprising executable software code of claim 15, wherein the code includes code to display at least one indicium of whether a sample polynucleotide of the first set of sample electrophoresis data includes a mutation.

17. The computer-readable medium comprising executable software code of claim 16, wherein the code includes code to display an indicium of whether the first set of sample electrophoresis data includes more than one sample polynucleotide.

18. The computer-readable medium comprising executable software code of claim 17, wherein the code includes code to display an indicium corresponding to each sample polynucleotide of the first set of sample electrophoresis data, each indicium being indicative of whether a respective one of the sample polynucleotides includes a mutation.

19. The computer-readable medium comprising executable software code of claim 16, comprising:

code to receive at least a second set of sample electrophoresis data;

code to process at least a subset of the second set of sample electrophoresis data to prepare a set of result data corresponding to the second set of sample electrophoresis data; and

code to display result data corresponding to the second set of sample electrophoresis data, the displayed result data including an indicium of whether a sample polynucleotide of the second set of sample electrophoresis data includes a mutation.

20. The computer-readable medium comprising executable software code of claim 14, comprising:

code to receive at least a second set of reference electrophoresis data;

code to receive user input defining members of a first group of sets of sample electrophoresis for processing with respect to the first set of reference electrophoresis data, the first group of sets including the first set of sample electrophoresis data;

code to receive user input defining members of a second group of sets of sample electrophoresis for processing with respect to the second set of reference electrophoresis data;

code to process at least a subset of each member of the first group and at least a subset of the first set of reference electrophoresis data to prepare respective sets of result data corresponding to members of the first group; and

code to process at least a subset of each member of the second group and at least a subset of the second set of reference electrophoresis data to prepare respective sets of result data corresponding to members of the second group.

21. The computer-readable medium comprising executable software code of claim 20, comprising code to simultaneously display result data corresponding to members of the first and second groups of sets of sample electrophoresis data.

22. The computer-readable medium comprising executable software code of claim 21, comprising code to display a plurality of indicia, each of the indicia indicative of whether a sample polynucleotide of a respective one of the sets of sample electrophoresis data includes a mutation.

23. The computer-readable medium comprising executable software code of claim 14, comprising code to normalize at least one of the subset of the first set of sample electrophoresis data and the subset of the first reference electrophoresis data and to process the normalized data.

24. The computer-readable medium comprising executable software code of claim 14, comprising code to receive user input indicative of a size of the subset of the first set of sample electrophoresis data and a size of the subset of the first set of reference electrophoresis data and to process the subsets of electrophoresis data to prepare the result data corresponding to the first set of sample electrophoresis data.

25. A method for interacting with a computer to determine the presence of mutation in at least one sample polynucleotide, comprising the steps of:

executing an application which includes one or more windows having one or more controls;

manipulating at least one of said controls to define members of a group of sample electrophoresis data;

manipulating at least one of said controls for defining a set of reference electrophoresis data to be used for processing members of the group;

manipulating at least one of said controls to select a first subset of each member of the group and a first subset of the reference electrophoresis data; and

manipulating at least one of said controls to execute code configured to process the first subsets of the members of the group and the first subset of the set of reference electrophoresis data to prepare result data corresponding to each member of the group, wherein the result data corresponding to each member of the group includes data indicative of whether a first sample polynucleotide of the corresponding sample electrophoresis data includes a mutation.

26. The method of claim 25, further comprising the steps of:

manipulating at least one of said controls to select a second subset of each member of the group and a second subset of the reference electrophoresis data; and

manipulating at least one of said controls to execute code configured to process the second subsets of the members of the group and the second subset of the set of reference electrophoresis data to prepare result data corresponding to each member of the group, wherein the result data corresponding to each member of the group includes data indicative of whether a second sample polynucleotide of the corresponding sample electrophoresis data includes a mutation.

27. The method of claim 26, further comprising determining the presence of an SNP or mutation in the sample compound on the basis of the plurality of detection value differences Δ

.

28. The method of claim 26, further comprising the steps of:

determining a number of peaks present in the reference electrophoresis data;

determining a number of peaks present in the sample electrophoresis data; and

determining the presence of an SNP or mutation in the sample compound of the biological sample and the basis of (1) the plurality of differences Δ and

(2) the number of peaks present in the reference and sample electrophoresis data.

29. The method of claim 26, comprising the steps of:

determining a migration coordinate difference Δ

_m between migration coordinates of the reference and sample peaks; and

wherein, the step of determining a plurality of detection value differences Δ

, comprises determining detection value differences between detection values of reference and sample electrophoresis data points that have migration coordinates differing by an amount Δ

_m.

30. The method of claim 26, comprising the steps of:

determining a migration coordinate difference Δ

_m between migration coordinates of the reference and sample peaks; and

prior to determining a plurality of detection value differences Δ

, aligning the migration coordinates of the reference and sample electrophoresis data on the basis of the migration coordinate difference Δ

_m.

26-1. A method of processing electrophoresis data obtained by temperature gradient electrophoresis (TGE) separation to provide data indicative of the presence of a single polynucleotide polymorphism (SNP) or a mutation in a sample compound of a biological sample, comprising:

providing reference electrophoresis data comprising a plurality of reference data points (dr_i, m_i), the reference data points defining at least one reference peak and having been obtained by TGE of at least one reference compound, and where, for the ith reference data point, dr_i is a detection value indicative of a detector signal and m_i is a migration coordinate;

providing sample electrophoresis data comprising a plurality of sample data points (ds_j, m_j), the sample data points defining at least one sample peak and having been obtained by TGE of at least one sample compound, and where, for the jth sample data point, dsj is a detection value indicative of a detector signal and mj is a migration coordinate;

normalizing the reference and sample electrophoresis data based on at least one detection value of the reference electrophoresis data and at least one detection value of the sample electrophoresis data;

determining a plurality of detection value differences Δ

between the reference and sample electrophoresis data, where the kth detection value difference Δ

_k is indicative of a difference between (1) the detection value dr_i of the reference electrophoresis data point having the migration coordinate m_i and (2) the detection value ds_j of the sample electrophoresis data point having the migration coordinate m_j; and

wherein the plurality of detection value differences Δ

are indicative of the presence of an SNP or mutation in the sample compound of the biological sample.

31. A method of processing electrophoresis data obtained by temperature gradient electrophoresis (TGE) separation to provide data indicative of the presence of a single polynucleotide polymorphism (SNP) or a mutation in a sample compound of a biological sample, comprising:

providing reference electrophoresis data comprising a plurality of reference data points (dr_i, m_i), the reference data points defining at least one reference peak and having been obtained by TGE of at least one reference compound, and where, for the ith reference data point, ds_i is a detection value indicative of a detector signal and m_i is a migration coordinate;

providing sample electrophoresis data comprising a plurality of sample data points (s_j, m_j), the sample data points defining at least one sample peak and having been obtained by TGE of at least one sample compound, and where, for the jth sample data point, s_j is a detection value indicative of a detector signal and mj is a migration coordinate;

normalizing the reference and sample electrophoresis data based on at least one detection value of the reference electrophoresis data and at least one detection value of the sample electrophoresis data; and

determining a covariance between the reference and sample electrophoresis data, wherein the covariance is indicative of the presence of an SNP or mutation in the sample compound of the biological sample.