Partitioning of polymorphic DNAs

• US 6,074,831 A
• Filed: 07/09/1998
• Issued: 06/13/2000
• Est. Priority Date: 07/09/1998
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Yakhini, Zohar, Webb, Peter Gregory, Roth, Ron M.
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): Epps, Janet
• Application Number:
  US09/112,435
• Time in Patent Office: 705 Days
• Field of Search: 435/6, 435/91.2, 435/91.5, 536/23.1, 536/24.33, 395/140, 395/147, 436/173, 436/501, 935/8, 935/77
• US Class Current: 435/6.18
• 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

Methods for applying graph theory techniques in methods to establish multiplexed assay formats for analyzing polymorphic DNAs are provided. These methods are used for designing and carrying out rapid and efficient processes for distinguishing target polymorphic DNA segments on the basis of variations in sequence and/or length. The methods are thus useful in the design of assays for determining identity, ancestry, predisposition to disease, or the presence or absence of a desired trait; genetic linkage analyses (gene mapping); and drug development.

Claims

1. A method for partitioning a set of polymorphic DNA molecules into two or more subsets, wherein the method comprises applying a graph theory technique to partition said polymorphic DNA molecules into two or more subsets, each subset then concurrently analyzed as a sample in a single measurement channel in a multiplexed DNA analysis to reveal which variant of a polymorphic DNA is present in the sample.

2. The method of claim 1, wherein the graph theory technique is a graph coloring technique.

3. The method of claim 2, wherein the graph coloring technique entails a coloring of interval graphs, said coloring being minimal.

4. The method of claim 2, wherein the graph coloring technique entails a coloring of arbitrary graphs using a smallest last order (SLO) technique.

5. The method of claim 3, wherein the graph coloring technique is interval graph coloring.

6. The method of claim 1, wherein the polymorphic DNA variants differ on the basis of length.

7. The method of claim 6, wherein the polymorphic DNA variants are microsatellite tandem repeat polymorphisms (STRPs).

8. The method of claim 1, wherein the polymorphic DNA variants differ on the basis of sequence.

9. The method of claim 8, wherein the polymorphic DNA variants are single nucleotide polymorphisms (SNPs).

10. The method of claim 1, wherein the multiplexed DNA analysis entails a separation of said subsets of polymorphic DNAs on the basis of length.

11. The method of claim 10, wherein said separation comprises an electrophoretic technique.

12. The method of claim 11, wherein said separation comprises capillary electrophoresis (CE).

13. The method of claim 11, wherein said separation comprises slab gel electrophoresis.

14. The method of claim 10, wherein said separation comprises a liquid chromatographic technique.

15. The method of claim 14, wherein said separation comprises high performance liquid chromatography (HPLC).

16. The method of claim 10, wherein the members of each said subset are labeled with a detectable label.

17. The method of claim 16, wherein the label is a fluorophore.

18. The method of claim 16, wherein the label is a mass tag.

19. The method of claim 18, wherein the label is a cleavable mass tag.

20. The method of claim 16, wherein each subset is assigned to a single gel lane in the gel electrophoresis.

21. The method of claim 16, wherein a plurality of subsets are assigned to a single gel lane in the gel electrophoresis and the subsets assigned to said single gel lane are differentially labeled relative to each other.

22. The method of claim 16, wherein each subset is assigned a mass tag label, and the set is analyzed using a combination of liquid chromatography and mass spectrometry (LC/MS).

23. The method of claim 1, wherein said multiplexed DNA analysis of each subset entails a mass analysis of the polymorphic DNAs.

24. The method of claim 23, wherein the polymorphic DNA variants are single nucleotide polymorphisms (SNPs).

25. The method of claim 24, wherein elements of each subset undergo a common enzymatic process and then are jointly analyzed by mass spectrometry in said multiplexed DNA analysis.

26. The method of claim 1, wherein partitioning of the set of polymorphic DNAs must satisfy constraints imposed by multiplexed PCR amplification techniques.

27. A method for partitioning a number of different types of molecules into subsets of the number of different types of molecules so that an analysis technique can be concurrently applied to a sample comprising different types of molecules selected from a subset to unambiguously determine the types of molecules present in the sample, the method comprising:

determining, for each different type of molecule, a set of possible results that can occur when the analysis technique is applied to the type of molecule; and

using a graph coloring technique to partition the different types of molecules into a smaller number of subsets of non-interfering types of molecules such that, for each subset of non-interfering types of molecules, the set of possible results that can occur for each type of molecule in the subset of non-interfering types of molecules does not contain a result that can occur for any other type of molecule in the subset of non-interfering types of molecules.

28. The method of claim 27 wherein the different types of molecules are DNA polymer molecules generated by amplification of DNA primers hybridized to polymorphic DNA molecules.

29. The method of claim 27 wherein the analysis technique is slab gel electrophoresis.

30. The method of claim 27 wherein the analysis technique is mass spectrometry.

31. The method of claim 27 wherein the analysis technique is capillary electrophoresis.

32. The method of claim 27 wherein the analysis technique is liquid chromatography.

33. The method of claim 27 wherein the different types of molecules are DNA polymer molecules, labeled with chemical tags, generated by amplification of DNA primers hybridized to polymorphic DNA molecules.

34. The method of claim 33 wherein the analysis technique is a combination of more than one of the following analysis techniques:

optical spectroscopy, mass spectrometry, radiometry, liquid chromatography, capillary electrophoresis, and slab gel electrophoresis.

35. The method of claim 33 wherein the analysis technique is mass spectrometry.

36. The method of claim 33 wherein the analysis technique is radiometry.

37. The method of claim 33 wherein the analysis technique is slab gel elctrophoresis.

38. The method of claim 33 wherein the analysis technique is optical spectroscopy.

39. The method of claim 27 wherein, in the graph coloring technique, the different types of molecules are considered to be vertices in an intersection graph, wherein an edge between two vertices indicates that sets of possible results related to different types of molecules represented by the two vertices contain at least one common possible result, wherein the vertices are colored so that vertices having a given color have no common edges, and wherein the types of molecules represented by all vertices having a given color are partitioned together as a subset of non-interfering types of molecules.

40. The method of claim 27 further including:

preparing a sample that contains an unknown mixture of different types of molecules chosen from a subset of non-interfering types of molecules; and

analyzing the sample using the analysis technique to determine the types of molecules present in the sample.

41. A system for partitioning a number of different types of molecules into subsets of the number of different types of molecules so that an analysis technique can be concurrently applied to a sample comprising different types of molecules selected from a subset to unambiguously determine the types of molecules present in the sample, the system comprising:

a computer having at least one data storage component and at least one processor;

a computer-readable list, stored in the data storage component, containing the different types of molecules;

for each type of molecule, a computer-readable list, stored in the data storage component, containing the possible results that can occur when the analysis technique is applied to the type of molecule; and

a computer program executed by the processor that applies a graph coloring technique to partition the computer-readable list of types of molecules into a list of subsets of non-interfering types of molecules such that, for each subset of non-interfering types of molecules, the set of possible results that can occur for each type of molecule in the subset of non-interfering types of molecules does not contain a result that can occur for any other type of molecule in the subset of non-interfering types of molecules.