Methods and products related to genotyping and DNA analysis

• US 6,703,228 B1
• Filed: 09/24/1999
• Issued: 03/09/2004
• Est. Priority Date: 09/25/1998
• Status: Expired due to Term

• Current Assignee: Massachusetts Institute of Technology
• Original Assignee: Massachusetts Institute of Technology
• Inventors: Charest, Alain, Housman, David E., Landers, John, Jordan, Barbara
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): ZHOU, SHUBO
• Application Number:
  US09/404,912
• Time in Patent Office: 1,628 Days
• Field of Search: 702/19, 702/20, 435/320.1, 435/325, 435/252.3, 435/6, 435/91.2, 536/23.1, 536/24.1, 536/24.3, 536/24.31, 536/24.32, 536/24.33
• US Class Current: 435/91.2
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2600/172 Haplotypes
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

The invention encompasses methods and products related to genotyping. The method of genotyping of the invention is based on the use of single nucleotide polymorphisms (SNPs) to perform high throughput genome scans. The high throughput method can be performed by hybridizing SNP allele-specific oligonucleotides and a reduced complexity genome (RCG). The invention also relates to methods of preparing the SNP specific oligonucleotides and RCGs, methods of fingerprinting, determining allele frequency for a SNP, characterizing tumors, generating a genomic classification code for a genome, identifying previously unknown SNPs, and related compositions and kits.

Claims

1. A method for detecting the presence or absence of a single nucteotide polymorphism (SNP) allele in a genomic DNA sample, the method comprising:

preparing a reduced complexity genome (RCG) from the genomic DNA sample, wherein the RCG is a randomly primed PCR-derived RCG, and

analyzing the RCG for the presence or absence of a SNP allele.

2. The method of claim 1, wherein the analysis comprises hybridizing a SNP-ASO and the RCG, wherein the SNP-ASO is complementary to one allele of a SNP, with the RCG, and wherein the presence or absence of the SNP is used to characterize the genomic DNA sample.

3. The method of claim 2, wherein the RCG is immobilized on a surface.

4. The method of claim 2, wherein the SNP-ASO is immobilized on a surface.

5. The method of claim 4, wherein a plurality of different SNP-ASOs are attached to the surface.

6. The method of claim 2, wherein the SNP-ASO is individually hybridized with a plurality of RCGs.

7. The method of claim 2, wherein the SNP-ASO is a plurality of SNP ASOs, at least a fraction which are labeled.

8. The method of claim 7, wherein an excess of a non-labeled SNP-ASO is added during the hybridization step, wherein the non-labeled oligonucleotide is complementary to a different allele of the same SNP than the labeled SNP-ASO.

9. The method of claim 7, further comprising performing a parallel hybridization reaction wherein the RCG is hybridized with a labeled SNP-ASO, wherein the oligonucleotide is complementary to a different allele of the same SNP than the labeled SNP-ASO.

10. The method of claim 9, wherein the two SNP-ASOs are distinguishably labeled.

11. The method of claim 7, an excess of non-labeled SNP-ASO is present during the hybridization.

12. The method of claim 7, wherein the label is a radioactive isotope.

13. The method of claim 12, further comprising the step of exposing the RCG to a film to produce a signal on the film which corresponds to the radioactively labeled hybridization products if the SNP is present in the RCG.

14. The method of claim 7, wherein the label is a fluorescent molecule.

15. The method of claim 14, further comprising the step of exposing the RCG to an automated fluorescence reader to generate an output signal which corresponds to the fluorescently labeled hybridization products if the SNP is present in the RCG.

16. The method of claim 7, wherein the plurality of SNP-ASOs are labeled with fluorescent molecules, each SNP-ASO of a particular sequence being labeled with a spectrally distinct fluorescent molecule from a SNP-ASO having a different sequence.

17. The method of claim 16, wherein the number of SNP-ASOs having a spectrally distinct fluorescent molecule is at least two.

18. The method of claim 16, wherein the number is selected from the group consisting of three, four and eight.

19. The method of claim 2, wherein a plurality of RCGs are labeled with fluorescent molecules, each RCG being labeled with a spectrally distinct fluorescent molecule, and wherein all of the RCGs having a spectrally distinct fluorescent molecule.

20. The method of claim 2, wherein the SNP-ASO is composed of from about 10 to about 50 nucleotide residues.

21. The method of claim 20, wherein the SNP-ASO is composed of from about 10 to about 25 nucleotide residues.

22. The method of claim 2, wherein the RCG is labeled.

23. The method of claim 2, wherein the genomic DNA sample is characterized by generating a genomic pattern based on the presence or absence of the allele of the SNP in the genomic DNA sample.

24. The method of claim 23, wherein the genomic pattern is a genomic classification code.

25. The method of claim 1, wherein the method further comprises identifying a genotype of the genomic DNA sample, whereby the genotype is identified by the presence or absence of the allele of the SNP in the RCG.

26. The method of claim 25, wherein the presence or absence of the SNP allele is analyzed in a plurality of genomic DNA samples selected randomly from a population, the method further comprising determining the allele frequency of the SNP allele in the population by comparing the number of genomic DNA samples in which the allele is detected and the number of genomic DNA samples analyzed.

27. The method of claim 1, wherein the genomic DNA sample is obtained from a tumor.

28. The method of claim 27, wherein a plurality of RCGs are prepared from genomic DNA samples isolated from a plurality of subjects and the plurality of RCGs are analyzed for the presence of the SNP.

29. The method of claim 1, wherein the RCG is prepared by performing degenerate oligonucleotide priming-polymerase chain reaction (DOP-PCR) using a degenerate oligonucleotide primer having a tag-(N)_x-TARGET nucleotide sequence, wherein the TARGET nucleotide sequence includes at least 7 TARGET nucleotide residues, wherein x is an integer from 0-9, and wherein each N is any nucleotide residue, and wherein the tag is a polynucleotide having from about 0 to about 20 nucleotides.

30. The method of claim 29, wherein the TARGET nucleotide sequence includes at least 8 nucleotide residues.

31. The method of claim 1, wherein the RCG is prepared by interspersed repeat sequence-polymerase chain reaction (IRS-PCR).

32. The method of claim 1, wherein the RCG is prepared by arbitrarily primed-polymerase chain reaction (AP-PCR).

33. The method of claim 1, wherein the RCG is prepared by adapter-polymerase chain reaction.

34. The method of claim 1, wherein the RCG is prepared by performing degenerate oligonucleotide priming-polymerase chain reaction using a degenerate oligonucleotide primer having a tag-(N)_x-TARGET nucleotide sequence, wherein the TARGET nucleotide sequence includes fewer than 7 TARGET nucleotide residues wherein x is an integer from 0 to 9, wherein each N is any nucleotide residues, and wherein the tag is a polynucleotide having from about 0-20 nucleotides.

35. The method of claim 34 wherein the TARGET nucleotide sequence includes at least 5 nucleotide residues.

36. The method of claim 34 wherein the TARGET nucleotide sequence includes at least 6 nucleotide residues.

37. The method of claim 1, wherein the RCG is prepared by performing multiple primed OP-PCR.

38. The method of claim 1, wherein the complexity of the genomic is reduced by 50%.

39. The method of claim 1, wherein the complexity of the genomic is reduced by 95%.

40. The method of claim 1, wherein the complexity of the genomic is reduced by 99%.