Complexity management of genomic DNA

• US 9,845,490 B2
• Filed: 12/03/2013
• Issued: 12/19/2017
• Est. Priority Date: 07/25/2001
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Matsuzaki, Hajime, Su, Xing, Walsh, Sean, Kennedy, Giulia, Mei, Rui
• Primary Examiner(s): Chunduru, Prabha
• Application Number:
  US14/095,907
• Publication Number:
  US 20150017632A1
• Time in Patent Office: 1,477 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.

Claims

1. A method of producing a second nucleic acid sample from a first nucleic acid sample, wherein said second nucleic acid sample is enriched with a collection of adaptor ligated target sequences, the method comprising:

fragmenting the first nucleic acid sample to produce sample fragments in a selected size range that comprises a collection of target sequences, wherein the fragmenting includes digestion with an enzyme or enzyme combination, wherein the collection of target sequences comprises between 10,000 and 3,000,000 single nucleotide polymorphisms, wherein greater than 80% of the single nucleotide polymorphisms in the collection of target sequences are at least 10 kilo bases and less than 500 kilo bases from another single nucleotide polymorphism, and wherein the average minimum distance between single nucleotide polymorphisms is between 10 kilo bases and 800 kilo bases;

ligating at least one synthetic adaptor to the sample fragments to produce the collection of adaptor ligated target sequences; and

generating the second nucleic acid sample by amplifying the sample fragments, wherein the collection of adaptor ligated target sequences is enriched in the second nucleic acid sample.

2. The method of claim 1, wherein the amplifying comprises PCR.

3. The method of claim 2, wherein the PCR uses a primer that is complementary to the adaptor.

4. The method of claim 2, wherein 20 to 50 cycles of PCR are used to amplify the sample fragments.

5. The method of claim 1, wherein the sample fragments are in a size range of 1 kb and less.

6. The method of claim 1, wherein the sample fragments are in a size range of 2 kb and less.

7. The method of claim 1, wherein the enzyme or enzyme combination includes at least one restriction enzyme.

8. The method of claim 7, wherein the at least one restriction enzyme has a six base recognition sequence.

9. The method of claim 1, wherein the enzyme or enzyme combination includes a type IIs endonuclease.

10. The method of claim 1, wherein the sample fragments in a size range of less than 1 kb comprise at least 0.01% of the first nucleic acid sample.

11. The method of claim 1, wherein the sample fragments in a size range of less than 1 kb comprise at least 0.5% of the first nucleic acid sample.

12. The method of claim 1, wherein the sample fragments in a size range of less than 1 kb comprise at least 3% of the first nucleic acid sample.

13. The method of claim 1, wherein the sample fragments in a size range of less than 1 kb comprise at least 12% of the first nucleic acid sample.

14. The method of claim 1, wherein the sample fragments in a size range of less than 1 kb comprise at least 50% of the first nucleic acid sample.

15. The method of claim 1, wherein the first nucleic acid sample is genomic DNA, DNA, cDNA derived from RNA or cDNA derived from mRNA.

16. The method of claim 1, wherein the target sequences are 800 base pairs long or less.

17. The method of claim 1, wherein the target sequences are 1000 base pairs long or less.

18. The method of claim 1, wherein the target sequences are 1200 base pairs long or less.

19. The method of claim 1, wherein the target sequences are 1500 base pairs long or less.

20. The method of claim 1, wherein the target sequences are 2000 base pairs long or less.

21. The method of claim 1, wherein the sample fragments enriched in said second nucleic acid sample is comprised of fragments that are about 2000 base pairs long or less.

22. The method of claim 1, wherein the sample fragments enriched in said second nucleic acid sample is comprised of fragments that are about 3000 base pairs long or less.

23. The method of claim 1, wherein the fragmenting, ligating and generating steps are performed in a single tube.

24. The method of claim 1, wherein two or more adaptors are ligated to the sample fragments so that some of the sample fragments have a first adaptor sequence ligated to one end and a second adaptor sequence ligated to the other end.

25. The method of claim 24, wherein the amplifying is by PCR with a first primer that is complementary to the first adaptor and a second primer that is complementary to the second adaptor.

26. The method of claim 1, wherein the adaptor comprises a complementary region comprising a first common sequence and the complement of the first common sequence and a region comprising a second common sequence on one strand and a third common sequence on the other strand, and wherein the second and third common sequences will not base pair under standard hybridization conditions.

27. The method of claim 26, wherein the amplifying is by PCR using a first primer that is complementary to the second common sequence and a second primer that is complementary to the third common sequence.

28. The method of claim 1, wherein at least one of the single nucleotide polymorphisms is associated with a phenotype.

29. The method of claim 1, wherein at least one of the single nucleotide polymorphisms is associated with a disease.

30. The method of claim 1, wherein at least one of the single nucleotide polymorphisms is associated with the efficacy of a drug.

31. The method of claim 1, wherein at least one of the single nucleotide polymorphisms is associated with a haplotype.