Complexity management of genomic DNA

• US 8,679,758 B2
• Filed: 08/06/2012
• Issued: 03/25/2014
• 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:
  US13/568,111
• Publication Number:
  US 20130137583A1
• Time in Patent Office: 596 Days
• Field of Search: None
• US Class Current: 435/6.12
• 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 analyzing single nucleotide polymorphisms (SNPs) comprising:

digesting a genomic DNA to provide fragments in a size range less than 1 kb and comprising SNPs of interest;

contacting the fragments in the size range with an array comprising probes specially designed to interrogate 10,000 to 1,500,000 SNPs on the fragments in the size range to produce a hybridization pattern; and

analyzing the hybridization pattern to identify which alleles of the SNPs are present.

2. The method of claim 1, wherein the genomic DNA is digested with an enzyme combination.

3. The method of claim 1, wherein the array comprising probes is designed to interrogate SNPs on fragments in a size range constituting less than 1% of the complexity of the genome.

4. The method of claim 1, wherein the size range is 100-500 bases.

5. The method of claim 1, wherein more than 80% of the SNPs are less than 500 kb from another SNP.

6. The method of claim 1, wherein the array comprising probes is specifically designed to interrogate at least 10,000-500,000 SNPs on the fragments in the size range.

7. The method of claim 1, wherein the array comprising probes is specifically designed to interrogate at least 50,000 SNPs on the fragments in the size range.

8. The method of claim 1, wherein the array comprising probes is specifically designed to interrogate only SNPs on fragments in the size range.

9. The method of claim 1, wherein the genomic DNA is a human genomic DNA.