Methods for genotyping polymorphisms in humans

• US 7,361,468 B2
• Filed: 07/05/2005
• Issued: 04/22/2008
• Est. Priority Date: 07/02/2004
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Chiles, Richard, Liu, Guoying, Yang, Geoffrey, Di, Xiaojun, Matsuzaki, Hajime, Hubbell, Earl A., Cawley, Simon, Mei, Rui, Webster, Teresa A.
• Primary Examiner(s): SWITZER, JULIET CAROLINE
• Application Number:
  US11/175,859
• Publication Number:
  US 20060024715A1
• Time in Patent Office: 1,022 Days
• Field of Search: None
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Claims

1. An array of oligonucleotides, the array consisting of:

a plurality of different allele specific perfect match probes attached to a solid support, wherein each allele specific perfect match probe consists of 20 to 50 contiguous nucleotides from a different sequence listed in SEQ ID Nos. 1-116,211 and wherein the plurality of different allele specific perfect match probes consists of at least one probe consisting of between 20 and 50 contiguous nucleotides from each of SEQ ID NOs. 1-116,211;

wherein each of the allele specific perfect match probes overlaps with nucleotide 26 of the sequence given in the respective SEQ ID NO, and each probe is perfectly complementary to one of the two possible alleles, and wherein each different allele specific perfect match probe is attached to a solid support in a known or determinable location of the array, wherein the two possible alleles are nucleotides allowed by the degenerate symbol at position 26 of the sequence given in the respective SEQ ID NO.

2. The array of claim 1 wherein the plurality of different allele specific perfect match probes consists of a first allele specific perfect match probe for the first allele of each SNP represented by SEQ ID Nos. 1-116,211 and a second allele specific perfect match probe for the second allele of each SNP represented by SEQ ID Nos. 1-116,211, wherein the SNP is represented by the degenerate nucleotide symbol at position 26 of the listed sequences, and the two alleles are nucleotides allowed by the degenerate symbol.

3. The array of claim 1 wherein each of the allele specific perfect match probes for a selected allele of a selected SNP varies from every other allele specific perfect match probe for that allele of that SNP in the position of the polymorphic base relative to the center of the probe.

4. The array of claim 3 wherein the polymorphic base in a probe is in a position selected from −

7, −

6, −

5, −

4, −

3, −

2, −

1, 0, 1, 2, 3, 4, 5, 6, or 7 relative to the center, where 0 is the central position of the probe.

5. The array of claim 4 wherein the probes are 25 bases in length.

6. The array of claim 1 wherein each allele specific perfect match probe is attached to a different bead.

7. A method of genotyping single nucleotide polymorphisms in parallel comprising:

obtaining a nucleic acid sample;

amplifying fragments of DNA in the nucleic acid sample;

hybridizing the amplified sample to the array of claim 1

analyzing the resulting hybridization pattern; and

determining the genotype of the sample for each of the single nucleotide polymorphisms.

8. The method of claim 7 wherein the solid support is a plurality of beads wherein each allele specific perfect match probe is attached to a different bead.

9. The method of claim 7 wherein the step of amplifying fragments of DNA in the nucleic acid sample comprises fragmenting the sample with at least one restriction enzyme, ligating an adapter to at least some of the fragments to generate adapter ligated fragments, and amplifying at least some of the adapter ligated fragments by polymerase chain reaction using a primer to the adapter.

10. The method of claim 9 wherein the at least one restriction enzyme is selected from the group consisting of XbaI and HindIII.

11. The method of claim 7 wherein the step of amplifying fragments of DNA in the nucleic acid sample comprises:

(a) fragmenting a first aliquot of the sample with a first restriction enzyme to generate a first fragmented aliquot;

(b) fragmenting a second aliquot of the sample with a second restriction enzyme to generate a second fragmented aliquot;

(c) ligating a first adapter to at least some of the fragments in the first fragmented aliquot;

(d) ligating a second adapter to at least some of the fragments in the second fragmented aliquot;

(e) amplifying at least some of the fragments from (c); and

,

(f) amplifying at least some of the fragments from (d); and

wherein the product of step (e) is hybridized to a first solid support and the product of step (f) is hybridized to a second solid support.

12. The method of claim 11 wherein the first restriction enzyme is XbaI, the second restriction enzyme is HindIII and the first primer and the second primer have the same sequence.

13. The method of claim 7 wherein the steps of analyzing the resulting hybridization pattern;

and determining the genotype of the sample for each of the single nucleotide polymorphisms are performed by a computer.

14. The method of claim 7 wherein the nucleic acid sample is from a human.

15. The method of claim 7 wherein the nucleic acid sample is from a non-human primate.