Polymorphism detection

• US 6,953,663 B1
• Filed: 06/27/2003
• Issued: 10/11/2005
• Est. Priority Date: 11/29/1995
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Ghandour, Ghassan, Sapolsky, Ronald
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US10/607,829
• Time in Patent Office: 837 Days
• Field of Search: 435/6, 536/23.1, 536/24.3
• US Class Current: 435/6.11
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2525/204 specific length of the oligonucleotides
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, e.g., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.

Claims

1. A method for detecting a polymorphism in a target nucleic acid sequence, comprising:

receiving hybridization intensities for a first group of probes that are complementary to said target nucleic acid sequence except that the group of probes includes all possible monosubstitutions of positions in said sequence that are within n bases of a base in said sequence that is complementary to said polymorphism, wherein n is from 0 to 5;

receiving hybridization intensities for a second and third group of probes complementary to marker-specific regions upstream and downstream of the polymorphism in the target nucleic acid sequence, wherein the third group of probes differs from the second set of probes at single bases corresponding to known mismatch positions; and

identifying the polymorphism by analyzing the hybridization intensities.

2. The method of claim 1, wherein the identifying the polymorphism comprises utilizing Principal Component Analysis.

3. The method of claim 1, wherein at least two alleles of the polymorphism are known.

4. The method of claim 1, wherein said first groups of probes comprises a plurality of different probes that are complementary to overlapping portions of said target nucleic acid sequence.

5. The method of claim 1, wherein the monosubstitutions occur at a plurality of distances from a 3′

end of said probes.

6. An method for detecting a polymorphism in a target nucleic acid sequence, said array comprising:

receiving hybridization intensities for a first group of probes that are complementary to said target nucleic acid sequence except that the group of probes includes all possible monosubstitutions of positions in said sequence that are within n bases of a base in said sequence that is complementary to said polymorphism;

receiving hybridization intensities for a second and third group of probes complementary to marker-specific regions upstream and downstream of the polymorphism in the target nucleic acid sequence, wherein the third group of probes differs from the second set of probes at single bases corresponding to known mismatch positions; and

identifying the polymorphism by analyzing the hybridization intensities.

7. The method of claim 6, wherein the identifying the polymorphism comprises utilizing Principal Component Analysis.

8. The method of claim 6, wherein at least two alleles of the polymorphism are known.

9. The method of claim 6, wherein said first groups of probes comprises a plurality of different probes that are complementary to overlapping portions of said target nucleic acid sequence.

10. The method of claim 6, wherein the monosubstitutions occur at a plurality of distances from a 3′

end of said probes.