Human genomic polymorphisms

• US 20060188875A1
• Filed: 10/31/2002
• Published: 08/24/2006
• Est. Priority Date: 09/18/2001
• Status: Abandoned Application

• Current Assignee: Perlegen Sciences, Inc.
• Original Assignee: Perlegen Sciences, Inc.
• Inventors: Berno, Anthony J., Hinds, David A., Patil, Nila, Cox, David R.
• Application Number:
  US10/284,444
• Publication Number:
  US 20060188875A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• 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 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

The invention provides nucleic acid segments of the human genome including polymorphic sites, SNP haplotype blocks, SNP haplotype patterns for each block and informative SNPs for each pattern. Allele-specific primers and probes hybridizing to regions flanking these sites are also provided. The nucleic acids, primers and probes are used in applications such as association studies and other genetic analyses.

Claims

1. A nucleic acid segment of between 10 and 201 contiguous bases from dbSNP.txt, wherein said nucleic acid segment includes either base at a SNP locus indicated in dbSNP.txt.

2. A complement of said nucleic acid segment of claim 1.

3. A SNP locus-specific oligonucleotide that hybridizes to said nucleic acid segment of claim 1.

4. A haplotype block from human chromosome 21 as described in group.txt.

5. A haplotype pattern from human chromosome 21 as described in pattern.txt.

6. A method of analyzing a nucleic acid from an individual comprising:

obtaining said nucleic acid and identifying a base occupying any one of said SNP loci indicated in dbSNP.txt.

7. The method of claim 6, wherein said nucleic acid is obtained from a plurality of individuals, and said base occupying any one of said SNP loci is determined in each of said plurality of individuals.

8. The method of claim 7, further comprising testing each of said plurality of individuals for a presence of a disease phenotype and correlating said presence of said disease phenotype with said base.

9. A computer-readable storage medium for storing data for access by an application program being executed on a data processing system comprising:

a data structure stored in said computer-readable storage medium, said data structure including information resident in a database used by said application program and including a plurality of records, each record of said plurality comprising information identifying a SNP locus indicated in dbSNP.txt.

10. The computer-readable storage medium of claim 9, wherein each record has a field identifying a base occupying said SNP locus and a location of said SNP locus.

11. The computer-readable storage medium of claim 10, wherein each record identifies a nucleic acid segment of between 10 and 100 bases from a sequence from dbSNP.txt including a SNP locus indicated therein, or the complement of said nucleic acid segment.

12. A signal carrying data for access by an application program being executed on a data processing system comprising:

a data structure encoded in said signal, said data structure including information resident in a database used by said application program and including a plurality of records, each record of the plurality comprising information identifying a SNP locus from dbSNP.txt.