Methods for genomic analysis

• US 20080026367A9
• Filed: 05/30/2003
• Published: 01/31/2008
• Est. Priority Date: 08/17/2001
• Status: Abandoned Application

• Current Assignee: Perlegen Sciences, Inc.
• Original Assignee: Perlegen Sciences, Inc.
• Inventors: Berno, Anthony, Hinds, David, Cox, David, Patil, Nila
• Application Number:
  US10/448,773
• Publication Number:
  US 20040029161A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G06Q 30/02 Marketing; Price estimation or determination; Fundraising
• 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 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16H 50/70 for mining of medical data, e.g. analysing previous cases of other patients
• CPC Class Codes: G16H 70/60 relating to pathologies

Abstract

The present invention relates to business methods for discovery of therapeutic and diagnostic products by identifying variations that occur in the human genome, relating these variations to one another, and, ultimately, relating these variations to the genetic bases of phenotype such as disease resistance, disease susceptibility or drug response.

Claims

1. A business method comprising:

identifying disease related loci by comparing frequencies of SNP haplotype patterns from essentially coding regions of individuals in a control group with frequencies of SNP haplotype patterns from essentially coding regions of individuals in a disease group, wherein differences in said frequencies indicate locations of disease-related genetic loci;

using said disease related loci in a discovery process; and

collaboratively or independently, marketing products from said discovery process.

2. The method of claim 1, wherein said control group comprises at least 16 individuals.

3. The method of claim 1, wherein said disease group comprises at least 16 individuals.

4. The method of claim 1, wherein said SNP haplotype patterns are determined using informative SNPs.

5. A business method comprising:

a. making an association between SNP haplotype patterns from coding regions of a genome and a phenotypic trait of interest by

i. building a baseline of SNP haplotype patterns from regions consisting essentially of coding regions of a genome;

ii. pooling genomic DNA from a population having a common phenotypic trait of interest;

iii. identifying said SNP haplotype patterns that are associated with said phenotypic trait of interest;

b. using said association in a discovery process; and

c. collaboratively or independently, marketing products from said discovery process.

6. The method of claim 5, wherein the phenotypic trait of interest is a drug response state.

7. The method of claim 6, wherein the drug response state is a responder state.

8. The method of claim 6, wherein the drug response state is a toxicity state.

10. The method of claim 5, wherein a technology provider provides discounted technology for said association, and receives equity in return for said discounted technology.

11. The method of claim 5, wherein said discovery process comprises identifying a pharmaceutical compound to address said phenotypic trait.

12. The method of claim 11, wherein said pharmaceutical compound is an antisense compound.

13. The method of claim 11, wherein said pharmaceutical compound is a small organic molecule.

14. The method of claim 11, wherein said pharmaceutical compound is an antibody.

15. The method of claim 11, wherein said pharmaceutical compound is a protein compound.

9. The method of claim I or 5 wherein the step of collaboratively or independently marketing products comprises receiving funds from a partner for making the association between the SNP patterns and the phenotypic trait.