The science behind our approach

Following are recent papers related to Perlegen and our approach to the discovery and validation of genetic content and its application in diagnostics. Abstracts of all articles are available; however, sign-in may be necessary to read the full text of the article.

• Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.
  Nature Genetics. 2008 May;40(5):631-37.
• Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides.
  Nature Genetics. 2008 Feb;40(2):149-51.
• Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
  New England Journal of Medicine. 2008 Feb 28;358(9):956-61.
• A genome-wide approach to identifying novel-imprinted genes.
  Human Genetics. 2008 Jan;122(6):625-34.
• A genomewide association study of skin pigmentation in a South Asian population.
  American Journal of Human Genetics. 2007 Dec;81(6):1119-32.
• Clinical predictors of glycosylated hemoglobin response to thiazolidinedione therapy.
  Diabetes Technology and Therapeutics. 2007 Dec;9(6):553-61.
• The genomic landscapes of human breast and colorectal cancers.
  Science. 2007 Nov 16;318(5853):1108-13
• Genome-wide detection and characterization of positive selection in human populations.
  Nature. 2007 Oct 18;449(7164):913-8.
• A second generation human haplotype map of over 3.1 million SNPs.
  Nature. 2007 Oct 18;449(7164):851-61.
• New models of collaboration in genome-wide association studies: the Genetic Association Information Network.
  Nature Genetics. 2007 Sep;39(9):1045-51.
• Evaluation of the SNP tagging approach in an independent population sample--array-based SNP discovery in Sami.
  Human Genetics. 2007 Sep;122(2):141-50.
• A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.
  Nature. 2007 Aug 30;448(7157):1050-3.
• In vitro human keratinocyte migration rates are associated with SNPs in the KRT1 interval.
  PLoS ONE. 2007 Aug 1;2(1):e697
• Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
  Science. 2007 Jul 20;317(5836):338-42.
• Genome-wide association study identifies novel breast cancer susceptibility loci.
  Nature. 28 June 2007;447:1087-1093
• A genomewide admixture map for Latino populations.
  American Journal of Human Genetics. 2007 Jun;80(6):1024-36.
• A genomewide single-nucleotide-polymorphism panel with high ancestry information for Mexican American admixture mapping.
  American Journal Human Genetics. 2007 Jun;80(6):1014-23.
• A Common Allele on Chromosome 9 Associated with Coronary Heart Disease.
  Science. 2007 Jun 8;316(5830):1488-91. Epub 2007 May 3.
• Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs.
  Human Molecular Genetics. 2007 Jan 1;16(1):36-49. Epub 2006 Nov 29
• Novel genes identified in a high-density genome wide association study for nicotine dependence.
  Human Molecular Genetics. 2007 Jan 1;16(1):24-35. Epub 2006 Dec 7.
• Design and validation of a population-based definition of the metabolic syndrome.
  Diabetes Care. 2006 Nov;29(11):2420-6.
• Perspectives on development of a combination pharmacogenomic diagnostic and drug product.
  Pharmacogenomics. 2006 Oct;7(7):1045-9. Review.
• A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping.
  American Journal of Human Genetics. 2006 Oct;79(4):640-9. Epub 2006 Aug 15.
• Allele-specific KRT1 expression is a complex trait.
  PLoS Genetics. 2006 Jun;2(6):e93. Epub 2006 Jun 9.
• Analysis of allelic differential expression in human white blood cells.
  Genome Research. 2006 Mar;16(3):331-9. Epub 2006 Feb 8.
• Common deletions and SNPs are in linkage disequilibrium in the human genome.
  Nature Genetics. 2006 Jan;38(1):82-5. Epub 2005 Dec 4.
• Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.
  Respiratory Research. 2005 Dec 10;6:145
• Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles.
  Genome Research. 2005 November; 15(11): 1511-1518.
• A haplotype map of the human genome.
  Nature. 2005 October 27; 437: 1299-1320.
• High-Resolution Whole-Genome Association Study of Parkinson Disease.
  American Journal of Human Genetics. 2005;77:685–693. Epub 2005 Sep 9.
• Fine-scale recombination patterns differ between chimpanzees and humans.
  Nature Genetics. 2005 Apr;37(4):429-34. Epub 2005 Feb 18.
• Whole Genome Patterns of Common DNA Variation in Three Human Populations.
  Science. 2005 Feb 18;307(5712):1072-1079.

Genotype Browser

• Application of Pooled Genotyping to Scan Candidate Regions for Association with HDL Cholesterol Levels.
  Human Genomics. 2004 Nov;1(6):421-34.

Supplemental Tables

• Segmental Phylogenetic Relationships of Inbred Mouse Strains Revealed by Fine-Scale Analysis of Sequence Variation Across 4.6 Mb of Mouse Genome.
  Genome Research. 2004 Aug;14(8):1493-1500.
• VISTA: Computational Tools for Comparative Genomics.
  Nucleic Acids Research. 2004 Jul 1;32(Web Server issue):W273-9.
• Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional.
  Genome Research. 2004 Mar;14(3):367-72.
• Matching strategies for genetic association studies in structured populations.
  American Journal of Human Genetics. 2004 Feb;74(2):317-25.
• Multi-species sequence comparison: the next frontier in genome annotation.
  Genome Biology. 2003, 4:122.
• Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates.
  Genome Research. 2003 Mar;13(3):341-6.
• Cross-species sequence comparisons: a review of methods and available resources.
  Genome Research. 2003 Jan;13(1):1-12. Review.
• Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21.
  Science. 2001 Nov 23;294(5547):1719-23.
• Evolutionarily conserved sequences on human chromosome 21.
  Genome Research. 2001 Oct;11(10):1651-9.