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Huang Y.,Columbia University | Hinds D.A.,Perlegen Sciences | Qi L.,University of California at Davis | Prentice R.L.,Fred Hutchinson Cancer Research Center
Genetic Epidemiology | Year: 2010

We examine the measurement properties of pooled DNA odds ratio estimates for 7,357 single nucleotide polymorphisms (SNPs) genotyped in a genome-wide association study of postmenopausal breast cancer. This study involved DNA pools formed from 125 cases or125 matched controls. Individual genotyping for these SNPs subsequently came available for a substantial majority of women included in seven pool pairs, providing the opportunity for a comparison of pooled DNA and individual odds ratio estimates and their variances. We find that the "per minor allele" odds ratio estimates from the pooled DNA comparisons agree fairly well with those from individual genotyping. Furthermore, the log-odds ratio variance estimates support a pooled DNA measurement model that we previously described, although with somewhat greater extra-binomial variation than was hypothesized in project design. Implications for the role of pooled DNA comparisons in the future genetic epidemiology research agenda are discussed. © 2010 Wiley-Liss, Inc. Source


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 3.11M | Year: 2005

DESCRIPTION (provided by applicant): The goal of this study is to identify the genetic determinants of late-onset Alzheimer's disease (AD). The proposed study uses Perlegen Sciences' high-density oligonucleotide array-based genotyping platform to genotype over 1.5 million single nucleotide polymorphisms (SNPs) across the genome in the context of a whole-genome association study of late-onset AD. Late-onset AD is a devastating neurodegenerative disease, characterized by the formation of pathogenic plaques in the brain, which affects as many as 10% of people 65 or older. The disease is complex, likely to involve the interaction of a number of genes, including apolipoprotein E, which increases risk and lowers age of onset. Studies aimed at identifying additional late-onset AD-susceptibility genes are ongoing. Using Perlegen Sciences' high-density array technology, SNPs associated with late-onset AD will be identified by measuring SNP allele frequency differences between 400 individuals with late-onset AD (cases) and 400 matched unaffected controls from samples in the NIMH AD Genetics Initiative collection. The initial 1.5 million SNP scan will be performed using separately pooled case and control DNA samples. A subset of these SNPs will be selected for verification based on the largest estimated allele frequency differences, haplotype structure and biological relevance. Genotyping the individual case and control samples, as well as a replicate population will verify the association of these SNPs with late-onset AD. The number of SNPs to be analyzed in this study is orders of magnitude higher than in previously published case-control studies, rendering this the most comprehensive search for genetic loci involved in AD. In addition to providing further evidence regarding the role of previously identified candidate loci, the study may also identify novel associations with unsuspected loci. Identification of new genetic factors associated with AD will lead to a better understanding of the molecular mechanisms underlying the disease and provide a basis for new approaches to treatment and prevention.


Patent
Perlegen Sciences and University of Cambridge | Date: 2015-06-12

Correlations between polymorphisms and breast cancer are provided. Methods of diagnosing, prognosing, and treating breast cancer are provided. Systems and kits for diagnosis, prognosis and treatment of breast cancer are provided. Methods of identifying breast cancer modulators are also described.


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 221.82K | Year: 2004

DESCRIPTION (provided by applicant): The goal of this study is to identify the genetic determinants of rheumatoid arthritis (RA). The proposed study uses Perlegen Sciences' high density oligonucleotide array-based genotyping platform to genotype over


Tian C.,Perlegen Sciences | Stokowski R.P.,Perlegen Sciences | Kershenobich D.,National Autonomous University of Mexico | Ballinger D.G.,Perlegen Sciences | And 2 more authors.
Nature Genetics | Year: 2010

Two genome-wide association studies (GWAS) have described associations of variants in PNPLA3 with nonalcoholic fatty liver and plasma liver enzyme levels. We investigated the contributions of these variants to liver disease in Mestizo subjects with a history of alcohol dependence. We found that rs738409 in PNPLA3 is strongly associated with alcoholic liver disease and clinically evident alcoholic cirrhosis (unadjusted OR= 2.25, P=1.7 × 10-10 ancestry-adjusted OR=1.79, P=1.9 × 10 -5). © 2010 Nature America, Inc. All rights reserved. Source

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