Info: math@vassar.edu -- Phone: 845.437.5525 Last updated: Nov 16, 2009Speaker: Rob Scharpf Johns Hopkins School of Public Health Dept of Biostatistics Title: Batch effects in SN arrays: Solutions for genotyping and copy number estimation Abstract Susceptibility to common diseases such as cancer and diabetes is influenced by genetic variation. Two forms of genetic variation are particularly common and can be assessed on a genome-wide scale using recent high throughput genotyping arrays: single nucleotide polymorphisms (SNPs) and copy number variants (CNVs). Many genome wide association studies (GWAS) have been carried out or are currently underway. The goal of these studies is to assess the contribution of genetic variation such as SNPs and CNVs to complex traits. The success and validity of a GWAS depends critically on the accuracy and precision of the locus- level estimates for genotype and copy number. However, underlying the copy number and genotype estimates reported in most biology journals is a much more complex and noisy data structure. In particular, nonbiological sources of variation (batch effects) in the normalized intensities between individuals are common and can affect the resulting inference. This talk will provide an overview of the technology, motivate the importance of batch effects, and describe robust solutions for genotyping and copy number estimation. When: Tuesday, November 17, 2009 Immediately following lunch at 12 noon Where: Rockefeller Hall 310, Vassar College
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