Quality Control of Affymetrix SNP Arrays by Imputation of Damaged Area

• Activity Number: 223
• Type: Contributed
• Date/Time: Monday, August 3, 2009 : 2:00 PM to 3:50 PM
• Sponsor: IMS
• Author(s): Ming Li*+ and Wenjiang Fu and Yalu Wen
• Companies: Michigan State University and Michigan State University and Michigan State University
• Keywords: Genotype Calling ; Array quanlity ; Genotyping accuracy ; mixed effect model

Abstract

A number of genotype calling methods have been studied for the Affymetrix high density SNP arrays, and the accuracy of genotype calling has been found to be highly dependent on the array quality, which has yet received enough attention. Although the SNP arrays of the HapMap samples have been used as gold-standard, we have found that a few HapMap arrays also have array quality issues.In this study, we examined the array images of all 90 HapMap samples on the Affymetrix 50K Xba arrays and studied the effect of the poor array quality of damaged areas on the genotyping calls. We further developed a mixed effect model to impute the probe intensities in the damaged areas. Based on the above results, we conclude that caution should be taken before applying genotype calling methods and our mixed effect model may help to improve the array quality to achieve high accuracy.