Robust DNA Copy Number Estimation and SNP Genotype Calling: A Single Array Approach

• Activity Number: 223
• Type: Contributed
• Date/Time: Monday, August 3, 2009 : 2:00 PM to 3:50 PM
• Sponsor: IMS
• Author(s): Wenjiang Fu*+ and Lin Wan and Kelian Sun and Qi Ding and Ming Li and Yalu Wen and Yuehua Cui and Robert C. Elston and Minping Qian
• Companies: Michigan State University and Peking University and Michigan State University and Michigan State University and Michigan State University and Michigan State University and Michigan State University and Case Western Reserve University and Peking University
• Keywords: DNA copy number ; Genotype calling ; HapMap sample ; Probe sequence binding ; Robust method ; SNP microarray

Abstract

DNA copy number estimation and SNP genotype calling offer promise in identifying disease alleles or biomarkers in genome-wide association studies. Although numerous methods have been studied for the Affymetrix SNP arrays, robust and highly accurate copy number estimation and SNP genotype calling methods are still in need given the rapid advancement of the microarray technology and the lack of report of robustness. In this paper, we take a probe intensity composite representation (PICR) approach by modeling array sequence binding. This approach provides an allelic copy number estimation through simple regression analysis and leads to a genotype calling method. Using the HapMap samples and a cell-line data of multiple copies of the X-chromosome, we demonstrate that our method is robust across laboratories and across array platforms, consistently achieves high accuracy on genotype calling.