Development of Analysis Pipeline for a Genome-Wide Association Study of Schizophrenia and Bipolar Disorders: An Integrated SNP, Gene, and Pathway Analysis

• Activity Number: 23
• Type: Topic Contributed
• Date/Time: Sunday, July 29, 2012 : 2:00 PM to 3:50 PM
• Sponsor: Section on Government Statistics
• Author(s): Clarence K. Zhang*+ and Hongyu Zhao and John Concato and J. Michael Gaziano and Philip Harvey and Larry Siever and Timothy O'Leary
• Companies: VA Clinical Epidemiology Research Center, VA Connecticut Healthcare System and Yale School of Public Health and VA Clinical Epidemiology Research Center, VA Connecticut Healthcare System and Massachusetts Area Veterans Research and Information Center, VA Boston Healthcare System and Miami Veteran Affairs Healthcare System and University of Miami and Bronx VA Medical Center and Mt Sinai School of Medicine and VA Office of Research and Development
• Keywords: Schizohprenia ; Bipolar disorder ; GWAS ; pathway ; association

Abstract

Schizophrenia and bipolar disorder are mental illnesses with substantial genetic components, and are prevalent diagnoses in the Veterans Health Administration (VHA). Genome wide association studies (GWAS) can identify genetic variants in multiple complex diseases. In this talk, we will introduce a GWAS study funded by the VA Cooperative Studies Program. Using a case-control design, we will compare the genomic variation of 9,000 Veterans with schizophrenia and 9,000 Veterans with bipolar disorder to the genomic variation of approximately 20,000 Veterans without these conditions. Given that the project is currently enrolling, our focus will be on development of the analysis pipeline that includes: data retrieval, genotype calling, quality control metrics, population stratification analysis, imputation, single marker association analysis, gene-based analysis, pathway based analysis, functional annotation, and other related studies. We will present data on enrollment and various quality measurements from an initial analysis. This project has the potential to advance the personalized treatment for two common mental disorders affecting veterans.