*PLEASE NOTE: This module is closed for registraiton. We suggest that you register for Module 7: Population Genetic Data Analysis instead.

This module assumes the material in Module 1 and serves as a foundation for many later modules.  This module will provide students with the basic tools to carry out genetic association analysis within the context of genome wide association studies (GWAS) and next-generation sequencing studies with considerable emphasis on hands-on learning.  Topics covered include: case-control (disease) association testing; quantitative trait analysis; quality control processes in GWAS; multi-locus testing using gene and pathway information; population structure and ancestry inference; association testing in the presence of population structure and/or relatedness; gene-environment and gene-gene interactions; basic rare variant association analysis in sequencing studies; advanced rare variant methods; sequence kernel association tests (SKAT); meta analysis; design considerations; and other emerging topics.  An important component of this module is in-class software exercises which will provide students with hands-on experience analyzing real data using state-of-the-art analysis tools for GWAS and next generation sequencing data.  Many software applications are implemented in R and the module will be most useful for students with basic familiarity with R, though all necessary R code will be provided.  Other public domain software that will be used include PLINK.

Background reading: Thornton, T., and McPeek, M.S. 2010. ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure.  Am. J. Hum. Genet. 86: 172-184. 
Wu, M.C., Lee, S., Cai, T., Li, Y., Boehnke, M., and Lin, X. 2011. Rare-variant association testing for sequencing data with the sequence kernel association test. Am. J. Hum. Genet. 89: 82-93.