This article is part of the supplement: Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci
Meta-genetic association of rheumatoid arthritis and PTPN22 using PedGenie 2.1
Division of Genetic Epidemiology, Department of Biomedical Informatics, University of Utah School of Medicine, 391 South Chipeta Way, Suite D, Salt Lake City, Utah 84108-1206, USA
BMC Proceedings 2007, 1(Suppl 1):S12 doi:Published: 18 December 2007
PedGenie beta version 2.1 is a unique, flexible, and easily implemented analysis software tool that is enhanced significantly by incorporation of meta-statistics to allow valid combined analysis of multiple studies, including mixtures of family-based and independent resources, in the detection of genetic association with common disease. Genetic Analysis Workshop 15 Problem 2 data, provided by the North American Rheumatoid Arthritis Consortium, were used to demonstrate PedGenie 2.1 meta-association testing of variants in the PTPN22 gene and rheumatoid arthritis across multiple resources containing both family-based and independent individuals. Our findings are generally consistent with previous reports for a panel of 14 single-nucleotide polymorphism (SNP) markers, including functional coding SNP R620W, in which the minor allele conferred a significant two-fold increased risk. More power to detect associations was achieved in certain analyses by using extra family-based samples, rather than restricting analyses to single cases randomly selected from each pedigree.