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This article is part of the supplement: Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci

Open Access Proceedings

Meta-genetic association of rheumatoid arthritis and PTPN22 using PedGenie 2.1

Karen Curtin*, Jathine Wong, Kristina Allen-Brady and Nicola J Camp

Author Affiliations

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

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BMC Proceedings 2007, 1(Suppl 1):S12  doi:

Published: 18 December 2007

Abstract

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.