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This article is part of the supplement: Genetic Analysis Workshop 17: Unraveling Human Exome Data

Open Access Proceedings

Identifying variants that contribute to linkage for dichotomous and quantitative traits in extended pedigrees

Wei-Min Chen12*, Ani Manichaikul12 and Stephen S Rich1

Author Affiliations

1 Center for Public Health Genomics, University of Virginia, West Complex, 6th Floor, Suite 6111, PO Box 800717, University of Virginia, Charlottesville, VA 22908, USA

2 Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA 22908, USA

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BMC Proceedings 2011, 5(Suppl 9):S68  doi:10.1186/1753-6561-5-S9-S68

Published: 29 November 2011

Abstract

Compared to genome-wide association analysis, linkage analysis is less influenced by allelic heterogeneity. The use of linkage information in large families should provide a great opportunity to identify less frequent variants. We perform a linkage scan for both dichotomous and quantitative traits in eight extended families. For the dichotomous trait, we identified one linkage region on chromosome 4q. For quantitative traits, we identified two regions on chromosomes 4q and 6p for Q1 and one region on chromosome 6q for Q2. To identify variants that contribute to these linkage signals, we performed standard association analysis in genomic regions of interest. We also screened less frequent variants in the linkage region based on the risk ratio and phenotypic distribution among carriers. Two rare variants at VEGFC and one common variant on chromosome 4q conferred the greatest risk for the dichotomous trait. We identified two rare variants on chromosomes 4q (VEGFC) and 6p (VEGFA) that explain 12.4% of the total phenotypic variance of trait Q1. We also identified four variants (including one at VNN3) on chromosome 6q that are able to drop the linkage LOD from 3.7 to 1.0. These results suggest that the use of classical linkage and association methods in large families can provide a useful approach to identifying variants that are responsible for diseases and complex traits in families.