Identifying Causal Rare Variants of Disease Through Family-based Analysis of Genetics Analysis Workshop 17 Data Set

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Identifying Causal Rare Variants of Disease Through Family-based Analysis of Genetics Analysis Workshop 17 Data Set

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Title: Identifying Causal Rare Variants of Disease Through Family-based Analysis of Genetics Analysis Workshop 17 Data Set
Author: Yip, Wai-Ki; De, Gourab; Raby, Benjamin Alexander; Laird, Nan M.

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Citation: Yip, Wai-Ki, Gourab De, Benjamin A Raby, and Nan Laird. 2011. Identifying causal rare variants of disease through family-based analysis of Genetics Analysis Workshop 17 data set. BMC Proceedings 5(Suppl 9): S21.
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Abstract: Linkage- and association-based methods have been proposed for mapping disease-causing rare variants. Based on the family information provided in the Genetic Analysis Workshop 17 data set, we formulate a two-pronged approach that combines both methods. Using the identity-by-descent information provided for eight extended pedigrees (n = 697) and the simulated quantitative trait Q1, we explore various traditional nonparametric linkage analysis methods; the best result is obtained by assuming between-family heterogeneity and applying the Haseman-Elston regression to each pedigree separately. We discover strong signals from two genes in two different families and weaker signals for a third gene from two other families. As an exploratory approach, we apply an association test based on a modified family-based association test statistic to all rare variants (frequency < 1% or < 3%) designated as causal for Q1. Family-based association tests correctly identified causal single-nucleotide polymorphisms for four genes (KDR, VEGFA, VEGFC, and FLT1). Our results suggest that both linkage and association tests with families show promise for identifying rare variants.
Published Version: doi:10.1186/1753-6561-5-S9-S21
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287856/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:8641842
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