Studying gene and gene-environment effects of uncommon and common variants on continuous traits: A marker-set approach using gene-trait similarity regression

Jung Ying Tzeng, Daowen Zhang, Monnat Pongpanich, Chris Smith, Mark I. McCarthy, Michèle M. Sale, Bradford B. Worrall, Fang Chi Hsu, Duncan C. Thomas, Patrick F. Sullivan

研究成果: Article

56 引文 斯高帕斯(Scopus)

摘要

Genomic association analyses of complex traits demand statistical tools that are capable of detecting small effects of common and rare variants and modeling complex interaction effects and yet are computationally feasible. In this work, we introduce a similarity-based regression method for assessing the main genetic and interaction effects of a group of markers on quantitative traits. The method uses genetic similarity to aggregate information from multiple polymorphic sites and integrates adaptive weights that depend on allele frequencies to accomodate common and uncommon variants. Collapsing information at the similarity level instead of the genotype level avoids canceling signals that have the opposite etiological effects and is applicable to any class of genetic variants without the need for dichotomizing the allele types. To assess gene-trait associations, we regress trait similarities for pairs of unrelated individuals on their genetic similarities and assess association by using a score test whose limiting distribution is derived in this work. The proposed regression framework allows for covariates, has the capacity to model both main and interaction effects, can be applied to a mixture of different polymorphism types, and is computationally efficient. These features make it an ideal tool for evaluating associations between phenotype and marker sets defined by linkage disequilibrium (LD) blocks, genes, or pathways in whole-genome analysis.

原文English
頁(從 - 到)277-288
頁數12
期刊American Journal of Human Genetics
89
發行號2
DOIs
出版狀態Published - 2011 八月 12

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

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