Joint identification of multiple genetic variants via elastic-net variable selection in a genome-wide association analysis

Annals of Human Genetics
Seoae ChoTaesung Park

Abstract

Unraveling the genetic background of common complex traits is a major goal in modern genetics. In recent years, genome-wide association (GWA) studies have been conducted with large-scale data sets of genetic variants. Most of those studies have relied on single-marker approaches that identify single genetic factors individually and can be limited in considering fully the joint effects of multiple genetic factors on complex traits. Joint identification of multiple genetic factors would be more powerful and would provide better prediction on complex traits since it utilizes combined information across variants. Here we propose a multi-stage approach for GWA analysis: (1) prescreening, (2) joint identification of putative SNPs based on elastic-net variable selection, and (3) empirical replication using bootstrap samples. Our approach enables an efficient joint search for genetic associations in GWA analysis. The suggested empirical replication method can be beneficial in GWA studies because one can avoid a costly, independent replication study while eliminating false-positive associations and focusing on a smaller number of replicable variants. We applied the proposed approach to a GWA analysis, and jointly identified 129 genetic ...Continue Reading

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Citations

May 25, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zitong Li, Mikko J Sillanpää
Jul 3, 2013·Bioinformatics·Chloé-Agathe AzencottKarsten M Borgwardt
Sep 14, 2012·Annals of Human Genetics·Hanni P Kärkkāinen, Mikko J Sillanpää
Jul 16, 2014·International Journal of Molecular Sciences·Jayoun KimTaesung Park
Nov 9, 2015·Cellular Immunology·Benjamin VincentJeffrey Frelinger
Sep 10, 2014·Genetic Epidemiology·Shaolong CaoYu-Ping Wang
Aug 13, 2015·PloS One·Yongkang Kim, Taesung Park
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Nov 4, 2016·Journal of Bioinformatics and Computational Biology·Sohee OhTaesung Park
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Jan 31, 2015·Cancer Informatics·Sungyeon HongTaesung Park
Jan 25, 2019·PloS One·Shuzhen SunCharles Chen
Aug 9, 2020·Psychotherapy Research : Journal of the Society for Psychotherapy Research·Philipp HerzogEva-Lotta Brakemeier
Jun 2, 2016·Statistical Applications in Genetics and Molecular Biology·Charles LaurinGitta Lubke
Mar 14, 2019·Statistical Applications in Genetics and Molecular Biology·Kevin HeYi Li
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Jan 19, 2011·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Elisa FrullantiTommaso A Dragani

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