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Genome-Wide Interaction-Based Association Analysis Identified Multiple New Susceptibility Loci for Common Diseases

Author

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  • Yang Liu
  • Haiming Xu
  • Suchao Chen
  • Xianfeng Chen
  • Zhenguo Zhang
  • Zhihong Zhu
  • Xueying Qin
  • Landian Hu
  • Jun Zhu
  • Guo-Ping Zhao
  • Xiangyin Kong

Abstract

Genome-wide interaction-based association (GWIBA) analysis has the potential to identify novel susceptibility loci. These interaction effects could be missed with the prevailing approaches in genome-wide association studies (GWAS). However, no convincing loci have been discovered exclusively from GWIBA methods, and the intensive computation involved is a major barrier for application. Here, we developed a fast, multi-thread/parallel program named “pair-wise interaction-based association mapping” (PIAM) for exhaustive two-locus searches. With this program, we performed a complete GWIBA analysis on seven diseases with stringent control for false positives, and we validated the results for three of these diseases. We identified one pair-wise interaction between a previously identified locus, C1orf106, and one new locus, TEC, that was specific for Crohn's disease, with a Bonferroni corrected P

Suggested Citation

  • Yang Liu & Haiming Xu & Suchao Chen & Xianfeng Chen & Zhenguo Zhang & Zhihong Zhu & Xueying Qin & Landian Hu & Jun Zhu & Guo-Ping Zhao & Xiangyin Kong, 2011. "Genome-Wide Interaction-Based Association Analysis Identified Multiple New Susceptibility Loci for Common Diseases," PLOS Genetics, Public Library of Science, vol. 7(3), pages 1-16, March.
    • Handle: RePEc:plo:pgen00:1001338
    DOI: 10.1371/journal.pgen.1001338
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    Cited by:

    1. Shuo Jiao & Li Hsu & Sonja Berndt & Stéphane Bézieau & Hermann Brenner & Daniel Buchanan & Bette J Caan & Peter T Campbell & Christopher S Carlson & Graham Casey & Andrew T Chan & Jenny Chang-Claude &, 2012. "Genome-Wide Search for Gene-Gene Interactions in Colorectal Cancer," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-14, December.
    2. Emily Mathieu, 2016. "AGGrEGATOr: A Gene-based GEne-Gene interActTiOn test for case-control association studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(2), pages 151-171, April.

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