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Accelerating Haplotype-Based Genome-Wide Association Study Using Perfect Phylogeny and Phase-Known Reference Data

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  • Yungang He
  • Cong Li
  • Christopher I Amos
  • Momiao Xiong
  • Hua Ling
  • Li Jin

Abstract

The genome-wide association study (GWAS) has become a routine approach for mapping disease risk loci with the advent of large-scale genotyping technologies. Multi-allelic haplotype markers can provide superior power compared with single-SNP markers in mapping disease loci. However, the application of haplotype-based analysis to GWAS is usually bottlenecked by prohibitive time cost for haplotype inference, also known as phasing. In this study, we developed an efficient approach to haplotype-based analysis in GWAS. By using a reference panel, our method accelerated the phasing process and reduced the potential bias generated by unrealistic assumptions in phasing process. The haplotype-based approach delivers great power and no type I error inflation for association studies. With only a medium-size reference panel, phasing error in our method is comparable to the genotyping error afforded by commercial genotyping solutions.

Suggested Citation

  • Yungang He & Cong Li & Christopher I Amos & Momiao Xiong & Hua Ling & Li Jin, 2011. "Accelerating Haplotype-Based Genome-Wide Association Study Using Perfect Phylogeny and Phase-Known Reference Data," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-8, July.
    • Handle: RePEc:plo:pone00:0022097
    DOI: 10.1371/journal.pone.0022097
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