Combined genotype and haplotype tests for region-based association studies.

Journal Article (Journal Article)

BACKGROUND: Although single-SNP analysis has proven to be useful in identifying many disease-associated loci, region-based analysis has several advantages. Empirically, it has been shown that region-based genotype and haplotype approaches may possess much higher power than single-SNP statistical tests. Both high quality haplotypes and genotypes may be available for analysis given the development of next generation sequencing technologies and haplotype assembly algorithms. RESULTS: As generally it is unknown whether genotypes or haplotypes are more relevant for identifying an association, we propose to use both of them with the purpose of preserving high power under both genotype and haplotype disease scenarios. We suggest two approaches for a combined association test and investigate the performance of these two approaches based on a theoretical model, population genetics simulations and analysis of a real data set. CONCLUSIONS: Based on a theoretical model, population genetics simulations and analysis of a central corneal thickness (CCT) Genome Wide Association Study (GWAS) data set we have shown that combined genotype and haplotype approach has a high potential utility for applications in association studies.

Full Text

Duke Authors

Cited Authors

  • Zakharov, S; Wong, TY; Aung, T; Vithana, EN; Khor, CC; Salim, A; Thalamuthu, A

Published Date

  • August 21, 2013

Published In

Volume / Issue

  • 14 /

Start / End Page

  • 569 -

PubMed ID

  • 23964661

Pubmed Central ID

  • PMC3852120

Electronic International Standard Serial Number (EISSN)

  • 1471-2164

Digital Object Identifier (DOI)

  • 10.1186/1471-2164-14-569


  • eng

Conference Location

  • England