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

Publication ,  Journal Article
Zakharov, S; Wong, TY; Aung, T; Vithana, EN; Khor, CC; Salim, A; Thalamuthu, A
Published in: BMC Genomics
August 21, 2013

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.

Duke Scholars

Published In

BMC Genomics

DOI

EISSN

1471-2164

Publication Date

August 21, 2013

Volume

14

Start / End Page

569

Location

England

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Models, Statistical
  • Models, Genetic
  • Linkage Disequilibrium
  • Humans
  • Haplotypes
  • Genotyping Techniques
  • Genome-Wide Association Study
  • Genetics, Population
  • Genetic Predisposition to Disease
 

Citation

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Zakharov, S., Wong, T. Y., Aung, T., Vithana, E. N., Khor, C. C., Salim, A., & Thalamuthu, A. (2013). Combined genotype and haplotype tests for region-based association studies. BMC Genomics, 14, 569. https://doi.org/10.1186/1471-2164-14-569
Zakharov, Sergii, Tien Yin Wong, Tin Aung, Eranga Nishanthie Vithana, Chiea Chuen Khor, Agus Salim, and Anbupalam Thalamuthu. “Combined genotype and haplotype tests for region-based association studies.BMC Genomics 14 (August 21, 2013): 569. https://doi.org/10.1186/1471-2164-14-569.
Zakharov S, Wong TY, Aung T, Vithana EN, Khor CC, Salim A, et al. Combined genotype and haplotype tests for region-based association studies. BMC Genomics. 2013 Aug 21;14:569.
Zakharov, Sergii, et al. “Combined genotype and haplotype tests for region-based association studies.BMC Genomics, vol. 14, Aug. 2013, p. 569. Pubmed, doi:10.1186/1471-2164-14-569.
Zakharov S, Wong TY, Aung T, Vithana EN, Khor CC, Salim A, Thalamuthu A. Combined genotype and haplotype tests for region-based association studies. BMC Genomics. 2013 Aug 21;14:569.
Journal cover image

Published In

BMC Genomics

DOI

EISSN

1471-2164

Publication Date

August 21, 2013

Volume

14

Start / End Page

569

Location

England

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Models, Statistical
  • Models, Genetic
  • Linkage Disequilibrium
  • Humans
  • Haplotypes
  • Genotyping Techniques
  • Genome-Wide Association Study
  • Genetics, Population
  • Genetic Predisposition to Disease