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Leveraging the HapMap correlation structure in association studies.

Noah Zaitlen1, Hyun Min Kang, Eleazar Eskin

  • 1Bioinformatics Program, University of California-San Diego, La Jolla, CA, USA.

American Journal of Human Genetics
|March 16, 2007
PubMed
Summary
This summary is machine-generated.

This study introduces WHAP, a novel method for indirect association in genetic studies. WHAP enhances power by leveraging SNP correlations for more efficient genomewide association studies.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Statistical genomics

Background:

  • High-throughput genotyping technologies enable genomewide association studies by measuring single-nucleotide polymorphism (SNP) allele frequencies.
  • Indirect association, using a subset of SNPs as proxies for uncollected ones, is crucial for association study efficiency.
  • Current multimarker methods for indirect association do not fully exploit SNP correlation structures.

Purpose of the Study:

  • To propose a novel multimarker indirect-association method, WHAP.
  • To improve the power of association studies by better utilizing the correlation structure between SNPs.
  • To provide a software implementation for widely used genotyping platforms.

Main Methods:

  • Developed WHAP, a novel multimarker indirect-association method based on weighted haplotype frequency differences.
  • Analyzed the power of WHAP compared to single-marker, multimarker, and traditional haplotype-based tests.
  • Empirically evaluated WHAP using HapMap reference panel data.

Main Results:

  • WHAP demonstrates a considerable gain in statistical power compared to existing methods.
  • Analytical and empirical evaluations confirm the enhanced power of the proposed method.
  • The method effectively utilizes the correlation structure between SNPs and their multimarker proxies.

Conclusions:

  • WHAP represents a significant advancement in multimarker indirect-association methods.
  • The proposed method offers increased power for genomewide association studies.
  • Software for Affymetrix 500k and Illumina HumanHap 550 chips is available.