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WHAP: haplotype-based association analysis.

Shaun Purcell1, Mark J Daly, Pak C Sham

  • 1Center for Human Genetic Research, MGH, Boston, MA, USA. shaun@pngu.mgh.harvard.edu

Bioinformatics (Oxford, England)
|November 23, 2006
PubMed
Summary
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This study introduces WHAP, a software tool for haplotype-based association analysis in genetic studies. It enables flexible testing of genetic variants and their effects on traits in various sample types.

Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Haplotype-based association analysis is crucial for understanding trait genetics.
  • Existing tools may lack flexibility in analyzing complex genetic architectures.

Purpose of the Study:

  • To introduce WHAP, a versatile software tool for haplotype-based association analysis.
  • To provide a flexible platform for dissecting genetic associations at multiple loci.

Main Methods:

  • Development of a C/C++ software tool (WHAP).
  • Implementation of various statistical tests including omnibus, haplotype-specific, and conditional likelihood ratio tests.
  • Support for single nucleotide polymorphism (SNP) and multiallelic marker data in population and family samples.

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Main Results:

  • WHAP offers a comprehensive suite of tests for quantitative and qualitative traits.
  • The tool allows flexible imposition of constraints on haplotype effects for conditional analyses.
  • Demonstrated utility in dissecting multi-locus associations.

Conclusions:

  • WHAP provides a powerful and flexible approach to haplotype-based association analysis.
  • The software facilitates detailed investigation of genetic variant effects and their independence.
  • Enables nuanced dissection of complex genetic associations.