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Testing for linkage and Hardy-Weinberg disequilibrium
1Statistical Advisory Service, Imperial College, South Kensington Campus, 8 Princes Gardens, London, UK. e.kulinskaya@ic.ac.uk
Annals of Human Genetics
|February 3, 2009
Summary
This study questions the exclusive use of two-sided tests for linkage disequilibrium (LD) and Hardy-Weinberg equilibrium (HWE). It proposes conditional p-values to achieve equivalent results for both one-sided and two-sided tests in genetic analyses.
Area of Science:
- Population genetics
- Statistical genetics
- Bioinformatics
Background:
- Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) are fundamental concepts in population genetics.
- Current statistical testing methods for HWE and LD may lack consistency and equivalence.
- The choice of statistical tests can impact inferences drawn from genetic data.
Purpose of the Study:
- To evaluate the necessity of exclusively using two-sided tests for LD.
- To compare the equivalence of different statistical tests for LD measures.
- To advocate for the use of conditional p-values in HWE and LD testing.
Main Methods:
- Analysis of statistical tests for Hardy-Weinberg equilibrium (HWE).
- Comparison of one-sided and two-sided tests for linkage disequilibrium (LD).
- Evaluation of exact and standard statistical tests for popular LD measures.
- Application of conditional p-values for HWE and LD assessment.
Main Results:
- The necessity of exclusively using two-sided tests for LD is challenged.
- Exact two-sided tests for popular LD measures are not equivalent.
- Standard statistical tests for LD are not equivalent, unlike one-sided tests.
- Conditional p-values offer equivalent results for one-sided and two-sided tests.
Conclusions:
- Conditional p-values provide a unified approach for testing HWE and LD.
- The proposed method enhances consistency in genetic data inference.
- This approach addresses inconsistencies arising from different LD testing methods.
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