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Sampling distribution of summary linkage disequilibrium measures
M D Teare1, A M Dunning, F Durocher
1Mathatical Modelling and Genetic Epidemiology, Division of Genomic Medicine, University of Sheffield, UK. m.d.teare@sheffield.ac.uk
Annals of Human Genetics
|August 14, 2002
Summary
Linkage disequilibrium (LD) measures like D' can be inflated in small sample sizes or extreme allele frequencies. The Delta statistic offers a more robust measure for association studies, unaffected by these factors.
Area of Science:
- Population genetics
- Statistical genetics
Background:
- Association studies rely on linkage disequilibrium (LD) measures.
- Common LD measures include D' and Delta, reflecting LD magnitude and mapping power, respectively.
Purpose of the Study:
- To investigate the sampling distribution of mean D' and Delta statistics.
- To assess the impact of sample size and allele frequencies on these LD measures.
Main Methods:
- Studied sampling distributions of mean D' and Delta.
- Analyzed effects of varying sample size and major allele frequencies.
- Illustrated findings with real SNP data from an Ashkenasi Jewish population.
Main Results:
- Mean D' estimates are substantially inflated with small sample sizes or extreme allele frequencies, especially when inferring haplotype frequencies.
- Smaller studies tend to show higher LD levels due to D' inflation.
- The Delta statistic is less affected by sample size and allele frequencies.
Conclusions:
- D' inflation can be mitigated using bootstrap correction and avoiding extreme allele frequency markers.
- Delta provides a more reliable measure for LD mapping power across different sample sizes and allele frequencies.
- These findings are crucial for accurate association study design and interpretation.