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Minor differences in haplotype frequency estimates can produce very large differences in heterogeneity test
1Academic Department of Psychiatry, Queen Mary's School of Medicine and Dentistry, London, UK. david.curtis@qmul.ac.uk
Comparing two software programs for genetic association studies revealed that minor variations in estimated haplotype frequencies can lead to substantial differences in statistical significance. This highlights the importance of careful interpretation in genetic research.
Area of Science:
- Population Genetics
- Statistical Genetics
- Bioinformatics
Background:
- Haplotype association tests commonly use likelihood ratio tests for case-control frequency heterogeneity.
- The DRD2 gene and heroin dependence association study provided data for analysis.
Purpose of the Study:
- To compare haplotype frequency estimation and likelihood ratio statistics generated by two software programs (MLOCUS and GENECOUNTING).
- To assess the empirical significance of results using permutation testing.
Main Methods:
- Utilized data from a heroin dependence and DRD2 gene association study.
- Employed MLOCUS and GENECOUNTING software for haplotype frequency estimation and likelihood ratio statistics.
- Conducted permutation testing for empirical significance assessment.
Main Results:
- Both programs produced similar, but not identical, haplotype frequency estimates.
- MLOCUS yielded a p-value of 1.8*10^-15, GENECOUNTING yielded 5.4*10^-4, and permutation testing yielded 2.8*10^-4.
- Significant discrepancies were observed in the likelihood ratio statistics between the two programs.
Conclusions:
- Discrepancies may arise because estimated combined haplotype frequencies are not constrained to be weighted averages of case/control frequencies.
- Minor variations in estimated haplotype frequencies can profoundly impact the likelihood ratio statistic and associated p-values.
- Emphasizes the need for caution when interpreting results from different software in genetic association studies.
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