The Essentiality of Reporting Hardy-Weinberg Equilibrium Calculations in Population-Based Genetic Association Studies

Population-based genetic association studies have proven to be a powerful tool inidentifying genes implicated in many complex human diseases that have a huge impacton public health. an essential quality control step in such studies is to undertakehardy-weinberg equilibrium (hwe) calculations. deviations from hwe in the controlgroup may reflect important problems including selection bias, population stratificationand genotyping errors. if hwe is violated, the inferences of these studies maythus be biased. we therefore aimed to examine the extent to which hwe calculationsare reported in genetic association studies published in cell journal(yakhteh) (cell j).using keywords pertaining to genetic association studies, eleven relevant articleswere identified of which ten provided full genotypic data. the genotype distribution of16 single nucleotide polymorphisms (snps) was re-analyzed for hwe by using threedifferent methods where appropriate. hwe was not reported in 60% of all articlesinvestigated. among those reporting, only one article provided calculations correctlyand in detail. therefore, 90% of articles analyzed failed to provide sufficient hwedata. interestingly, three articles had significant hwe deviation in their control groupsof which one highly deviated from hwe expectations (p= 9.8×10-12). we thus showthat hwe calculations are under-reported in genetic association studies publishedin this journal. furthermore, the conclusions of the three studies showing significanthwe in their control groups should be treated cautiously as they may be potentiallymisleading. we therefore recommend that reporting of detailed hwe calculationsshould become mandatory for such studies in the future.