Importance of hardy-weinberg equilibrium testing in snp analysis
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If genotype or allele frequencies deviate significantly from HWE, it can indicate Systematic errors in genotyping, Unexpected population structure, Presence of homologous regions in the genome, Association with trait in case-control studies. Since the last of those is least likely, so deviation from HWE is an indicator that a marker should be discarded. It is true unless adjacent markers in LD with one another both violate HWE.
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