Figure 3.
Illustration of output from the Web tool (see Materials and Methods section and http://www.oege.org/software/hwe-mr-calc.shtml) developed for Hardy-Weinberg equilibrium (HWE) analysis with estimations of possible ascertainment bias. In this example, the user input was genotype group counts of 5,236 (commoner homozygotes), 4,050 (heterozygotes), and 714 (rarer homozygotes). The output χ2 value of 3.32 approaches but does not reach statistical significance (at P < 0.05). The table of solutions for perfect HWE (χ2 = 0) shows, in red, the count that would be necessary if one of the 3 groups were accordingly adjusted. The differences from observed counts identify the possible missingnesses or excesses, which can then be considered in a subsequent genotype-phenotype or Mendelian randomization analysis. Hz, homozygotes; SNPs, single nucleotide polymorphisms. (TRG, SR, and INMD represent the authors’ initials.)