The effect of ethnic and racial population substructuring on the estimation of multi-locus fixed-bin VNTR RFLP genotype probabilities.

Four East Asian ethnic and four racial VNTR RFLP Southern California databases were used to determine the impact of population substructure on fixed-bin genotype probability estimates. Two calculations were used for population-level probabilities: Stratified sampling, which takes substructuring into account, and pooling, which ignores it. Using 1000 four-locus genotypes, the relative difference between probabilities calculated with the stratified and the pooled methods did not exceed one order of magnitude out of about 11 orders of magnitude for East-Asian racial genotypes. Pooled estimates differed from cognate ethnic values by less than one order of magnitude out of about six. These findings suggest substructuring of races by major ethnic groups does not lead to large errors. Racial genotype probability variances were on average about twice the ethnic variances. Multi-racial total population probabilities calculated by the pooled and stratified methods differed by less than one order of magnitude out of five.