Analysis of genotype frequencies and interlocus association for the PM, DQA1, and D1S80 loci in four populations

Allele frequencies of the LDLR, HBGG, GYPA, D7S8, GC, DQA1, and D1S80 loci are presented and genotypes are analyzed for each of four ethnic groups: Af rican Americans (n = 200), US Caucasians (n = 200), US Hispanics (n = 200), and Japanese (n = 89). Hardy-Weinberg genotypic proportions were observed in all but two of the 28 population-locus tests undertaken. Those two insta nces are attributable to type I statistical error. Gametic equilibrium amon g loci is an assumption invoked for application of the product rule to util ize the discriminatory power from two or more loci simultaneously. Two stat istical methods, a genotype matching statistic and log,linear modeling, wer e used to evaluate gametic disequilibrium. The match statistic, comparing o bserved to expected likelihood of genotypic identity for seven loci among p airs of individuals within the database, revealed only one statistically si gnificant deviation among 20 tests. As expected, the probability of match w as generally lowest in the test on all ethnic groups combined, indicating t hat allele frequencies differ among ethnic groups for some of the loci. Thi s was confirmed with the statistic 8 to measure ethnic stratification, in w hich about 0.10 of the genetic variation is apportioned among the four ethn ic groups for four of the structural loci (LDLR, HBGG, GC, and DQA1), while for GYPA, D7S8, and D1S80, variation is more uniformly distributed among e thnic groups. Log-linear modeling was also applied to the Eve PM loci. The most parsimonious log-linear model included only three higher order terms: the two-way interactions of three of the PM loci with ethnic group. These t hree instances (LDLR, HBGG, and GC) indicated differences in allele frequen cies between ethnic groups. No two or higher way interaction (disequilibriu m) was observed among loci. In summary, the assumptions of Hardy-Weinberg a nd gametic equilibrium that facilitate the use of the five PM loci, DQA1 an d D1S80 in forensic applications are consistent with the allele and genotyp e frequencies observed in these populations.