Human leukocyte antigen-A, -B, -C, -DRB1 allele and haplotype frequencies in Americans originating from southern Europe: contrasting patterns of population differentiation between Italian and Spanish Americans.

High-resolution DNA sequencing was used to identify the human leukocyte antigen (HLA) -A, -B, -C, and -DRB1 alleles found in 552 individuals from the United States indicating Southern European (Italian or Spanish) heritage. A total of 46 HLA-A, 80 HLA-B, 32 HLA-C, and 50 DRB1 alleles were identified. Frequent alleles included A02:01:01G (allele frequency = 0.26 in Italian Americans and 0.22 in Spanish Americans); B07:02:01G (Italian Americans allele frequency = 0.11); B44:03 (Spanish Americans allele frequency = 0.07); C04:01:01G and C07:01:01G (allele frequency = 0.13 and 0.16, respectively, in Italian Americans; 0.15 and 0.12, respectively, in Spanish Americans); and DRB107:01:01 (allele frequency = 0.12 in each population). The action of balancing selection was inferred at the HLA-B and -C loci in both populations. The A01:01:01G-C07:01:01G-B08:01:01G-DRB103:01:01 haplotype was the most frequent A-C-B-DRB1 haplotype in Italian Americans (haplotype frequency = 0.049), and was the second most frequent haplotype in Spanish Americans (haplotype frequency = 0.021). A29:02:01-C16:01:01-B44:03-DRB107:01:01 was the most frequent A-C-B-DRB1 in Spanish Americans (haplotype frequency = 0.023), and was observed at a frequency of 0.015 in Italian Americans. Pairwise F'(st) values measuring the degree of differentiation between these Southern European American populations as well as European and European American populations suggest that Spanish Americans constitute a distinct subset of the European American population, most similar to Mexican Americans, whereas Italian Americans cannot be distinguished from the larger European American population.