Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population

Standardized genotyping of HLA STR by CE as surrogate for HLA class I and II markers and for identification of HLA identical siblings

“…For prediction of HLA‐B,‐C haplotypes, the STR haplotypes of D6S2678 and D6S2792 had slightly more and stronger LD than those of D6S2691 and D6S2678. Haplotypes of D6S2792, D6S2789 and of D6S2691, D6S2789 showed lesser and weaker LD with individual HLA‐B and ‐C alleles and HLA‐B,‐C haplotypes, which might be due to the lower degree of polymorphism of D6S2691 and D6S2789 and their increased distance to HLA‐B and –C compared with D6S2678 and D6S2792 . All two‐locus STR haplotypes had more LD with HLA‐B,‐C haplotypes than the corresponding individual STR loci, but most HLA haplotypes were predicted by combining the LD of individual STR loci and their haplotypes.…”

“…Parents and siblings have been routinely typed for HLA‐A, ‐B, ‐C, and –DRB1 (low‐resolution typing by serology and/or DNA sequence‐specific primer). Genotyping of the eight STR loci D6S2972, D6S2906, D6S2691, D6S2678, D6S2792, D6S2789, D6S273, and DQIV was performed by CE on an ABI 310 or an ABI 3130 Genetic Analyser (Applied Biosystems by Life Technologies, Carlsbad, CA, USA) by comparison with locus‐specific sequenced allelic ladders after PCR with fluorescent‐labeled primers as previously described .…”

“…Based on phasing information, 576 full haplotypes of four HLA and eight STR loci were deduced. Haplotypes from three families were not taken into consideration because of recombination events within the HLA region in two cases and a de novo mutation at the D6S2678 locus in another case (a maternal allele *20 mutated to *21) as described elsewhere . In some families only one parent was available.…”

“…As results from previous studies with HLA STRs were not comparable due to a lack of common allele designation, names for loci and definition of primer sets, such a standardized nomenclature was suggested for these microsatellites . For the eight HLA STR loci used in this study (D6S2972, D6S2906 (C3_3_6), D6S2691 (C2_4_4), D6S2678 (C1_4_4), D6S2792 (TNFa), D6S2789 (TNFd), D6S273, and DQIV (M2_4_32)) such a sequence‐based nomenclature was defined by use of publicly available reference DNA samples . Furthermore, a population study carried out in an Austrian population showed that these loci offer a considerable degree of polymorphism, which is a prerequisite for their use in this study.…”