Novel associations among HLA-DQA1 and-DQB1 alleles, revealed by high-resolution sequence-based typing (SBT)

Althought it is a valuable tool for the identification of HLA alleles, sequ ence-based typing (SBT) presents difficulties when used to determine HLA-DQ A1 and -DQB1 alleles Specifically, some HLA-DQA1 alleles have a three-base deletion at codon 56 of exon 2 that interferes with the sequencing read. Mo reover, the frequently used primers for HLA-DQB1 may co-amplify the HLA-DQB 2 pseudogene. To overcome these problems, we amplified DQA1 exon 2 using fi ve group-specific polymerase chain reactions (PCRs) which allowed separatio n of deleted from non-deleted DQA1 alleles DQB1 exon 2 was amplified using two group-specific amplifications. To increase typing resolution, we also a nalyzed DQA1 exons 1, 3 and 4 and DQB1 exon 3 by PCR using sequence-specifi c primers (PCR-SSP) or SET analysis. Using this method we found some import ant associations between DQA1 and DQB1 alleles: DQA1*05011 and DQB1*0201, D QA1*0505 and DQB1*03011, DQA1*01021 and DQB1*06, DQA1*01022 and DQB1*0502.