Analysis for 2 samples with HLA-DQB1 allele dropout at exon 2 in sequence-based typing

Abstract

To explore the reason for HLA-DQB1 allele dropout during routine sequence-based typing(SBT) in order to improve the accuracy of typing. Two thousand samples derived from HLA high-resolution typing laboratory were typed for HLA-DQB1 locus using an AlleleSEQR HLA-DQB1 SBT kit. Non-conclusive results and "abnormal" sequencing samples were retyped using a LABType rSSO HD HLA-DQB1 kit and further analyzed with both sequence-specific primers and group-specific primers and sequenced for haplotype analysis. Among the 2000 samples, 2 samples with no conclusive result were identified. The heterozygosity was confirmed with both the LAB Type SSO HD HLA-DQB1 kit and PCR-SBT in house method. Subsequent HLA-DQB1 cloning and haplotype sequencing have elucidated that HLA-DQB1*02:02 dropped out at exon 2 for the first sample and HLA-DQB1*02:01:01 dropped out at exon 2 for the second sample during PCR amplification. No novel nucleotide mutation was found. Our results indicated that preferential amplification at exon 2 of DQB1 may result in allele dropout in exon 2 sequences during HLA-DQB1 SBT test. This may provide useful information for HLA genotyping.