Identification of a novel HLA‐DPB1 allele (DPB1*1902) by haplotype‐specific extraction and nucleotide sequencing†

Abstract

The DPB1*1902 allele resulted from a single-nucleotide substitution at codon 35 (TTC --> CTC/F --> L) of exon 2 of DPB1*0402 or 0602.

SNP-specific extraction of haplotype-resolved targeted genomic regions

“…Also, its potential to generate short-range haplotype information has been confirmed and utilized successfully for characterizing new HLA alleles and resolve HLA typing ambiguities (22,24,25,29,30). We demonstrate that by haploseparating and tiling neighboring regions we can generate phased sequence information of almost 150 kb.…”

“…By selectively targeting unique genomic variation, including SNPs, individual molecular haplotypes can be isolated and characterized. This method has been used extensively to resolve short-range HLA allele ambiguities and determine new HLA alleles (25,29,30). …”

“…DNA was purified from blood by conventional isolation methods such as the Qiagen EZ1 magnetic separation kit from 350 μl of whole blood or ethanol precipitation (25) from 5–7 ml of whole blood.…”

HLA class II DPB1 and DRB1 polymorphisms associated with genetic susceptibility to beryllium toxicity

“…For ambiguities or inconsistent patterns of primer amplifications, sequence-based typing was performed and confirmed by bi-directional sequencing-based typing of exon 2 (AlleleSEQR HLA-DPB1 SBT kit; Atria Genetics, South San Francisco, California USA). A new allele was identified and was named DPB1*1902 25. DRB1 typing was performed by sequence-based typing.…”

Identification of a New HLA-B Allele (B*1576) by Haplotype Specific Extraction

“…Haplotype specific extraction provides a rapid, automated method for determining true (i.e. non-statistically derived) and previously unknown haplotypes, directly from genomic DNA, without requiring any familial information [4][5][6][7][8][9][10]. The method does not rely on amplification-based phasing methods which can be affected by polymorphic variation and eliminates the need for cloning or subcloning for the characterization of new alleles.…”