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

Abstract

Routine typing of a potential bone marrow donor by sequence-specific oligonucleotide probes and sequence based typing produced inconclusive subtyping results, suggesting a new allele. A magnetic bead-based method, haplotype specific extraction (HSE), was used to separate the diploid sample into its haploid components. The sample was then re-typed using standard sequence-based typing (SBT), revealing a new human leukocyte antigen (HLA) allele, since named B*1576. HSE used in conjunction with standard SBT is a convenient and simple tool for resolving ambiguous and novel allele combinations without the need for amplification or subcloning.

In contrast to other stimulatory natural killer cell immunoglobulin-like receptor loci, several KIR2DS5 alleles predominate in African Americans

“…When required, PCR products were cloned using the TOPO TA cloning kit (Invitrogen). Qiagen HaploPrep reagents 488A ( KIR2DS2 ) and 744d22 ( KIR2DS4 ) (Valencia, CA) were used to isolate alleles [23] in some cases following manufacturer’s instructions.…”

In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM

“…For example, one promising approach is to use DNA haplotype-specific extraction of the gene from the sample using a commercially available extraction kit, such as the solid-phase, capture-based EZ1 HaploPrep kit from Qiagen [88], and then resequencing the unresolved haplotype. The DNA haplotype-specific extraction procedure can extract genomic regions of up to 50 kb of contiguous sequence without amplication or concentration of the extracted DNA, and it has been used successfully to genotype and haplotype HLA class I and class II genes [84,[89][90][91][92][93] including adjoining genes such as HLA-B, MICA and HLA-C [89].…”

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

“…Molecular haplotyping has been successfully used to describe a novel HLA DPB allele. This technology has been previously used to describe novel HLA B alleles (3, 4). It, therefore, appears that there is an alternative technology to the traditional way for characterizing new HLA alleles, by amplification and subcloning, which is a much simpler and direct method.…”