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Derivation of HLA types from shotgun sequence datasets

2012; BioMed Central; Volume: 4; Issue: 12 Linguagem: Inglês

10.1186/gm396

1756-994X

Robin M. Warren, Gina Choe, Douglas J Freeman, Mauro Castellarin, Sarah Munro, Richard A. Moore, Robert A. Holt,

Herpesvirus Infections and Treatments

Abstract The human leukocyte antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype. We describe HLAminer, a computational method for identifying HLA alleles directly from shotgun sequence datasets ( http://www.bcgsc.ca/platform/bioinfo/software/hlaminer ). This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.