title: Derivation of HLA types from shotgun sequence datasets.
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.
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.
authors.forename: René L
authors.initials: RL
authors.lastname: Warren
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.
authors.forename: Gina
authors.initials: G
authors.lastname: Choe
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.
authors.forename: Douglas J
authors.initials: DJ
authors.lastname: Freeman
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.
authors.forename: Mauro
authors.initials: M
authors.lastname: Castellarin
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.
authors.forename: Sarah
authors.initials: S
authors.lastname: Munro
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada.
authors.forename: Richard
authors.initials: R
authors.lastname: Moore
authors.affiliation: BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada ; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Holt