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- Title
Derivation of HLA types from shotgun sequence datasets.
- Authors
Warren, René L.; Gina Choe; Freeman, Douglas J.; Castellarin, Mauro; Munro, Sarah; Moore, Richard; Holt, Robert A.
- 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.
- Subjects
HLA histocompatibility antigens; GENETIC polymorphisms; GENETIC research; GENOMES; GENETICS
- Publication
Genome Medicine, 2012, Vol 4, Issue 12, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/gm396