Derivation of HLA types from shotgun sequence datasets

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 prod...

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Bibliographic Details
Published in:Genome medicine 2012-12, Vol.4 (12), p.95-95, Article 95
Main Authors: Warren, René L, Choe, Gina, Freeman, Douglas J, Castellarin, Mauro, Munro, Sarah, Moore, Richard, Holt, Robert A
Format: Article
Language:English
Subjects:
Genes
Genetic aspects
Genomes
Genomics
Histocompatibility antigens
HLA histocompatibility antigens
Method
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Summary: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.
ISSN:1756-994X
1756-994X
DOI:10.1186/gm396