Derivation of HLA Types from Shotgun Sequence Datasets

Resource type
Date created
2012
Authors/Contributors
Author: Warren, Rene
Author: Choe, Gina
Author: Munro, Sarah
Author: Holt, Robert
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 webcite). 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.
Document
Published as
Genome Medicine 2012, 4:95 doi:10.1186/gm396
Publication title
Genome Medicine
Document title
Derivation of HLA Types from Shotgun Sequence Datasets
Date
2012
Volume
4
Issue
95
Publisher DOI
10.1186/gm396
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
Member of collection
Attachment Size
gm396.pdf 2.07 MB