PMID- 23228053
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20140520
LR  - 20231104
IS  - 1756-994X (Print)
IS  - 1756-994X (Electronic)
IS  - 1756-994X (Linking)
VI  - 4
IP  - 12
DP  - 2012
TI  - Derivation of HLA types from shotgun sequence datasets.
PG  - 95
LID - 10.1186/gm396 [doi]
AB  - 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.
FAU - Warren, Rene L
AU  - Warren RL
AD  - BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British 
      Columbia V5Z 1L3, Canada.
FAU - Choe, Gina
AU  - Choe G
AD  - BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British 
      Columbia V5Z 1L3, Canada.
FAU - Freeman, Douglas J
AU  - Freeman DJ
AD  - BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British 
      Columbia V5Z 1L3, Canada.
FAU - Castellarin, Mauro
AU  - Castellarin M
AD  - BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British 
      Columbia V5Z 1L3, Canada.
FAU - Munro, Sarah
AU  - Munro S
AD  - BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British 
      Columbia V5Z 1L3, Canada.
FAU - Moore, Richard
AU  - Moore R
AD  - BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British 
      Columbia V5Z 1L3, Canada.
FAU - Holt, Robert A
AU  - Holt RA
AD  - 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.
LA  - eng
PT  - Journal Article
DEP - 20121210
PL  - England
TA  - Genome Med
JT  - Genome medicine
JID - 101475844
PMC - PMC3580435
EDAT- 2012/12/12 06:00
MHDA- 2012/12/12 06:01
PMCR- 2012/12/10
CRDT- 2012/12/12 06:00
PHST- 2012/06/08 00:00 [received]
PHST- 2012/10/12 00:00 [revised]
PHST- 2012/12/10 00:00 [accepted]
PHST- 2012/12/12 06:00 [entrez]
PHST- 2012/12/12 06:00 [pubmed]
PHST- 2012/12/12 06:01 [medline]
PHST- 2012/12/10 00:00 [pmc-release]
AID - gm396 [pii]
AID - 10.1186/gm396 [doi]
PST - epublish
SO  - Genome Med. 2012 Dec 10;4(12):95. doi: 10.1186/gm396. eCollection 2012.