PMID- 29415772
OWN - NLM
STAT- MEDLINE
DCOM- 20180816
LR  - 20181113
IS  - 1474-760X (Electronic)
IS  - 1474-7596 (Print)
IS  - 1474-7596 (Linking)
VI  - 19
IP  - 1
DP  - 2018 Feb 7
TI  - Kourami: graph-guided assembly for novel human leukocyte antigen allele 
      discovery.
PG  - 16
LID - 10.1186/s13059-018-1388-2 [doi]
LID - 16
AB  - Accurate typing of human leukocyte antigen (HLA) is important because HLA genes 
      play important roles in immune responses and disease genesis. Previously 
      available computational methods are database-matching approaches and their 
      outputs are inherently limited by the completeness of already known types, making 
      them unsuitable for discovery of novel alleles. We have developed a graph-guided 
      assembly technique for classical HLA genes, which can construct allele sequences 
      given high-coverage whole-genome sequencing data. Our method delivers highly 
      accurate HLA typing, comparable to the current state-of-the-art methods. Using 
      various data, we also demonstrate that our method can type novel alleles.
FAU - Lee, Heewook
AU  - Lee H
AD  - Computational Biology Department, School of Computer Science, Carnegie Mellon 
      University, Pittsburgh, PA, USA.
FAU - Kingsford, Carl
AU  - Kingsford C
AD  - Computational Biology Department, School of Computer Science, Carnegie Mellon 
      University, Pittsburgh, PA, USA. carlk@cs.cmu.edu.
LA  - eng
GR  - CCF-1256087/Division of Computing and Communication Foundations/International
GR  - R01 HG007104/HG/NHGRI NIH HHS/United States
GR  - GBMF4554/Gordon and Betty Moore Foundation/International
GR  - R01HG007104/HG/NHGRI NIH HHS/United States
GR  - CCF-1319998/Division of Computing and Communication Foundations/International
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20180207
PL  - England
TA  - Genome Biol
JT  - Genome biology
JID - 100960660
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Alleles
MH  - Genome
MH  - HLA Antigens/*genetics
MH  - Haplotypes
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Terminology as Topic
MH  - Whole Genome Sequencing
PMC - PMC5804087
COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. COMPETING INTERESTS: 
      The authors declare that they have no competing interests. PUBLISHER'S NOTE: 
      Springer Nature remains neutral with regard to jurisdictional claims in published 
      maps and institutional affiliations.
EDAT- 2018/02/09 06:00
MHDA- 2018/08/17 06:00
PMCR- 2018/02/07
CRDT- 2018/02/09 06:00
PHST- 2017/05/17 00:00 [received]
PHST- 2018/01/08 00:00 [accepted]
PHST- 2018/02/09 06:00 [entrez]
PHST- 2018/02/09 06:00 [pubmed]
PHST- 2018/08/17 06:00 [medline]
PHST- 2018/02/07 00:00 [pmc-release]
AID - 10.1186/s13059-018-1388-2 [pii]
AID - 1388 [pii]
AID - 10.1186/s13059-018-1388-2 [doi]
PST - epublish
SO  - Genome Biol. 2018 Feb 7;19(1):16. doi: 10.1186/s13059-018-1388-2.