PMID- 29858814
OWN - NLM
STAT- MEDLINE
DCOM- 20190304
LR  - 20200313
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 1802
DP  - 2018
TI  - Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami.
PG  - 235-247
LID - 10.1007/978-1-4939-8546-3_17 [doi]
AB  - Accurate typing of human leukocyte antigen (HLA) is essential for successful 
      organ transplantation and HLA genes are heavily associated with various diseases. 
      Widely used typing assays often involve a set of specially designed primers or 
      probes requiring additional experiments. With the maturing of high-throughput 
      sequencing (HTS) technologies, whole genome sequencing (WGS) as well as other HTS 
      assays are becoming more accessible even in the clinical settings. We describe 
      various computational methods capable of directly typing HLA genes using HTS data 
      including Kourami, our HLA assembler. Kourami is the first HLA assembler capable 
      of discovering novel alleles. Kourami assembles full-length sequences across the 
      peptide-binding regions of HLA genes. Here, we focus on how a user would use 
      Kourami on a new sample. We demonstrate the application by typing HLA alleles 
      from a recently published WGS data with validated HLA types using Kourami.
FAU - Lee, Heewook
AU  - Lee H
AD  - Computational Biology Department, School of Computer Science, Carnegie Mellon 
      University, Pittsburgh, PA, USA. heewookl@cs.cmu.edu.
FAU - Kingsford, Carl
AU  - Kingsford C
AD  - Computational Biology Department, School of Computer Science, Carnegie Mellon 
      University, Pittsburgh, PA, USA.
LA  - eng
GR  - R01 GM122935/GM/NIGMS NIH HHS/United States
GR  - R01 HG007104/HG/NHGRI NIH HHS/United States
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.
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
SB  - IM
MH  - *Algorithms
MH  - Alleles
MH  - Base Sequence
MH  - Genome, Human
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Sequence Alignment
MH  - Software
MH  - Whole Genome Sequencing
OTO - NOTNLM
OT  - Assembly
OT  - Bioinformatics in silico
OT  - HLA
OT  - High-throughput
OT  - WGS
OT  - Whole genome sequencing
EDAT- 2018/06/03 06:00
MHDA- 2019/03/05 06:00
CRDT- 2018/06/03 06:00
PHST- 2018/06/03 06:00 [entrez]
PHST- 2018/06/03 06:00 [pubmed]
PHST- 2019/03/05 06:00 [medline]
AID - 10.1007/978-1-4939-8546-3_17 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2018;1802:235-247. doi: 10.1007/978-1-4939-8546-3_17.