PMID- 32124313
OWN - NLM
STAT- MEDLINE
DCOM- 20210208
LR  - 20210208
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 2120
DP  - 2020
TI  - Rapid High-Resolution Typing of Class I HLA Genes by Nanopore Sequencing.
PG  - 93-99
LID - 10.1007/978-1-0716-0327-7_6 [doi]
AB  - Nanopore sequencing, enabled initially by the MinION device from Oxford Nanopore 
      Technologies (ONT), is the only technology that offers portable, single-molecule 
      sequencing and ultralong reads. The technology is ideal for the typing of human 
      leukocyte antigen (HLA) genes for transplantation and cancer immunotherapy. 
      However, such applications have been hindered by the high error rate of nanopore 
      sequencing reads. We developed the workflow and bioinformatic pipeline, Athlon 
      (accurate typing of human leukocyte antigen by Oxford Nanopore), to perform 
      high-resolution typing of Class I HLA genes by nanopore sequencing. The method 
      features a novel algorithm for candidate allele selection, followed by error 
      correction through consensus building. Here, we describe the protocol of using 
      Athlon packaged in a VirtualBox image for the above application.
FAU - Liu, Chang
AU  - Liu C
AD  - Department of Pathology and Immunology, Washington University School of Medicine, 
      St. Louis, MO, USA. cliu32@wustl.edu.
FAU - Berry, Rick
AU  - Berry R
AD  - PlatformSTL, St. Louis, MO, USA.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Genomics/methods
MH  - HLA Antigens/*genetics
MH  - High-Throughput Nucleotide Sequencing/methods
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Nanopore Sequencing/*methods
MH  - Software
MH  - Workflow
OTO - NOTNLM
OT  - HLA typing
OT  - Human leukocyte antigen (HLA)
OT  - Nanopore sequencing
OT  - Targeted sequencing
EDAT- 2020/03/04 06:00
MHDA- 2021/02/09 06:00
CRDT- 2020/03/04 06:00
PHST- 2020/03/04 06:00 [entrez]
PHST- 2020/03/04 06:00 [pubmed]
PHST- 2021/02/09 06:00 [medline]
AID - 10.1007/978-1-0716-0327-7_6 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2020;2120:93-99. doi: 10.1007/978-1-0716-0327-7_6.