PMID- 31832057
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231019
IS  - 1660-3796 (Print)
IS  - 1660-3818 (Electronic)
IS  - 1660-3796 (Linking)
VI  - 46
IP  - 5
DP  - 2019 Oct
TI  - Bioinformatics Strategies, Challenges, and Opportunities for Next Generation 
      Sequencing-Based HLA Genotyping.
PG  - 312-325
LID - 10.1159/000502487 [doi]
AB  - The advent of next generation sequencing (NGS) has altered the face of genotyping 
      the human leukocyte antigen (HLA) system in clinical, stem cell donor registry, 
      and research contexts. NGS has led to a dramatically increased sequencing 
      throughput at high accuracy, while being more time and cost efficient than 
      precursor technologies. This has led to a broader and deeper profiling of the key 
      genes in the human immunogenetic make-up. The rapid evolution of sequencing 
      technologies is evidenced by the development of varied short-read sequencing 
      platforms with differing read lengths and sequencing capacities to long-read 
      sequencing platforms capable of profiling full genes without fragmentation. 
      Concomitantly, there has been development of a diverse set of computational 
      analyses and software tools developed to deal with the various strengths and 
      limitations of the sequencing data generated by the different sequencing 
      platforms. This review surveys the different modalities involved in generating 
      NGS HLA profiling sequence data. It systematically describes various 
      computational approaches that have been developed to achieve HLA genotyping to 
      different degrees of resolution. At each stage, this review enumerates the 
      drawbacks and advantages of each of the platforms and analysis approaches, thus 
      providing a comprehensive picture of the current state of HLA genotyping 
      technologies.
CI  - Copyright (c) 2019 by S. Karger AG, Basel.
FAU - Klasberg, Steffen
AU  - Klasberg S
AD  - DKMS Life Science Lab, Dresden, Germany.
FAU - Surendranath, Vineeth
AU  - Surendranath V
AD  - DKMS Life Science Lab, Dresden, Germany.
FAU - Lange, Vinzenz
AU  - Lange V
AD  - DKMS Life Science Lab, Dresden, Germany.
FAU - Schofl, Gerhard
AU  - Schofl G
AD  - DKMS Life Science Lab, Dresden, Germany.
LA  - eng
PT  - Journal Article
PT  - Review
DEP - 20190906
PL  - Switzerland
TA  - Transfus Med Hemother
JT  - Transfusion medicine and hemotherapy : offizielles Organ der Deutschen 
      Gesellschaft fur Transfusionsmedizin und Immunhamatologie
JID - 101176417
PMC - PMC6876610
OTO - NOTNLM
OT  - Genotyping
OT  - Human leukocyte antigen
OT  - Next generation sequencing
COIS- The authors have no conflicts of interest to declare.
EDAT- 2019/12/14 06:00
MHDA- 2019/12/14 06:01
PMCR- 2019/09/06
CRDT- 2019/12/14 06:00
PHST- 2019/05/12 00:00 [received]
PHST- 2019/07/30 00:00 [accepted]
PHST- 2019/12/14 06:00 [entrez]
PHST- 2019/12/14 06:00 [pubmed]
PHST- 2019/12/14 06:01 [medline]
PHST- 2019/09/06 00:00 [pmc-release]
AID - tmh-0046-0312 [pii]
AID - 10.1159/000502487 [doi]
PST - ppublish
SO  - Transfus Med Hemother. 2019 Oct;46(5):312-325. doi: 10.1159/000502487. Epub 2019 
      Sep 6.