Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop.
NGS HLA typing
Proficiency testing
Quality control
Reference cell panel
Journal
Human immunology
ISSN: 1879-1166
Titre abrégé: Hum Immunol
Pays: United States
ID NLM: 8010936
Informations de publication
Date de publication:
Apr 2019
Apr 2019
Historique:
received:
17
08
2018
revised:
10
01
2019
accepted:
30
01
2019
pubmed:
10
2
2019
medline:
31
7
2019
entrez:
10
2
2019
Statut:
ppublish
Résumé
The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
Identifiants
pubmed: 30738112
pii: S0198-8859(19)30127-2
doi: 10.1016/j.humimm.2019.01.009
pmc: PMC6446570
mid: NIHMS1521785
pii:
doi:
Substances chimiques
HLA Antigens
0
Types de publication
Journal Article
Review
Langues
eng
Pagination
228-236Subventions
Organisme : NIAID NIH HHS
ID : R01 AI128775
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM109030
Pays : United States
Organisme : Department of Health
ID : RP-PG-0310-1003
Pays : United Kingdom
Organisme : NINDS NIH HHS
ID : U19 NS095774
Pays : United States
Informations de copyright
Copyright © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
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