Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type.
Exome
HLA
Human leukocyte antigen
MHC
Next generation sequencing
Pharmacogenetics
Pharmacogenomics
Journal
Human immunology
ISSN: 1879-1166
Titre abrégé: Hum Immunol
Pays: United States
ID NLM: 8010936
Informations de publication
Date de publication:
Aug 2020
Aug 2020
Historique:
received:
21
12
2019
revised:
15
05
2020
accepted:
03
06
2020
pubmed:
18
6
2020
medline:
10
6
2021
entrez:
18
6
2020
Statut:
ppublish
Résumé
We explored the feasibility of obtaining accurate HLA type using pre-existing NGS data not generated for HLA purposes. 83 exomes and 500 targeted NGS pharmacogenomic panels were analyzed using Omixon HLA Explore, OptiType, and/or HLA-Genotyper software. Results were compared against clinical HLA genotyping. 765 (94.2%) Omixon and 769 (94.7%) HLA-Genotyper of 812 germline allele calls across class I/II loci and 402 (99.5%) of 404 OptiType class I calls were concordant to the second field (i.e. HLA-A*02:01). An additional 19 (2.3%) Omixon, 39 (4.8%) HLA-Genotyper, and 2 (0.5%) OptiType allele calls were first field concordant (i.e. HLA-A*02). Using Omixon, four alleles (0.4%) were discordant and 24 (3.0%) failed to call, while 4 alleles (0.4%) were discordant using HLA-Genotyper. Tumor exomes were also evaluated and were 85.4%, 91.6%, and 100% concordant (Omixon and HLA-Genotyper with 96 alleles tested, and Optitype with 48 class I alleles, respectively). The 15 exomes and 500 pharmacogenomic panels were 100% concordant for each pharmacogenomic allele tested. This work has broad implications spanning future clinical care (pharmacogenomics, tumor response to immunotherapy, autoimmunity, etc.) and research applications.
Identifiants
pubmed: 32546429
pii: S0198-8859(20)30337-2
doi: 10.1016/j.humimm.2020.06.002
pmc: PMC7721171
mid: NIHMS1645538
pii:
doi:
Substances chimiques
HLA Antigens
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
423-429Subventions
Organisme : NCI NIH HHS
ID : P50 CA116201
Pays : United States
Informations de copyright
Copyright © 2020 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Blood. 2007 Dec 15;110(13):4576-83
pubmed: 17785583
Nucleic Acids Res. 2015 Jan;43(Database issue):D423-31
pubmed: 25414341
J Immunol Res. 2014;2014:971818
pubmed: 25126587
Mayo Clin Proc. 2015 Oct;90(10):1327-37
pubmed: 26434960
Clin Pharmacol Ther. 2012 Apr;91(4):734-8
pubmed: 22378157
Tissue Antigens. 2009 Nov;74(5):393-403
pubmed: 19845894
Nat Biotechnol. 2015 Nov;33(11):1152-8
pubmed: 26372948
Mol Med Today. 1999 Apr;5(4):178-86
pubmed: 10203751
Clin Pharmacol Ther. 2016 Aug;100(2):160-9
pubmed: 26857349
BMC Genomics. 2017 Feb 14;18(1):161
pubmed: 28196473
J Natl Cancer Inst. 2017 Jul 1;109(7):
pubmed: 28376176
Clin Pharmacol Ther. 2013 Feb;93(2):153-8
pubmed: 23232549
Pharmacogenomics. 2012 Aug;13(11):1285-306
pubmed: 22920398
Tissue Antigens. 2009 Feb;73(2):95-170
pubmed: 19140825
Biol Blood Marrow Transplant. 2019 Aug;25(8):e268-e269
pubmed: 31145991
Int J Epidemiol. 2020 Feb 1;49(1):23-24k
pubmed: 31378813
Bioinformatics. 2014 Dec 1;30(23):3310-6
pubmed: 25143287
Cancer Immunol Immunother. 2017 Feb;66(2):259-271
pubmed: 28040849
Tumori. 2001 Mar-Apr;87(2):S40-3
pubmed: 11401225
Tissue Antigens. 2013 Apr;81(4):194-203
pubmed: 23510415
Per Med. 2017 Sep;14(5):383-388
pubmed: 29181084
Tissue Antigens. 2012 Oct;80(4):305-16
pubmed: 22861646
Arch Pathol Lab Med. 2017 Jun;141(6):806-812
pubmed: 28234015
Immunogenetics. 2005 Nov;57(10):717-29
pubmed: 16215732
Annu Rev Pharmacol Toxicol. 2019 Jan 6;59:463-486
pubmed: 30134124
Hum Immunol. 2015 Dec;76(12):928-38
pubmed: 26027777
Clin Pharmacol Ther. 2018 Apr;103(4):574-581
pubmed: 29392710
Pharmacogenomics. 2018 Mar;19(4):321-331
pubmed: 29469671
Discov Med. 2013 Sep;16(87):93-101
pubmed: 23998445
J Mol Diagn. 2016 May;18(3):438-445
pubmed: 26947514
Science. 2018 Feb 2;359(6375):582-587
pubmed: 29217585
Pharmacogenomics. 2016 Oct;17(15):1629-1636
pubmed: 27648637