Full-Length Characterization of Novel HLA-DRB1 Alleles for Reference Database Submission.
DRB1
Genotyping
HLA
Novel allele
PCR
Primer
Sequencing
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
22
6
2024
pubmed:
22
6
2024
entrez:
22
6
2024
Statut:
ppublish
Résumé
The prerequisite for successful HLA genotyping is the integrity of the large allele reference database IPD-IMGT/HLA. Consequently, it is in the laboratories' best interest that the data quality of submitted novel sequences is high. However, due to its long and variable length, the gene HLA-DRB1 presents the biggest challenge and as of today only 16% of the HLA-DRB1 alleles in the database are characterized in full length. To improve this situation, we developed a protocol for long-range PCR amplification of targeted HLA-DRB1 alleles. By subsequently combining both long-read and short-read sequencing technologies, our protocol ensures phased and error-corrected sequences of reference grade quality. This dual redundant reference sequencing (DR2S) approach is of particular importance for correctly resolving the challenging repeat regions of DRB1 intron 1. Until today, we used this protocol to characterize and submit 384 full-length HLA-DRB1 sequences to IPD-IMGT/HLA.
Identifiants
pubmed: 38907896
doi: 10.1007/978-1-0716-3874-3_10
doi:
Substances chimiques
HLA-DRB1 Chains
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
145-156Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Robinson J, Barker DJ, Georgiou X et al (2020) IPD-IMGT/HLA Database. Nucleic Acids Res 48:D948–D955
pubmed: 31667505
Gerritsen KEH, Groeneweg M, Meertens CMH et al (2015) Full-length HLA-DRB1 coding sequences generated by a hemizygous RNA-SBT approach. Tissue Antigens 86:333–342
doi: 10.1111/tan.12654
pubmed: 26396036
Klasberg S, Schmidt AH, Lange V et al (2021) DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples. BMC Bioinformatic 22:236
doi: 10.1186/s12859-021-04153-0
Albrecht V, Zweiniger C, Surendranath V et al (2017) Dual redundant sequencing strategy: full-length gene characterisation of 1056 novel and confirmatory HLA alleles. HLA 90:79–87
doi: 10.1111/tan.13057
pubmed: 28547825
pmcid: 6084308
Schöne B, Fuhrmann M, Surendranath V et al (2019) TypeLoader2: automated submission of novel HLA and killer-cell immunoglobulin-like receptor alleles in full length. HLA 93:195–202
doi: 10.1111/tan.13508
pubmed: 30821128
pmcid: 6594033