Evidence map›Paper›PMID 38400869›Full record

ArticleImmunogenetics2024

Resolving unknown nucleotides in the IPD-IMGT/HLA database by extended and full-length sequencing of HLA class I and II alleles.

Christina E M Voorter, Mathijs Groeneweg, Timo I Olieslagers, Ingrid Fae, Gottfried F Fischer, Marco Andreani, Maria Troiano, Blanka Vidan-Jeras, Sendi Montanic, Bouke G Hepkema and 3 more

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In one paragraph

Article in Immunogenetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Christina E M VoorterDepartment of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands. c.voorter@mumc.nl.
Mathijs GroenewegDepartment of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
Timo I OlieslagersDepartment of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
Ingrid FaeDepartment for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria.
Gottfried F FischerDepartment for Transfusion Medicine and Cell Therapy, Medical University Vienna, Vienna, Austria.
Marco AndreaniLaboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy.
Maria TroianoLaboratorio di Immunogenetica dei Trapianti, Dipartimento di Oncoematologia, Ospedale Pediatrico Bambino Gesù, Rome, Italy.
Blanka Vidan-JerasTissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia.
Sendi MontanicTissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia.
Bouke G HepkemaTransplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Laura B BungenerTransplantation Immunology, Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Marcel G J TilanusDepartment of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
Lotte WietenDepartment of Transplantation Immunology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In the past, identification of HLA alleles was limited to sequencing the region of the gene coding for the peptide binding groove, resulting in a lack of sequence information in the HLA database, challenging HLA allele assignment software programs. We investigated full-length sequences of 19 HLA class I and 7 HLA class II alleles, and we extended another 47 HLA class I alleles with sequences of 5' and 3' UTR regions that were all not yet available in the IPD-IMGT/HLA database. We resolved 8638 unknown nucleotides in the coding sequence of HLA class I and 2139 of HLA class II. Furthermore, with full-length sequencing of the 26 alleles, more than 90 kb of sequence information was added to the non-coding sequences, whereas extension of the 47 alleles resulted in the addition of 5.5 kb unknown nucleotides to the 5' UTR and > 31.7 kb to the 3' UTR region. With this information, some interesting features were observed, like possible recombination events and lineage evolutionary origins. The continuing increase in the availability of full-length sequences in the HLA database will enable the identification of the evolutionary origin and will help the community to improve the alignment and assignment accuracy of HLA alleles.

Indexed as

Biological EvolutionNucleotides3' Untranslated RegionsAllelesCell Membrane3' Untranslated RegionsNucleotidesExtended sequencesFull-length sequencingGroup-specific Sanger sequencingHuman leucocyte antigenNGS

Identifiers

PMID38400869
PMCPMC10944811

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