High resolution HLA genotyping with third generation sequencing technology—A multicentre study
Article Swipe
Stéphane Bühler
,
Maja Nørgaard
,
Rudi Steffensen
,
Kirstine Kløve‐Mogensen
,
Bjarne Kuno Møller
,
Rebecca Großmann
,
Sylvie Ferrari‐Lacraz
,
Claudia Lehmann
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1111/tan.15632
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1111/tan.15632
Molecular HLA typing techniques are currently undergoing a rapid evolution. While real‐time PCR is established as the standard method in tissue typing laboratories regarding allocation of solid organs, next generation sequencing (NGS) for high‐resolution HLA typing is becoming indispensable but is not yet suitable for deceased donors. By contrast, high‐resolution typing is essential for stem cell transplantation and is increasingly required for questions relating to various disease associations. In this multicentre clinical study, the TGS technique using nanopore sequencing is investigated applying NanoTYPE™ kit and NanoTYPER™ software (Omixon Biocomputing Ltd., Budapest, Hungary) regarding the concordance of the results with NGS and its practicability in diagnostic laboratories. The results of 381 samples show a concordance of 99.58% for 11 HLA loci, HLA‐A , ‐B , ‐C , ‐DRB1 , ‐DRB3 , ‐DRB4 , ‐DRB5 , ‐DQA1 , ‐DQB1 , ‐DPA1 and ‐DPB1 . The quality control (QC) data shows a very high quality of the sequencing performed in each laboratory, 34,926 (97.15%) QC values were returned as ‘passed’, 862 (2.4%) as ‘inspect’ and 162 (0.45%) as ‘failed’. We show that an ‘inspect’ or ‘failed’ QC warning does not automatically lead to incorrect HLA typing. The advantages of nanopore sequencing are speed, flexibility, reusability of the flow cells and easy implementation in the laboratory. There are challenges, such as exon coverage and the handling of large amounts of data. Finally, nanopore sequencing presents potential for applications in basic research within the field of epigenetics and genomics and holds significance for clinical concerns.
Related Topics
Concepts
Typing
Nanopore sequencing
Concordance
Human leukocyte antigen
DNA sequencing
Computer science
Genotyping
Computational biology
Biology
Genetics
Genotype
Antigen
Gene
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1111/tan.15632
- OA Status
- hybrid
- Cited By
- 4
- References
- 29
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4401517840
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4401517840Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1111/tan.15632Digital Object Identifier
- Title
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High resolution
HLA genotyping with third generation sequencing technology—A multicentre studyWork title - Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-08-01Full publication date if available
- Authors
-
Stéphane Bühler, Maja Nørgaard, Rudi Steffensen, Kirstine Kløve‐Mogensen, Bjarne Kuno Møller, Rebecca Großmann, Sylvie Ferrari‐Lacraz, Claudia LehmannList of authors in order
- Landing page
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https://doi.org/10.1111/tan.15632Publisher landing page
- Open access
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://doi.org/10.1111/tan.15632Direct OA link when available
- Concepts
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Typing, Nanopore sequencing, Concordance, Human leukocyte antigen, DNA sequencing, Computer science, Genotyping, Computational biology, Biology, Genetics, Genotype, Antigen, GeneTop concepts (fields/topics) attached by OpenAlex
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4Total citation count in OpenAlex
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2025: 2, 2024: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.high‐resolution | 33, 49 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5023894554, https://openalex.org/A5021991466 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 8 |
| corresponding_institution_ids | https://openalex.org/I4210106256, https://openalex.org/I4210125843 |
| citation_normalized_percentile.value | 0.89849378 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |