{"doi":"10.1111/tan.15020","title":"Complete sequences of six major histocompatibility complex haplotypes, including all the major <scp>MHC</scp> class <scp>II</scp> structures","abstract":"Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.06%-0.49% in a 1000 Genomes Project read remapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.","journal":"HLA","year":2023,"id":331155,"datarank":0.8879290679015761,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"self_citation_contribution":0.515098080672772,"citation_network_contribution":0.37283098722880414,"self_endowment_contribution":0.515098080672772,"citer_contribution":0.37283098722880414,"corpus_percentile":77.24916840720972,"corpus_rank":2942,"citation_count":30,"citer_count":22,"citers_with_citation_signal":16,"citers_with_endowment":16,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8667,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":988631,"name":"Stephan Scholz","orcid":"0000-0002-8383-9498","position":1,"is_corresponding":false},{"id":19724,"name":"Nicholas R. Pollock","orcid":"0000-0003-0114-528X","position":2,"is_corresponding":false},{"id":441902,"name":"William Palmer","orcid":"0000-0002-0348-6339","position":3,"is_corresponding":false},{"id":774981,"name":"Katherine M. Kichula","orcid":"0000-0002-9817-3043","position":4,"is_corresponding":false},{"id":989007,"name":"Daniel Strelow","orcid":null,"position":5,"is_corresponding":false},{"id":989008,"name":"Duyen Bao Le","orcid":null,"position":6,"is_corresponding":false},{"id":989009,"name":"Dana Belick","orcid":null,"position":7,"is_corresponding":false},{"id":1056640,"name":"Lisanna Hülse","orcid":null,"position":8,"is_corresponding":false},{"id":59534,"name":"Tobias Lautwein","orcid":"0000-0002-3872-3613","position":9,"is_corresponding":false},{"id":988632,"name":"Thorsten Wachtmeister","orcid":"0000-0002-6760-2458","position":10,"is_corresponding":false},{"id":59557,"name":"Tassilo Erik Wollenweber","orcid":"0000-0001-7953-9903","position":11,"is_corresponding":false},{"id":988633,"name":"Birgit Henrich","orcid":"0000-0002-0565-5773","position":12,"is_corresponding":false},{"id":74498,"name":"Karl Köhrer","orcid":"0000-0003-3644-2022","position":13,"is_corresponding":false},{"id":255080,"name":"Peter Parham","orcid":"0000-0003-0530-5922","position":14,"is_corresponding":false},{"id":19714,"name":"Lisbeth A. Guethlein","orcid":"0000-0002-1301-8301","position":15,"is_corresponding":false},{"id":19722,"name":"Paul J. Norman","orcid":"0000-0001-8370-7703","position":16,"is_corresponding":false},{"id":19739,"name":"Alexander T Dilthey","orcid":"0000-0002-6394-4581","position":17,"is_corresponding":false},{"id":553732,"name":"Torsten Houwaart","orcid":"0000-0002-4525-7593","position":0,"is_corresponding":true}],"reference_count":72,"raw_metadata":null,"created_at":"2026-07-19T01:09:19.317824Z","pmid":"36932816","pmcid":"PMC10986641","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":83.3333,"fair_a":62.5,"fair_i":20.0,"fair_r":58.3333,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Whole-genome Nanopore, Illumina and PacBio HiFi sequencing data generated as part of this study and the generated MHC assemblies were submitted to NCBI BioProject PRJNA764575.","grounded":true,"rationale":"The paper provides a BioProject accession (PRJNA764575), which is a persistent identifier scheme accepted at 'yes'. 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[majority verdict 'partial' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Whole-genome Nanopore, Illumina and PacBio HiFi sequencing data generated as part of this study and the generated MHC assemblies were submitted to NCBI BioProject PRJNA764575.","grounded":true,"rationale":"The data availability statement provides a route to the data with no stated precondition. 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Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any file format for the released data.","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Whole-genome Nanopore, Illumina and PacBio HiFi sequencing data generated as part of this study and the generated MHC assemblies were submitted to NCBI BioProject PRJNA764575.","why":"The dataset identifier (BioProject PRJNA764575) appears only in the body text (data availability statement), not in the reference list. [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). 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[majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":null,"why":"The paper uses IPD-IMGT/HLA, a community standard for HLA allele nomenclature, to compare the assemblies. 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper mentions BioSample IDs for data from another study (reference 9) in Table S2, providing identifiers for external resources. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. 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Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:37:07.268279Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}