{"doi":"10.1016/j.xgen.2024.100674","title":"Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes","abstract":"The Long-Read Personalized OncoGenomics (POG) dataset comprises a cohort of 189 patient tumors and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the POG program and the Marathon of Hope Cancer Centres Network includes DNA and RNA short-read sequence data, analytics, and clinical information. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. Long-range phasing facilitates the discovery of allelically differentially methylated regions (aDMRs) and allele-specific expression, including recurrent aDMRs in the cancer genes RET and CDKN2A. Germline promoter methylation in MLH1 can be directly observed in Lynch syndrome. Promoter methylation in BRCA1 and RAD51C is a likely driver behind homologous recombination deficiency where no coding driver mutation was found. This dataset demonstrates applications for long-read sequencing in precision medicine and is available as a resource for developing analytical approaches using this technology.","journal":"Cell Genomics","year":2024,"id":421198,"datarank":0.8223978046976396,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.3025374192776805,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.3025374192776805,"corpus_percentile":75.46994662334649,"corpus_rank":3172,"citation_count":31,"citer_count":26,"citers_with_citation_signal":17,"citers_with_endowment":17,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9462,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":546771,"name":"Erin Pleasance","orcid":"0000-0002-5104-042X","position":1,"is_corresponding":false},{"id":1214020,"name":"Jeremy Fan","orcid":null,"position":2,"is_corresponding":false},{"id":1213315,"name":"Vahid Akbari","orcid":"0000-0002-9621-8180","position":3,"is_corresponding":false},{"id":1213316,"name":"Glenn Chang","orcid":"0000-0003-4008-1725","position":4,"is_corresponding":false},{"id":831341,"name":"Katherine Dixon","orcid":"0000-0002-7334-888X","position":5,"is_corresponding":false},{"id":848743,"name":"Veronika Csizmók","orcid":null,"position":6,"is_corresponding":false},{"id":1167603,"name":"Signe MacLennan","orcid":"0009-0000-0021-375X","position":7,"is_corresponding":false},{"id":299030,"name":"Vanessa Porter","orcid":"0000-0002-7167-4884","position":8,"is_corresponding":false},{"id":986730,"name":"Andrew Galbraith","orcid":"0009-0001-1345-8833","position":9,"is_corresponding":false},{"id":734682,"name":"Cameron J. Grisdale","orcid":"0000-0003-1923-6972","position":10,"is_corresponding":false},{"id":299033,"name":"Luka Culibrk","orcid":"0000-0003-1208-1920","position":11,"is_corresponding":false},{"id":830426,"name":"John H. Dupuis","orcid":"0000-0003-0780-9454","position":12,"is_corresponding":false},{"id":924296,"name":"Richard Corbett","orcid":null,"position":13,"is_corresponding":false},{"id":507107,"name":"James Hopkins","orcid":"0000-0003-3552-2629","position":14,"is_corresponding":false},{"id":300361,"name":"Reanne Bowlby","orcid":null,"position":15,"is_corresponding":false},{"id":18721,"name":"Pawan Pandoh","orcid":"0000-0001-6374-235X","position":16,"is_corresponding":false},{"id":1213317,"name":"Duane E. Smailus","orcid":"0000-0002-7526-3409","position":17,"is_corresponding":false},{"id":1214021,"name":"Dean Cheng","orcid":null,"position":18,"is_corresponding":false},{"id":14217,"name":"Tina Wong","orcid":null,"position":19,"is_corresponding":false},{"id":1213318,"name":"Connor Frey","orcid":"0000-0002-4080-3030","position":20,"is_corresponding":false},{"id":847795,"name":"Yaoqing Shen","orcid":"0000-0002-7978-0008","position":21,"is_corresponding":false},{"id":722512,"name":"Eleanor Lewis","orcid":null,"position":22,"is_corresponding":false},{"id":53922,"name":"Luis F. Paulin","orcid":"0000-0003-2567-3773","position":23,"is_corresponding":false},{"id":49032,"name":"Fritz J. Sedlazeck","orcid":"0000-0001-6040-2691","position":24,"is_corresponding":false},{"id":816381,"name":"Jessica Nelson","orcid":"0000-0002-6062-6051","position":25,"is_corresponding":false},{"id":547452,"name":"Eric Chuah","orcid":null,"position":26,"is_corresponding":false},{"id":13836,"name":"Karen Mungall","orcid":"0000-0002-9092-4391","position":27,"is_corresponding":false},{"id":416547,"name":"Richard A. Moore","orcid":"0000-0002-3572-0572","position":28,"is_corresponding":false},{"id":18724,"name":"Robin Coope","orcid":"0000-0002-4685-3506","position":29,"is_corresponding":false},{"id":13835,"name":"Andrew J. Mungall","orcid":"0000-0002-0905-2742","position":30,"is_corresponding":false},{"id":22202,"name":"Melissa K. McConechy","orcid":"0000-0002-1965-1095","position":31,"is_corresponding":false},{"id":734681,"name":"Laura M. Williamson","orcid":"0000-0001-7353-6533","position":32,"is_corresponding":false},{"id":774089,"name":"Kasmintan A. Schrader","orcid":"0000-0002-7413-4314","position":33,"is_corresponding":false},{"id":22215,"name":"Stephen Yip","orcid":"0000-0002-8514-9861","position":34,"is_corresponding":false},{"id":13784,"name":"Marco A. Marra","orcid":"0000-0001-7146-7175","position":35,"is_corresponding":false},{"id":536671,"name":"Janessa Laskin","orcid":"0000-0002-0161-9329","position":36,"is_corresponding":false},{"id":14377,"name":"Steven J.M. Jones","orcid":"0000-0003-3394-2208","position":37,"is_corresponding":false},{"id":1213314,"name":"Kieran O’Neill","orcid":"0000-0001-7609-5905","position":0,"is_corresponding":true}],"reference_count":130,"raw_metadata":null,"created_at":"2026-07-19T01:57:36.298171Z","pmid":"39406235","pmcid":"PMC11605692","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":72.2222,"fair_a":68.75,"fair_i":60.0,"fair_r":50.0,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":72.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Genomic and transcriptomic sequence datasets for long-read and short-read platforms have been deposited at the European Genome-Phenome Archive (EGA; https://ega-archive.org/ ) as part of study EGA: EGAS00001001159, as listed in the key resources table , with accession numbers as listed in Table S1 .","grounded":true,"rationale":"The paper provides a persistent identifier string (EGAS00001001159) in the EGA scheme, which is a registered repository accession pattern.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"European Genome-Phenome Archive (EGA)","grounded":false,"rationale":"The paper names the European Genome-Phenome Archive (EGA) as the repository holding the study's data. 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For sensitive/human clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","why":"The only gatekeeper named for additional data access is the lead contact, a natural person, and no institutional gatekeeper is specified for the deposited data. [majority verdict 'partial' (3/5 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. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence in the paper states when the data become available or how long they persist, beyond the act of deposition. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) 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.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper."],"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":"2026-07-20T11:34:46.846227Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}