{"doi":"10.1038/s41588-024-01720-y","title":"Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis","abstract":"We report a multi-ancestry genome-wide association study on liver cirrhosis and its associated endophenotypes, alanine aminotransferase (ALT) and γ-glutamyl transferase. Using data from 12 cohorts, including 18,265 cases with cirrhosis, 1,782,047 controls, up to 1 million individuals with liver function tests and a validation cohort of 21,689 cases and 617,729 controls, we identify and validate 14 risk associations for cirrhosis. Many variants are located near genes involved in hepatic lipid metabolism. One of these, PNPLA3 p.Ile148Met, interacts with alcohol intake, obesity and diabetes on the risk of cirrhosis and hepatocellular carcinoma (HCC). We develop a polygenic risk score that associates with the progression from cirrhosis to HCC. By focusing on prioritized genes from common variant analyses, we find that rare coding variants in GPAM associate with lower ALT, supporting GPAM as a potential target for therapeutic inhibition. In conclusion, this study provides insights into the genetic underpinnings of cirrhosis.","journal":"Nature Genetics","year":2024,"id":417690,"datarank":1.3895833003028988,"base_score":4.1588830833596715,"endowment":4.1588830833596715,"self_citation_contribution":0.6238324625039509,"citation_network_contribution":0.7657508377989479,"self_endowment_contribution":0.6238324625039509,"citer_contribution":0.7657508377989479,"corpus_percentile":85.10868724375338,"corpus_rank":1926,"citation_count":63,"citer_count":56,"citers_with_citation_signal":29,"citers_with_endowment":29,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7638,"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":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":733445,"name":"Garðar Sveinbjörnsson","orcid":"0000-0003-2429-9468","position":1,"is_corresponding":false},{"id":253978,"name":"Marijana Vujković","orcid":"0000-0003-4924-5714","position":2,"is_corresponding":false},{"id":830484,"name":"Anne-Sofie Seidelin","orcid":null,"position":3,"is_corresponding":false},{"id":1204023,"name":"Helene Gellert‐Kristensen","orcid":"0000-0002-9771-9876","position":4,"is_corresponding":false},{"id":651412,"name":"Gustav Ahlberg","orcid":"0000-0003-0066-2779","position":5,"is_corresponding":false},{"id":55683,"name":"Vinicius Tragante","orcid":"0000-0002-8223-8957","position":6,"is_corresponding":false},{"id":1204024,"name":"Søren A Rand","orcid":"0000-0002-1892-1911","position":7,"is_corresponding":false},{"id":683386,"name":"Joseph Brancale","orcid":"0000-0002-1948-5103","position":8,"is_corresponding":false},{"id":502791,"name":"Sílvia Vilarinho","orcid":"0000-0002-2099-4212","position":9,"is_corresponding":false},{"id":288808,"name":"Pia R. Lundegaard","orcid":"0000-0002-8284-1844","position":10,"is_corresponding":false},{"id":428089,"name":"Erik Sørensen","orcid":"0000-0002-5002-9077","position":11,"is_corresponding":false},{"id":428087,"name":"Christian Erikstrup","orcid":"0000-0001-6551-6647","position":12,"is_corresponding":false},{"id":568613,"name":"Mie Topholm Bruun","orcid":"0000-0002-8819-5388","position":13,"is_corresponding":false},{"id":1177319,"name":"Bitten Aagaard Jensen","orcid":null,"position":14,"is_corresponding":false},{"id":13083,"name":"Søren Brunak","orcid":"0000-0003-0316-5866","position":15,"is_corresponding":false},{"id":568608,"name":"Karina Banasik","orcid":"0000-0003-2489-2499","position":16,"is_corresponding":false},{"id":40998,"name":"Henrik Ullum","orcid":"0000-0001-7306-9058","position":17,"is_corresponding":false},{"id":21845,"name":"Niek Verweij","orcid":"0000-0002-4303-7685","position":18,"is_corresponding":false},{"id":240616,"name":"Luca A. 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Morgan","orcid":"0000-0003-1328-0307","position":27,"is_corresponding":false},{"id":388337,"name":"Tae‐Hwi Schwantes‐An","orcid":"0000-0001-6387-0095","position":28,"is_corresponding":false},{"id":85808,"name":"Daniel Dochtermann","orcid":"0000-0001-9513-5124","position":29,"is_corresponding":false},{"id":11352,"name":"Saiju Pyarajan","orcid":"0000-0002-9047-3762","position":30,"is_corresponding":false},{"id":11259,"name":"Philip S. Tsao","orcid":"0000-0001-7274-9318","position":31,"is_corresponding":false},{"id":270841,"name":"Triin Laisk","orcid":"0000-0003-1501-9030","position":32,"is_corresponding":false},{"id":14660,"name":"Reedik Mägi","orcid":"0000-0002-2964-6011","position":33,"is_corresponding":false},{"id":263005,"name":"Julia Kozlitina","orcid":"0000-0001-7720-2290","position":34,"is_corresponding":false},{"id":265223,"name":"Anne Tybjærg‐Hansen","orcid":null,"position":35,"is_corresponding":false},{"id":190012,"name":"David A. 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In clinical / human-subjects, describe the data with OMOP CDM, CDISC SDTM or HL7 FHIR.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard (e.g., MIAME, BIDS, an ontology) is named in the text; only generic terms like 'GWAS' are used.","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We used PLINK 2.0 (https://www.cog-genomics.org/plink/2.0/)","why":"The paper names specific software tools (e.g., PLINK 2.0, METAL) used to produce the data, providing proper nouns and version information. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No README, data dictionary, or codebook is named to accompany the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The study's own data (GWAS summary statistics) are not sensitive and are openly available without a gatekeeper; the 'upon request' clause applies to other data, not the main dataset.","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":"The paper does not state when the data become available or how long they persist; no timing or retention commitment is made.","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.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","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."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:14:27.174620Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}