{"doi":"10.1038/s42003-022-03702-4","title":"Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program","abstract":"The genetic determinants of fasting glucose (FG) and fasting insulin (FI) have been studied mostly through genome arrays, resulting in over 100 associated variants. We extended this work with high-coverage whole genome sequencing analyses from fifteen cohorts in NHLBI's Trans-Omics for Precision Medicine (TOPMed) program. Over 23,000 non-diabetic individuals from five race-ethnicities/populations (African, Asian, European, Hispanic and Samoan) were included. Eight variants were significantly associated with FG or FI across previously identified regions MTNR1B, G6PC2, GCK, GCKR and FOXA2. We additionally characterize suggestive associations with FG or FI near previously identified SLC30A8, TCF7L2, and ADCY5 regions as well as APOB, PTPRT, and ROBO1. Functional annotation resources including the Diabetes Epigenome Atlas were compiled for each signal (chromatin states, annotation principal components, and others) to elucidate variant-to-function hypotheses. We provide a catalog of nucleotide-resolution genomic variation spanning intergenic and intronic regions creating a foundation for future sequencing-based investigations of glycemic traits.","journal":"Communications Biology","year":2022,"id":260032,"datarank":0.581667776467426,"base_score":2.833213344056216,"endowment":2.833213344056216,"self_citation_contribution":0.42498200160843247,"citation_network_contribution":0.15668577485899346,"self_endowment_contribution":0.42498200160843247,"citer_contribution":0.15668577485899346,"corpus_percentile":66.31082230989402,"corpus_rank":4356,"citation_count":16,"citer_count":12,"citers_with_citation_signal":9,"citers_with_endowment":9,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9222,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":235841,"name":"Sheila M. 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Hasbani","orcid":"0000-0001-9874-3440","position":10,"is_corresponding":false},{"id":286564,"name":"Paul S. de Vries","orcid":"0000-0003-0964-0111","position":11,"is_corresponding":false},{"id":24948,"name":"Jennifer A. Brody","orcid":"0000-0001-8509-148X","position":12,"is_corresponding":false},{"id":24765,"name":"Bertha Hidalgo","orcid":"0000-0002-2556-1969","position":13,"is_corresponding":false},{"id":24754,"name":"Xiuqing Guo","orcid":"0000-0002-5264-5068","position":14,"is_corresponding":false},{"id":25004,"name":"James A. Perry","orcid":"0000-0001-5050-2074","position":15,"is_corresponding":false},{"id":22061,"name":"Jeffrey R. O’Connell","orcid":"0000-0002-7046-6688","position":16,"is_corresponding":false},{"id":282181,"name":"Samantha Lent","orcid":"0000-0003-0844-5621","position":17,"is_corresponding":false},{"id":24828,"name":"May E. Montasser","orcid":"0000-0002-9558-5456","position":18,"is_corresponding":false},{"id":218536,"name":"Brian E. 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Peralta","orcid":"0000-0002-8811-5579","position":28,"is_corresponding":false},{"id":24680,"name":"Stella Aslibekyan","orcid":null,"position":29,"is_corresponding":false},{"id":430814,"name":"Abigail S. Baldridge","orcid":"0000-0002-1573-0554","position":30,"is_corresponding":false},{"id":278982,"name":"Alain G. Bertoni","orcid":"0000-0002-7503-6273","position":31,"is_corresponding":false},{"id":218549,"name":"Lawrence F. Bielak","orcid":"0000-0002-3443-8030","position":32,"is_corresponding":false},{"id":738683,"name":"Chung-Shiuan Chen","orcid":"0000-0001-8895-9651","position":33,"is_corresponding":false},{"id":30759,"name":"Yii‐Der Ida Chen","orcid":"0000-0003-1741-3517","position":34,"is_corresponding":false},{"id":557633,"name":"Won Jung Choi","orcid":"0000-0001-8953-1059","position":35,"is_corresponding":false},{"id":270034,"name":"Mark O. Goodarzi","orcid":"0000-0001-6364-5103","position":36,"is_corresponding":false},{"id":51218,"name":"James S. Floyd","orcid":"0000-0002-0365-9041","position":37,"is_corresponding":false},{"id":24975,"name":"Marguerite R. Irvin","orcid":"0000-0002-1442-2023","position":38,"is_corresponding":false},{"id":336893,"name":"Rita R. Kalyani","orcid":"0000-0002-1530-6884","position":39,"is_corresponding":false},{"id":218540,"name":"Tanika N. Kelly","orcid":"0000-0002-7348-4451","position":40,"is_corresponding":false},{"id":557636,"name":"Seonwook Lee","orcid":"0000-0003-3373-2956","position":41,"is_corresponding":false},{"id":22056,"name":"Ching‐Ti Liu","orcid":"0000-0002-0703-0742","position":42,"is_corresponding":false},{"id":274747,"name":"Douglas P. Loesch","orcid":"0000-0001-5716-4557","position":43,"is_corresponding":false},{"id":11268,"name":"JoAnn E. Manson","orcid":"0000-0002-9426-7595","position":44,"is_corresponding":false},{"id":372286,"name":"Ryan L. 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[majority verdict 'yes' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"Code availability This study did not rely on custom code or mathematical algorithms.","grounded":true,"rationale":"The paper explicitly states that no custom code was used and provides no code.","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"The Analysis Commons was funded by R01HL131136.","grounded":true,"rationale":"A grant number is provided in the Acknowledgements.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not mention a license for the data.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"http://t2d.hugeamp.org/","why":"The paper gives a URL for the data, which is not a persistent identifier scheme. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not specify the file format of the released data.","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"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).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Code availability This study did not rely on custom code or mathematical algorithms.","why":"The paper explicitly states that no custom code was used and provides no code.","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The summary results generated during this study are available at the AMP-T2D Portal, http://t2d.hugeamp.org/.","why":"The dataset identifier appears only in the body text, not in the reference list.","gain":4.17,"priority":"important","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"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.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The summary results generated during this study are available at the AMP-T2D Portal, http://t2d.hugeamp.org/. Fasting Insulin: https://t2d.hugeamp.org/dinspector.html?dataset=TOPMed_frz5b_pooled_FI_WGS. Fasting Glucose: https://t2d.hugeamp.org/dinspector.html?dataset=TOPMed_frz5b_pooled_FG_WGS. Accession codes for genotype and phenotype files by cohort may be found in Supplementary Table 1.","why":"The statement points to a public repository with functional links (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide an itemised inventory or description of the dataset's content. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The summary results generated during this study are available at the AMP-T2D Portal, http://t2d.hugeamp.org/.","why":"The paper states the data are available but does not apply an explicit access-rights label. [majority verdict 'partial' (3/5 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 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":"The paper does not indicate that the data conform to a community standard vocabulary. [majority verdict 'no' (3/5 passes agreed)]","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":"Models were fit using GENetic Estimation and Inference in Structured samples (GENESIS) in the Analysis Commons cloud-computing platform.","why":"The paper names the specific software used to produce the summary results. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"The paper does not mention a README, codebook, or schema accompanying the data.","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 summary results are publicly available and no gatekeeper is named.","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 a persistence commitment or an availability timeline for the data. [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.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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. 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Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list."],"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":"2026-07-20T12:03:45.548851Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}