{"doi":"10.1038/nature15394","title":"An integrated map of structural variation in 2,504 human genomes","abstract":"Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.","journal":"Nature","year":2015,"id":9605,"datarank":9.071817689328547,"base_score":7.8961806086154915,"endowment":7.8961806086154915,"self_citation_contribution":1.1844270912923238,"citation_network_contribution":7.887390598036223,"self_endowment_contribution":1.1844270912923238,"citer_contribution":7.887390598036223,"corpus_percentile":98.38322890075037,"corpus_rank":210,"citation_count":2686,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7647,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-09-30","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":13956,"name":"Tobias Rausch","orcid":"0000-0001-5773-5620","position":1,"is_corresponding":false},{"id":61976,"name":"Marianne K. 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Konkel","orcid":"0000-0002-3190-1667","position":10,"is_corresponding":false},{"id":19876,"name":"Ankit Malhotra","orcid":"0000-0002-1905-0732","position":11,"is_corresponding":false},{"id":35179,"name":"Adrian M. Stütz ","orcid":null,"position":12,"is_corresponding":false},{"id":19736,"name":"Xinghua Shi","orcid":"0000-0003-4662-3177","position":13,"is_corresponding":false},{"id":51032,"name":"Francesco Paolo Casale","orcid":"0000-0002-5450-1981","position":14,"is_corresponding":false},{"id":13341,"name":"Jieming Chen","orcid":"0000-0003-3767-9486","position":15,"is_corresponding":false},{"id":35201,"name":" Fereydoun Hormozdiari","orcid":"0000-0003-2703-9274","position":16,"is_corresponding":false},{"id":62043,"name":"Gargi Dayama","orcid":"0000-0003-1349-8998","position":17,"is_corresponding":false},{"id":13086,"name":"Calvin Wing Yiu Chan","orcid":"0000-0002-3656-7709","position":18,"is_corresponding":false},{"id":62049,"name":"Maika Malig","orcid":"0000-0002-2535-6607","position":19,"is_corresponding":false},{"id":19738,"name":"Mark J. P. Chaisson","orcid":"0000-0001-5395-1457","position":20,"is_corresponding":false},{"id":29310,"name":"Seva Kashin","orcid":"0009-0008-1432-8249","position":23,"is_corresponding":false},{"id":35176,"name":" Hugo Y. K. Lam","orcid":"0000-0002-0564-6105","position":26,"is_corresponding":false},{"id":18870,"name":"Xinmeng Jasmine Mu","orcid":"0000-0002-8079-0828","position":27,"is_corresponding":false},{"id":61927,"name":"Zhuoyi Huang","orcid":"0000-0001-9149-295X","position":28,"is_corresponding":false},{"id":2971,"name":"Danny Antaki","orcid":"0000-0003-0381-7801","position":29,"is_corresponding":false},{"id":27807,"name":"Taejeong Bae","orcid":"0000-0002-4626-3725","position":30,"is_corresponding":false},{"id":61982,"name":"Eliza Cerveira","orcid":"0000-0001-8915-3334","position":31,"is_corresponding":false},{"id":80277,"name":"Peter Chines","orcid":null,"position":32,"is_corresponding":false},{"id":13351,"name":"Zechen Chong","orcid":"0000-0001-5750-1808","position":33,"is_corresponding":false},{"id":3646,"name":"Hans Clevers","orcid":"0000-0002-3077-5582","position":34,"is_corresponding":false},{"id":29317,"name":"Princy Parsana","orcid":"0000-0001-5784-9636","position":35,"is_corresponding":false},{"id":32248,"name":"Fred R. 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Jaffe","orcid":"0000-0001-8739-568X","position":45,"is_corresponding":false},{"id":1753,"name":"Richard A. Gibbs","orcid":"0000-0002-1356-5698","position":46,"is_corresponding":false},{"id":36370,"name":"Christopher E. Mason","orcid":"0000-0002-1850-1642","position":48,"is_corresponding":false},{"id":70732,"name":"Mauricio O. Carneiro","orcid":null,"position":49,"is_corresponding":false},{"id":1751,"name":"Donna M. Muzny","orcid":"0000-0002-3055-0359","position":50,"is_corresponding":false},{"id":62050,"name":"Bradley J. Nelson","orcid":"0000-0002-7739-7996","position":51,"is_corresponding":false},{"id":2973,"name":"Amina Noor","orcid":null,"position":52,"is_corresponding":false},{"id":62052,"name":"Nicholas F. Parrish","orcid":"0000-0002-6971-8016","position":53,"is_corresponding":false},{"id":80278,"name":"Matthew Pendleton","orcid":"0000-0002-7465-4459","position":54,"is_corresponding":false},{"id":62017,"name":"Andrew Quitadamo","orcid":"0000-0001-8748-4586","position":55,"is_corresponding":false},{"id":13950,"name":"Benjamin Raeder","orcid":"0000-0002-9494-8884","position":56,"is_corresponding":false},{"id":5797,"name":"Eric E. Schadt","orcid":"0000-0002-7892-8808","position":57,"is_corresponding":false},{"id":61986,"name":"Mallory Romanovitch","orcid":null,"position":58,"is_corresponding":false},{"id":80279,"name":"Andreas Schlattl","orcid":"0009-0008-1357-355X","position":59,"is_corresponding":false},{"id":2004,"name":"Robert Sebra","orcid":"0000-0001-9267-2426","position":60,"is_corresponding":false},{"id":62671,"name":"Andrey A. Shabalin","orcid":"0000-0003-0309-6821","position":61,"is_corresponding":false},{"id":5931,"name":"Andreas Untergasser","orcid":null,"position":62,"is_corresponding":false},{"id":35180,"name":" Jerilyn A. 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[majority verdict 'no' (4/5 passes agreed)]","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data deposits Sequencing data, archive accessions and supporting datasets including GRCh37 variant call files comprising the extended SV Analysis Group release set, a ‘readme’ describing differences to the phase 3 marker paper variant release 16 , and a GRCh38 version of our callset, are available at http://www.1000genomes.org/phase-3-structural-variant-dataset . DGV archive accession: estd219.","why":"The strongest identifier is a web URL (http://www.1000genomes.org/phase-3-structural-variant-dataset) which is not a persistent identifier scheme; the DGV accession is not in the accepted PID list. [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. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No specific file format token (e.g., VCF, BAM) is named for the released data; 'variant call files' is a generic description.","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":null,"why":"No code repository or locator is mentioned; only third-party tools are named.","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":"Data deposits Sequencing data, archive accessions and supporting datasets including GRCh37 variant call files comprising the extended SV Analysis Group release set, a ‘readme’ describing differences to the phase 3 marker paper variant release 16 , and a GRCh38 version of our callset, are available at http://www.1000genomes.org/phase-3-structural-variant-dataset . DGV archive accession: estd219.","why":"The dataset identifier (DGV accession and URL) appears only in the body text, not as a reference-list entry.","gain":4.17,"priority":"important","scored":true},{"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":"Data deposits Sequencing data, archive accessions and supporting datasets including GRCh37 variant call files comprising the extended SV Analysis Group release set, a ‘readme’ describing differences to the phase 3 marker paper variant release 16 , and a GRCh38 version of our callset, are available at http://www.1000genomes.org/phase-3-structural-variant-dataset . DGV archive accession: estd219.","why":"The paper describes the action of accessing the data via URL and accession but does not use an explicit access-level label like 'open access'.","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":"no","current":0.0,"evidence":null,"why":"No data/metadata community standard (e.g., MIAME, BIDS, ontology) is named; the reference assembly GRCh37 is a reference genome, not a data standard.","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":"using two independent mapping algorithms—BWA and mrsFAST—and performed SV discovery and genotyping using an ensemble of nine different algorithms","why":"The text names specific tools and algorithms (BWA, mrsFAST) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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 genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are human-subject but are stated to be publicly available with no named gatekeeper; no gatekeeper clause exists.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). 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":"No identifier (accession, DOI, RRID) is given for any external resource that the data depend on. [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. 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 states when the data become available or how long they persist; no temporal commitment is made. [majority verdict 'no' (4/5 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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list."],"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":"2026-07-20T10:45:20.199820Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}