{"doi":"10.1093/ije/dyad018","title":"Design and quality control of large-scale two-sample Mendelian randomization studies","abstract":"Background: Mendelian randomization (MR) studies are susceptible to metadata errors (e.g. incorrect specification of the effect allele column) and other analytical issues that can introduce substantial bias into analyses. We developed a quality control (QC) pipeline for the Fatty Acids in Cancer Mendelian Randomization Collaboration (FAMRC) that can be used to identify and correct for such errors. Methods: We collated summary association statistics from fatty acid and cancer genome-wide association studies (GWAS) and subjected the collated data to a comprehensive QC pipeline. We identified metadata errors through comparison of study-specific statistics to external reference data sets (the National Human Genome Research Institute-European Bioinformatics Institute GWAS catalogue and 1000 genome super populations) and other analytical issues through comparison of reported to expected genetic effect sizes. Comparisons were based on three sets of genetic variants: (i) GWAS hits for fatty acids, (ii) GWAS hits for cancer and (iii) a 1000 genomes reference set. Results: We collated summary data from 6 fatty acid and 54 cancer GWAS. Metadata errors and analytical issues with the potential to introduce substantial bias were identified in seven studies (11.6%). After resolving metadata errors and analytical issues, we created a data set of 219 842 genetic associations with 90 cancer types, generated in analyses of 566 665 cancer cases and 1 622 374 controls. Conclusions: In this large MR collaboration, 11.6% of included studies were affected by a substantial metadata error or analytical issue. By increasing the integrity of collated summary data prior to their analysis, our protocol can be used to increase the reliability of downstream MR analyses. Our pipeline is available to other researchers via the CheckSumStats package (https://github.com/MRCIEU/CheckSumStats).","journal":"International Journal of Epidemiology","year":2023,"id":357222,"datarank":0.6201876070676834,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.21398007690235182,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.21398007690235182,"corpus_percentile":68.13645857507542,"corpus_rank":4120,"citation_count":14,"citer_count":9,"citers_with_citation_signal":4,"citers_with_endowment":4,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6638,"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":29.1667,"fair_percentile":43.01436869458881,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":469254,"name":"Maria Carolina Borges","orcid":"0000-0001-7785-4547","position":1,"is_corresponding":false},{"id":424645,"name":"Kimberley Burrows","orcid":"0000-0002-3208-0389","position":2,"is_corresponding":false},{"id":305438,"name":"Rozenn N. Lemaître","orcid":"0000-0002-7038-1844","position":3,"is_corresponding":false},{"id":228668,"name":"Sean Harrison","orcid":"0000-0002-7966-0700","position":4,"is_corresponding":false},{"id":78822,"name":"Stephen Burgess","orcid":"0000-0001-5365-8760","position":5,"is_corresponding":false},{"id":236702,"name":"Xuling Chang","orcid":"0000-0001-7471-4768","position":6,"is_corresponding":false},{"id":542704,"name":"Jason Westra","orcid":"0000-0002-4754-1395","position":7,"is_corresponding":false},{"id":369709,"name":"Nikhil K. Khankari","orcid":"0000-0002-8802-4431","position":8,"is_corresponding":false},{"id":874458,"name":"Kostas K Tsilidis","orcid":null,"position":9,"is_corresponding":false},{"id":78831,"name":"Tom R Gaunt","orcid":"0000-0003-0924-3247","position":10,"is_corresponding":false},{"id":21773,"name":"Gibran Hemani","orcid":"0000-0003-0920-1055","position":11,"is_corresponding":false},{"id":564973,"name":"Jie Zheng","orcid":"0000-0002-4265-6695","position":12,"is_corresponding":false},{"id":55366,"name":"Thérèse Truong","orcid":"0000-0002-2943-6786","position":13,"is_corresponding":false},{"id":55345,"name":"Tracy A. O’Mara","orcid":"0000-0002-5436-3232","position":14,"is_corresponding":false},{"id":55382,"name":"Amanda B. Spurdle","orcid":"0000-0003-1337-7897","position":15,"is_corresponding":false},{"id":231303,"name":"Matthew H. Law","orcid":"0000-0002-4303-8821","position":16,"is_corresponding":false},{"id":264807,"name":"Susan L. Slager","orcid":"0000-0002-5173-4712","position":17,"is_corresponding":false},{"id":260278,"name":"Brenda M. Birmann","orcid":"0000-0002-7550-5498","position":18,"is_corresponding":false},{"id":1029676,"name":"Fatemeh Saberi Hosnijeh","orcid":"0000-0002-7572-9715","position":19,"is_corresponding":false},{"id":329377,"name":"Daniela Mariosa","orcid":"0000-0001-8181-1419","position":20,"is_corresponding":false},{"id":5679,"name":"Christopher I. Amos","orcid":"0000-0002-8540-7023","position":21,"is_corresponding":false},{"id":816784,"name":"Rayjean J Hung","orcid":null,"position":22,"is_corresponding":false},{"id":39347,"name":"Wei Zheng","orcid":"0000-0003-1226-070X","position":23,"is_corresponding":false},{"id":39449,"name":"Marc J. Gunter","orcid":"0000-0001-5472-6761","position":24,"is_corresponding":false},{"id":1528,"name":"George Davey Smith","orcid":"0000-0002-1407-8314","position":25,"is_corresponding":false},{"id":78829,"name":"Caroline Relton","orcid":"0000-0003-2052-4840","position":26,"is_corresponding":false},{"id":78830,"name":"Richard M Martin","orcid":"0000-0002-7992-7719","position":27,"is_corresponding":false},{"id":305423,"name":"Nathan Tintle","orcid":"0000-0003-1447-9107","position":28,"is_corresponding":false},{"id":218649,"name":"Ulrike Peters","orcid":"0000-0001-5666-9318","position":29,"is_corresponding":false},{"id":472445,"name":"Terri Rice","orcid":null,"position":30,"is_corresponding":false},{"id":252204,"name":"Iona Cheng","orcid":"0000-0003-4132-2893","position":31,"is_corresponding":false},{"id":218621,"name":"Mark A. Jenkins","orcid":"0000-0002-8964-6160","position":32,"is_corresponding":false},{"id":608335,"name":"Steve Gallinger","orcid":null,"position":33,"is_corresponding":false},{"id":883538,"name":"Alex J. Cornish","orcid":"0000-0002-3966-3501","position":34,"is_corresponding":false},{"id":917328,"name":"Amit Sud","orcid":"0000-0002-6133-0164","position":35,"is_corresponding":false},{"id":338822,"name":"Jayaram Vijayakrishnan","orcid":"0000-0002-8284-2249","position":36,"is_corresponding":false},{"id":264805,"name":"Margaret Wrensch","orcid":"0000-0002-3070-7600","position":37,"is_corresponding":false},{"id":38786,"name":"Mattias Johansson","orcid":"0000-0002-3116-5081","position":38,"is_corresponding":false},{"id":304439,"name":"Aaron D. Norman","orcid":"0000-0002-4208-2708","position":39,"is_corresponding":false},{"id":109497,"name":"Alison P. Klein","orcid":"0000-0003-2737-8399","position":40,"is_corresponding":false},{"id":503082,"name":"Alyssa Clay‐Gilmour","orcid":"0000-0001-9998-4879","position":41,"is_corresponding":false},{"id":1151,"name":"André Franke","orcid":"0000-0003-1530-5811","position":42,"is_corresponding":false},{"id":305416,"name":"Andres V Ardisson Korat","orcid":"0000-0003-4599-2245","position":43,"is_corresponding":false},{"id":842918,"name":"Bill Wheeler","orcid":null,"position":44,"is_corresponding":false},{"id":16675,"name":"Björn Nilsson","orcid":"0000-0001-5542-0254","position":45,"is_corresponding":false},{"id":395251,"name":"Caren E. Smith","orcid":"0000-0002-9511-1103","position":46,"is_corresponding":false},{"id":236703,"name":"Chew‐Kiat Heng","orcid":"0000-0002-7309-9473","position":47,"is_corresponding":false},{"id":781899,"name":"Ci Song","orcid":"0000-0002-0947-9068","position":48,"is_corresponding":false},{"id":1030273,"name":"David Riadi","orcid":null,"position":49,"is_corresponding":false},{"id":665371,"name":"Elizabeth B. Claus","orcid":"0000-0001-9867-8124","position":50,"is_corresponding":false},{"id":571032,"name":"Eva Ellinghaus","orcid":"0000-0003-2914-3382","position":51,"is_corresponding":false},{"id":390241,"name":"Evgenia Ostroumova","orcid":"0000-0003-4729-1733","position":52,"is_corresponding":false},{"id":1030274,"name":"Hosnijeh","orcid":null,"position":53,"is_corresponding":false},{"id":427900,"name":"Florent de Vathaire","orcid":"0000-0002-8374-9281","position":54,"is_corresponding":false},{"id":1029677,"name":"Giovanni Cugliari","orcid":"0000-0002-6080-0718","position":55,"is_corresponding":false},{"id":13056,"name":"Giuseppe Matullo","orcid":"0000-0003-0674-7757","position":56,"is_corresponding":false},{"id":764197,"name":"Irene Oi‐Lin Ng","orcid":"0000-0001-7532-2029","position":57,"is_corresponding":false},{"id":302818,"name":"James R. Cerhan","orcid":"0000-0002-7482-178X","position":58,"is_corresponding":false},{"id":1107107,"name":"Jeanette E Passow","orcid":null,"position":59,"is_corresponding":false},{"id":270071,"name":"Jia Nee Foo","orcid":"0000-0001-9899-2308","position":60,"is_corresponding":false},{"id":383608,"name":"Jiali Han","orcid":"0000-0002-1949-4907","position":61,"is_corresponding":false},{"id":20712,"name":"Jianjun Liu","orcid":"0000-0002-3255-3019","position":62,"is_corresponding":false},{"id":14321,"name":"Jill S. Barnholtz‐Sloan","orcid":"0000-0001-6190-9304","position":63,"is_corresponding":false},{"id":307,"name":"Joellen M. Schildkraut","orcid":"0000-0002-0990-9339","position":64,"is_corresponding":false},{"id":240511,"name":"John M. Maris","orcid":"0000-0002-8088-7929","position":65,"is_corresponding":false},{"id":409685,"name":"Joseph L. Wiemels","orcid":"0000-0003-4838-9951","position":66,"is_corresponding":false},{"id":929566,"name":"Kari Hemminki","orcid":"0000-0002-2769-3316","position":67,"is_corresponding":false},{"id":389186,"name":"Keming Yang","orcid":"0000-0001-9722-8041","position":68,"is_corresponding":false},{"id":21903,"name":"Lambertus A. Kiemeney","orcid":"0000-0002-2368-1326","position":69,"is_corresponding":false},{"id":240062,"name":"Lang Wu","orcid":"0000-0001-9938-3627","position":70,"is_corresponding":false},{"id":264809,"name":"Laufey T. Ámundadóttir","orcid":"0000-0003-1859-8971","position":71,"is_corresponding":false},{"id":70186,"name":"Marc‐Henri Stern","orcid":"0000-0002-8100-2272","position":72,"is_corresponding":false},{"id":625032,"name":"Marie-Christine Boutron","orcid":null,"position":73,"is_corresponding":false},{"id":30757,"name":"Mark M. Iles","orcid":"0000-0002-2603-6509","position":74,"is_corresponding":false},{"id":241831,"name":"Mark P. 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Taylor","orcid":"0000-0003-0163-1421","position":84,"is_corresponding":false},{"id":231298,"name":"Puya Gharahkhani","orcid":"0000-0002-4203-5952","position":85,"is_corresponding":false},{"id":15705,"name":"Quinn T. Ostrom","orcid":"0000-0003-3469-7558","position":86,"is_corresponding":false},{"id":302477,"name":"Rachael Z. Stolzenberg‐Solomon","orcid":"0000-0003-3698-7006","position":87,"is_corresponding":false},{"id":390744,"name":"Rajkumar Dorajoo","orcid":"0000-0001-6608-2051","position":88,"is_corresponding":false},{"id":254457,"name":"Richard S. Houlston","orcid":"0000-0002-5268-0242","position":89,"is_corresponding":false},{"id":226434,"name":"Robert B. Jenkins","orcid":"0000-0002-4049-694X","position":90,"is_corresponding":false},{"id":32676,"name":"Sharon J. Diskin","orcid":"0000-0002-7200-8939","position":91,"is_corresponding":false},{"id":21999,"name":"Sonja I. Berndt","orcid":"0000-0001-5230-0652","position":92,"is_corresponding":false},{"id":501916,"name":"Spiridon Tsavachidis","orcid":null,"position":93,"is_corresponding":false},{"id":19984,"name":"Stefan Enroth","orcid":"0000-0002-5056-9137","position":94,"is_corresponding":false},{"id":1030278,"name":"Stephen J. Channock","orcid":null,"position":95,"is_corresponding":false},{"id":218619,"name":"Tabitha A. Harrison","orcid":"0000-0002-4173-7530","position":96,"is_corresponding":false},{"id":361123,"name":"Tessel E. Galesloot","orcid":"0000-0002-2717-3679","position":97,"is_corresponding":false},{"id":21882,"name":"Ulf Gyllensten","orcid":"0000-0002-6316-3355","position":98,"is_corresponding":false},{"id":74232,"name":"Vijai Joseph","orcid":"0000-0002-7933-151X","position":99,"is_corresponding":false},{"id":78832,"name":"Philip C Haycock","orcid":"0000-0001-5001-3350","position":0,"is_corresponding":true}],"reference_count":101,"raw_metadata":null,"created_at":"2026-07-19T01:13:34.795336Z","pmid":"38587501","pmcid":"PMC10555669","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":33.3333,"fair_a":25.0,"fair_i":40.0,"fair_r":50.0,"fair_zscore":-0.2091,"fair_rationale":{"fair_score":29.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":33.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No persistent identifier scheme (DOI, Handle, ARK, or repository accession) is assigned to the paper's own compiled dataset. [majority verdict 'no' (3/5 passes agreed)]","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":"Full GWAS summary data for the included cancer studies can be downloaded from Open GWAS ( https://gwas.mrcieu.ac.uk/) or the GWAS catalogue FTP site ( https://www.ebi.ac.uk/gwas/home)","grounded":false,"rationale":"The paper names Open GWAS, GWAS catalogue, and University of Bristol data repository as repositories holding the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Full GWAS summary data for the included cancer studies can be downloaded from Open GWAS ( https://gwas.mrcieu.ac.uk/) or the GWAS catalogue FTP site ( https://www.ebi.ac.uk/gwas/home), or obtained by direct correspondence with the relevant study. Supplementary Table S5 contains further details on the underlying source for each cancer GWAS summary-data set, such as Open GWAS identifiers and columns indicating whether the data were downloaded from the GWAS catalogue or obtained by correspondence. Full GWAS summary data for cancers generated in UK Biobank, under application number 15825, can be downloaded from either Open GWAS or the University of Bristol data repository at https://doi.org/10.5523/bris.aed0u12w0ede20olb0m77p4b9. Summary genetic data corresponding to the fatty acid SNP set (i.e. a subset of the full summary data) for all cancer studies can be found at the following github repository:https:// github.com/mightyphil2000/fatty-acids/tree/master/outcome_data/ data/harmonised.","grounded":false,"rationale":"The data availability statement points to repositories (Open GWAS, GWAS catalogue, University of Bristol repository) with persistent links. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"After resolving metadata errors and analytical issues, we created a data set of 219 842 genetic associations with 90 cancer types, generated in analyses of 566 665 cancer cases and 1 622 374 controls.","grounded":true,"rationale":"The dataset is described in a single prose sentence without an itemised inventory of files or variables.","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier or link for the paper's own compiled dataset appears in the reference list or body text; only identifiers for underlying studies are given.","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":25.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Full GWAS summary data for the included cancer studies can be downloaded from Open GWAS ( https://gwas.mrcieu.ac.uk/) or the GWAS catalogue FTP site ( https://www.ebi.ac.uk/gwas/home)","grounded":false,"rationale":"The primary routes to the data are through public repositories (Open GWAS, GWAS catalogue, University of Bristol repository) with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"Full GWAS summary data for the included cancer studies can be downloaded from Open GWAS ( https://gwas.mrcieu.ac.uk/) or the GWAS catalogue FTP site ( https://www.ebi.ac.uk/gwas/home), or obtained by direct correspondence with the relevant study.","grounded":false,"rationale":"The statement describes download actions from repositories without applying an explicit access-level label like 'open access' or 'restricted'. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"Full GWAS summary data for the included cancer studies can be downloaded from Open GWAS ( https://gwas.mrcieu.ac.uk/) or the GWAS catalogue FTP site ( https://www.ebi.ac.uk/gwas/home), or obtained by direct correspondence with the relevant study.","grounded":false,"rationale":"The paper uses summary statistics which are not considered sensitive human-subject data, and no gatekeeper is named for the data.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence addresses how long the data persist or when they become available, so class 3 (no). [majority verdict 'no' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"We manually mapped the cancer name for each data set to the experimental factor ontology (EFO).","grounded":true,"rationale":"The paper explicitly states use of the Experimental Factor Ontology, a community standard vocabulary.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"15825","grounded":false,"rationale":"The paper gives the UK Biobank application number 15825, an identifier for an external resource, so class 1 (yes). 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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":"2026-07-20T12:10:39.827059Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}