Association Rule Mining for Genome-Wide Association Studies through Gibbs Sampling

Association Rule Mining for Genome-Wide Association Studies through Gibbs Sampling | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Association Rule Mining for Genome-Wide Association Studies through Gibbs Sampling Guoqi Qian, Pei-Yun Sun This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1768333/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 16 Oct, 2023 Read the published version in International Journal of Data Science and Analytics → Version 1 posted 7 You are reading this latest preprint version Abstract Finding associations between genetic markers and a phenotypic trait such as coronary artery disease (CAD) is of primary interest in genome-wide association studies (GWAS). A major challenge in GWAS is the involved genomic data often contain large number of genetic markers and the underlying genotype-phenotype relationship is mostly complex. Current statistical and machine learning methods lack the power to tackle this challenge with effectiveness and efficiency. In this paper we develop a stochastic search method to mine the genotype-phenotype associations from GWAS data. The new method generalizes the well-established association rule mining (ARM) framework for searching for the most important genotype-phenotype association rules, where we develop a multinomial Gibbs sampling algorithm and use it together with the Apriori algorithm to overcome the overwhelming computing complexity in ARM in GWAS. Three simulation studies based on synthetic data are used to assess the performance of our developed method, delivering the anticipated results. Finally, we illustrate the use of the developed method through a case study of CAD GWAS. Gibbs sampling association rule mining genome-wide association study genotype-phenotype association epistatic interaction Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 16 Oct, 2023 Read the published version in International Journal of Data Science and Analytics → Version 1 posted Editorial decision: Major revision 03 Jul, 2023 Reviews received at journal 03 Aug, 2022 Reviewers agreed at journal 12 Jul, 2022 Reviewers invited by journal 12 Jul, 2022 Editor assigned by journal 04 Jul, 2022 Submission checks completed at journal 20 Jun, 2022 First submitted to journal 17 Jun, 2022 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-1768333","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":114770126,"identity":"96346ac0-0aa7-4089-a1d7-034a08ed3193","order_by":0,"name":"Guoqi Qian","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA6UlEQVRIie3PvQrCMBDA8ZOCDmrnlqK+QkpBEMRnySE4Cz6AguDkCwh9BIeK4MdW6OBSzRpwqXsHxUXQwdMuihA6OuQPyU0/LgHQ6f421gYwaJ5GdIX5SC8jmJ9AlI1cxBRzN0n7AtelMia4gbopeeFaURBbpp7rsyNux9Ulwxg8W3LDUREm46ZTIRJE1ZWFE8BAcshDDi+yvhEZEjHuSiKmLxK+twARziQvKrfYsjigv3Q9IksLY8udxadJy1cQU0SLJH10aoHYL86XTbth7rqRTBUE6LPw8QyLTmGkAgAi/CI6nU6n++0JsV9UyyI0MeEAAAAASUVORK5CYII=","orcid":"","institution":"University of Melbourne","correspondingAuthor":true,"prefix":"","firstName":"Guoqi","middleName":"","lastName":"Qian","suffix":""},{"id":114770127,"identity":"c7650602-f6e4-4d2e-8b38-6aa20dd3db0e","order_by":1,"name":"Pei-Yun Sun","email":"","orcid":"","institution":"University of Melbourne","correspondingAuthor":false,"prefix":"","firstName":"Pei-Yun","middleName":"","lastName":"Sun","suffix":""}],"badges":[],"createdAt":"2022-06-17 10:59:09","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-1768333/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-1768333/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s41060-023-00456-y","type":"published","date":"2023-10-16T15:01:34+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":23058655,"identity":"8398ef1e-0091-4c70-b1c0-b6ac23b2df50","added_by":"auto","created_at":"2022-06-24 16:46:47","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":386418,"visible":true,"origin":"","legend":"","description":"","filename":"GibbsARMGWAS.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1768333/v1_covered.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Association Rule Mining for Genome-Wide Association Studies through Gibbs Sampling","fulltext":[{"header":"Full Text","content":"This preprint is available for \u003ca href='/article/rs-1768333/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e."}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"international-journal-of-data-science-and-analytics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"jdsa","sideBox":"Learn more about [International Journal of Data Science and Analytics](http://link.springer.com/journal/41060)","snPcode":"41060","submissionUrl":"https://submission.nature.com/new-submission/41060/3","title":"International Journal of Data Science and Analytics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Gibbs sampling, association rule mining, genome-wide association study, genotype-phenotype association, epistatic interaction","lastPublishedDoi":"10.21203/rs.3.rs-1768333/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1768333/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Finding associations between genetic markers and a phenotypic trait such as coronary artery disease (CAD) is of primary interest in genome-wide association studies (GWAS). 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