{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T16:06:57Z","timestamp":1792426017690,"version":"4.5.0"},"reference-count":103,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,10,30]],"date-time":"2020-10-30T00:00:00Z","timestamp":1604016000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91935302"],"award-info":[{"award-number":["91935302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61922020"],"award-info":[{"award-number":["61922020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61771331"],"award-info":[{"award-number":["61771331"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Over the last decade, genome-wide association studies (GWAS) have discovered thousands of genetic variants underlying complex human diseases and agriculturally important traits. These findings have been utilized to dissect the biological basis of diseases, to develop new drugs, to advance precision medicine and to boost breeding. However, the potential of GWAS is still underexploited due to methodological limitations. Many challenges have emerged, including detecting epistasis and single-nucleotide polymorphisms (SNPs) with small effects and distinguishing causal variants from other SNPs associated through linkage disequilibrium. These issues have motivated advancements in GWAS analyses in two contrasting cultures\u2014statistical modelling and machine learning. In this review, we systematically present the basic concepts and the benefits and limitations in both methods. We further discuss recent efforts to mitigate their weaknesses. Additionally, we summarize the state-of-the-art tools for detecting the missed signals, ultrarare mutations and gene\u2013gene interactions and for prioritizing SNPs. Our work can offer both theoretical and practical guidelines for performing GWAS analyses and for developing further new robust methods to fully exploit the potential of GWAS.<\/jats:p>","DOI":"10.1093\/bib\/bbaa263","type":"journal-article","created":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T19:12:49Z","timestamp":1600110769000},"source":"Crossref","is-referenced-by-count":38,"title":["Revisiting genome-wide association studies from statistical modelling to machine learning"],"prefix":"10.1093","volume":"22","author":[{"given":"Shanwen","family":"Sun","sequence":"first","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences at the University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benzhi","family":"Dong","sequence":"additional","affiliation":[{"name":"College of Computer Science and Engineering, Northeast Forestry University, Harbin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences at the University of Electronic Science and Technology of China, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,30]]},"reference":[{"key":"2021072112310784800_ref1","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nrg1521","article-title":"Genome-wide association studies for common diseases and complex traits","volume":"6","author":"Hirschhorn","year":"2005","journal-title":"Nat Rev Genet"},{"key":"2021072112310784800_ref2","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/s41576-019-0127-1","article-title":"Benefits and limitations of genome-wide association studies","volume":"20","author":"Tam","year":"2019","journal-title":"Nat Rev 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