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Deep learning is challenging in genome-wide association studies (GWAS) with high-dimensional genomic data. Here we propose a novel three-step approach (SWAT-CNN) for identification of genetic variants using deep learning to identify phenotype-related single nucleotide polymorphisms (SNPs) that can be applied to develop accurate disease classification models. In the first step, we divided the whole genome into nonoverlapping fragments of an optimal size and then ran convolutional neural network (CNN) on each fragment to select phenotype-associated fragments. In the second step, using a Sliding Window Association Test (SWAT), we ran CNN on the selected fragments to calculate phenotype influence scores (PIS) and identify phenotype-associated SNPs based on PIS. In the third step, we ran CNN on all identified SNPs to develop a classification model. We tested our approach using GWAS data from the Alzheimer\u2019s Disease Neuroimaging Initiative (ADNI) including (N\u00a0=\u2009981; cognitively normal older adults (CN)\u2009=\u2009650 and AD\u2009=\u2009331). Our approach identified the well-known APOE region as the most significant genetic locus for AD. Our classification model achieved an area under the curve (AUC) of 0.82, which was compatible with traditional machine learning approaches, random forest and XGBoost. SWAT-CNN, a novel deep learning\u2013based genome-wide approach, identified AD-associated SNPs and a classification model for AD and may hold promise for a range of biomedical applications.<\/jats:p>","DOI":"10.1093\/bib\/bbac022","type":"journal-article","created":{"date-parts":[[2022,2,10]],"date-time":"2022-02-10T15:10:14Z","timestamp":1644505814000},"source":"Crossref","is-referenced-by-count":71,"title":["Deep learning-based identification of genetic variants: application to Alzheimer\u2019s disease classification"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1765-5735","authenticated-orcid":false,"given":"Taeho","family":"Jo","sequence":"first","affiliation":[{"name":"Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana Alzheimer\u2019s Disease Research Center, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana University Network Science Institute , Bloomington, IN , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7624-3872","authenticated-orcid":false,"given":"Kwangsik","family":"Nho","sequence":"additional","affiliation":[{"name":"Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana Alzheimer\u2019s Disease Research Center, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana University Network Science Institute , Bloomington, IN , USA"},{"name":"Center for Computational Biology and Bioinformatics, Indiana University School of Medicine , Indianapolis, IN , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5357-9966","authenticated-orcid":false,"given":"Paula","family":"Bice","sequence":"additional","affiliation":[{"name":"Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana Alzheimer\u2019s Disease Research Center, Indiana University School of Medicine , Indianapolis, IN , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1376-8532","authenticated-orcid":false,"given":"Andrew J","family":"Saykin","sequence":"additional","affiliation":[{"name":"Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana Alzheimer\u2019s Disease Research Center, Indiana University School of Medicine , Indianapolis, IN , USA"},{"name":"Indiana University Network Science Institute , Bloomington, IN , USA"},{"name":"Department of Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis, IN , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"For The Alzheimer\u2019s Disease 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