{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:35:12Z","timestamp":1780317312436,"version":"3.54.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,6,24]],"date-time":"2020-06-24T00:00:00Z","timestamp":1592956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Science Foundation CCF","award":["1763191"],"award-info":[{"award-number":["1763191"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21 MD012867-01"],"award-info":[{"award-number":["R21 MD012867-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30AG059307"],"award-info":[{"award-number":["P30AG059307"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Silicon Valley Foundation and the Chan-Zuckerberg Initiative"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Interpreting genetic variants of unknown significance (VUS) is essential in clinical applications of genome sequencing for diagnosis and personalized care. Non-coding variants remain particularly difficult to interpret, despite making up a large majority of trait associations identified in genome-wide association studies (GWAS) analyses. Predicting the regulatory effects of non-coding variants on candidate genes is a key step in evaluating their clinical significance. Here, we develop a machine-learning algorithm, Inference of Connected expression quantitative trait loci (eQTLs) (IRT), to predict the regulatory targets of non-coding variants identified in studies of eQTLs. We assemble datasets using eQTL results from the Genotype-Tissue Expression (GTEx) project and learn to separate positive and negative pairs based on annotations characterizing the variant, gene and the intermediate sequence. IRT achieves an area under the receiver operating characteristic curve (ROC-AUC) of 0.799 using random cross-validation, and 0.700 for a more stringent position-based cross-validation. Further evaluation on rare variants and experimentally validated regulatory variants shows a significant enrichment in IRT identifying the true target genes versus negative controls. In gene-ranking experiments, IRT achieves a top-1 accuracy of 50% and top-3 accuracy of 90%. Salient features, including GC-content, histone modifications and Hi-C interactions are further analyzed and visualized to illustrate their influences on predictions. IRT can be applied to any VUS of interest and each candidate nearby gene to output a score reflecting the likelihood of regulatory effect on the expression level. These scores can be used to prioritize variants and genes to assist in patient diagnosis and GWAS follow-up studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Codes and data used in this work are available at https:\/\/github.com\/miaecle\/eQTL_Trees.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa254","type":"journal-article","created":{"date-parts":[[2020,4,17]],"date-time":"2020-04-17T11:13:55Z","timestamp":1587122035000},"page":"4440-4448","source":"Crossref","is-referenced-by-count":8,"title":["Predicting target genes of non-coding regulatory variants with IRT"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0148-7055","authenticated-orcid":false,"given":"Zhenqin","family":"Wu","sequence":"first","affiliation":[{"name":"Department of Chemistry, Stanford University , CA 94305, USA"},{"name":"Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, 94305 CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilah M","family":"Ioannidis","sequence":"additional","affiliation":[{"name":"Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, 94305 CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Zou","sequence":"additional","affiliation":[{"name":"Department of Biomedical Data Science, Stanford University School of Medicine , Stanford, 94305 CA, USA"},{"name":"Chan-Zuckerberg Biohub , San Francisco, 94158 CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,6,24]]},"reference":[{"key":"2023062213510479400_btaa254-B1","doi-asserted-by":"crossref","DOI":"10.1101\/416685","article-title":"Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks","author":"Agarwal","year":"2018"},{"key":"2023062213510479400_btaa254-B2","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1093\/bioinformatics\/btq134","article-title":"Permutation importance: a corrected feature importance measure","volume":"26","author":"Altmann","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062213510479400_btaa254-B3","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1016\/j.jid.2016.01.013","article-title":"Identification of susceptibility loci for cutaneous squamous cell carcinoma","volume":"136","author":"Asgari","year":"2016","journal-title":"J. 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