{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T14:19:25Z","timestamp":1768486765759,"version":"3.49.0"},"posted":{"date-parts":[[2019,9,20]]},"group-title":"Cancer Biology","reference-count":65,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2019,9,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Most breast cancer (BC) risk-associated variants (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting miRNA genes and\/or miRNA-binding. To test this we adapted two miRNA-binding prediction algorithms \u2014 TargetScan and miRanda \u2014 to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant (\n                  <jats:italic>P<\/jats:italic>\n                  \u2264 5 \u00d7 10\n                  <jats:sup>\u22128<\/jats:sup>\n                  ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3\u2019UTRs of putative miRNA target genes were predicted to alter miRNA\u2237mRNA pair binding stability in five candidate target genes. Of these, we propose\n                  <jats:italic>RNF115<\/jats:italic>\n                  , at locus 1q21.1, as a strong novel target gene associated with BC risk, and re-inforce the role of miRNA mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.\n                <\/jats:p>","DOI":"10.1101\/777318","type":"posted-content","created":{"date-parts":[[2019,9,21]],"date-time":"2019-09-21T05:15:11Z","timestamp":1569042911000},"source":"Crossref","is-referenced-by-count":0,"title":["Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0021-9702","authenticated-orcid":false,"given":"Ana","family":"Jacinta-Fernandes","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0702-6700","authenticated-orcid":false,"given":"Joana M.","family":"Xavier","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5226-3441","authenticated-orcid":false,"given":"Ramiro","family":"Magno","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2789-8303","authenticated-orcid":false,"given":"Joel G.","family":"Lage","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0454-9207","authenticated-orcid":false,"given":"Ana-Teresa","family":"Maia","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019092210290266000_777318v1.1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1133"},{"key":"2019092210290266000_777318v1.2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1229"},{"key":"2019092210290266000_777318v1.3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0060108"},{"key":"2019092210290266000_777318v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.10.012"},{"key":"2019092210290266000_777318v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/ng.840"},{"key":"2019092210290266000_777318v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.01.002"},{"key":"2019092210290266000_777318v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2014.11.009"},{"key":"2019092210290266000_777318v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2016.07.017"},{"key":"2019092210290266000_777318v1.9","doi-asserted-by":"publisher","DOI":"10.1186\/bcr3169"},{"key":"2019092210290266000_777318v1.10","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.12818"},{"key":"2019092210290266000_777318v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(04)00045-5"},{"key":"2019092210290266000_777318v1.12","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-08-2129"},{"key":"2019092210290266000_777318v1.13","doi-asserted-by":"publisher","DOI":"10.2147\/OTT.S108787"},{"key":"2019092210290266000_777318v1.14","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-09-3541"},{"key":"2019092210290266000_777318v1.15","doi-asserted-by":"publisher","DOI":"10.1002\/humu.22159"},{"key":"2019092210290266000_777318v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms12868"},{"key":"2019092210290266000_777318v1.17","doi-asserted-by":"publisher","DOI":"10.1126\/science.1222794"},{"key":"2019092210290266000_777318v1.18","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.06633"},{"key":"2019092210290266000_777318v1.19","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2003-5-1-r1"},{"key":"2019092210290266000_777318v1.20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx331"},{"key":"2019092210290266000_777318v1.21","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-10-0527"},{"key":"2019092210290266000_777318v1.22","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.29978"},{"key":"2019092210290266000_777318v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2007.09.021"},{"key":"2019092210290266000_777318v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/srep32700"},{"key":"2019092210290266000_777318v1.25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003212"},{"key":"2019092210290266000_777318v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/ng.669"},{"key":"2019092210290266000_777318v1.27","doi-asserted-by":"publisher","DOI":"10.1158\/1557-3125.ADVBC15-A31"},{"key":"2019092210290266000_777318v1.28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts089"},{"key":"2019092210290266000_777318v1.29","doi-asserted-by":"publisher","DOI":"10.1126\/science.1262110"},{"key":"2019092210290266000_777318v1.30","doi-asserted-by":"publisher","DOI":"10.1158\/1940-6207.CAPR-08-0012"},{"key":"2019092210290266000_777318v1.31","first-page":"5132","article-title":"Chemopreventive 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