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However, most transcriptome-wide association approaches primarily model local (\n                    <jats:italic>cis<\/jats:italic>\n                    ) genetic effects, leaving much of gene regulation unexplained. Here, we show that incorporating distal (\n                    <jats:italic>trans<\/jats:italic>\n                    ) regulatory effects improves the prediction of gene expression and the identification of disease-associated genes. Using RNA sequencing data from six human post-mortem brain regions, we developed INGENE and MODULE, two models capturing the combined influence of candidate\n                    <jats:italic>trans-<\/jats:italic>\n                    acting variants within gene coexpression networks. Integrating these models with conventional\n                    <jats:italic>cis<\/jats:italic>\n                    -based predictors improved gene expression imputation (maximum likelihood estimation, \u03b1\u2009=\u20090.05) for 18,744 genes across regions. Applying this framework to Psychiatric Genomics Consortium wave 3 genotypes identified 766 genes associated with schizophrenia (\n                    <jats:italic>P<\/jats:italic>\n                    <jats:sub>FDR<\/jats:sub>\n                    \u2009&lt;\u20090.01), including 641 not previously reported by transcriptome-wide analyses. These findings highlight the contribution of distal regulatory mechanisms and gene network interactions to schizophrenia risk.\n                  <\/jats:p>","DOI":"10.1038\/s41588-026-02646-3","type":"journal-article","created":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T09:02:48Z","timestamp":1782118968000},"page":"1559-1572","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Co-expression-based models improve eQTL predictions for transcriptome-wide association studies and highlight new schizophrenia-associated genes"],"prefix":"10.1038","volume":"58","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3724-9456","authenticated-orcid":false,"given":"Fabiana","family":"Rossi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonardo","family":"Sportelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6979-7404","authenticated-orcid":false,"given":"Gianluca C.","family":"Kikidis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7816-668X","authenticated-orcid":false,"given":"Giulia","family":"Grassi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabio","family":"Di Camillo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Bertolino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0878-1131","authenticated-orcid":false,"given":"Giuseppe","family":"Blasi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Borcuk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9062-571X","authenticated-orcid":false,"given":"Daniela","family":"Fusco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8746-3037","authenticated-orcid":false,"given":"Thomas M.","family":"Hyde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4210-6052","authenticated-orcid":false,"given":"Joel E.","family":"Kleinman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9573-0601","authenticated-orcid":false,"given":"Davide","family":"Marnetto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0556-0165","authenticated-orcid":false,"given":"Silvia","family":"Pellegrini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9654-3266","authenticated-orcid":false,"given":"Antonio","family":"Rampino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedetto","family":"Vitiello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3622-835X","authenticated-orcid":false,"given":"Stephan","family":"Ripke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Braun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Kraft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2419-4351","authenticated-orcid":false,"given":"Sintia Iole","family":"Belangero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulo R.","family":"Menezes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3382-4754","authenticated-orcid":false,"given":"Celso","family":"Arango","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6980-4053","authenticated-orcid":false,"given":"James T. 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