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Here we represent the first comprehensive meta-analysis of urinary metabolite GWAS studies, aiming to consolidate existing data on metabolite-SNP associations, evaluate consistency across studies, and unravel novel genetic links. Following an extensive literature review and data collection through the EMBL-EBI GWAS Catalog, PubMed, and metabolomix.com, we employed a sample size-based meta-analytic approach to evaluate the significance of previously reported GWAS associations. Our analysis identified 48 independent lead SNPs correlated with the levels of 14 unique urinary metabolites: alanine, 3-aminoisobutyrate, betaine, creatine, creatinine, formate, glycine, glycolate, histidine, 2-hydroxybutyrate, lysine, threonine, trimethylamine, and tyrosine. Notably, the results revealed a novel locus for tyrosine (rs4594899,\n                    <jats:italic>SLC12A7,<\/jats:italic>\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20096.6\u2009\u00d7\u200910\n                    <jats:sup>\u20139<\/jats:sup>\n                    , N\u2009=\u20092623), and three newly associated independent SNPs within known loci: one for glycine (rs1755615,\n                    <jats:italic>GLDC<\/jats:italic>\n                    ,\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20092.4\u2009\u00d7\u200910\n                    <jats:sup>\u201310<\/jats:sup>\n                    , N\u2009=\u20095319), and two for 3-aminoisobutyrate (rs79053399,\n                    <jats:italic>RAI14<\/jats:italic>\n                    ,\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20096.9\u2009\u00d7\u200910\n                    <jats:sup>\u201310<\/jats:sup>\n                    , N\u2009=\u20094656; rs36071744,\n                    <jats:italic>TTC23L,<\/jats:italic>\n                    <jats:italic>P<\/jats:italic>\n                    \u2009=\u20092.97\u2009\u00d7\u200910\n                    <jats:sup>\u201310<\/jats:sup>\n                    , N\u2009=\u20094872). These findings underscore the potential of urinary metabolite GWAS meta-analyses in revealing novel genetic factors that may aid in the understanding of disease processes and highlight the necessity for larger and more comprehensive future studies.\n                  <\/jats:p>","DOI":"10.1038\/s41598-025-07518-0","type":"journal-article","created":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T04:16:25Z","timestamp":1751343385000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Meta-analysis of urinary metabolite GWAS studies identifies novel genome-wide significant loci"],"prefix":"10.1038","volume":"15","author":[{"given":"Jihan K.","family":"Zaki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakub","family":"Tomasik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jade A.","family":"McCune","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oren A.","family":"Scherman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabine","family":"Bahn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,7,1]]},"reference":[{"key":"7518_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s43586-021-00056-9","volume":"1","author":"E Uffelmann","year":"2021","unstructured":"Uffelmann, E. et al. Genome-wide association studies. Nat. Rev. Methods Primers 1, 1\u201321 (2021).","journal-title":"Nat. Rev. Methods Primers"},{"key":"7518_CR2","doi-asserted-by":"publisher","first-page":"e1000282","DOI":"10.1371\/journal.pgen.1000282","volume":"4","author":"C Gieger","year":"2008","unstructured":"Gieger, C. et al. Genetics meets metabolomics: A genome-wide association study of metabolite profiles in human serum. PLoS Genet. 4, e1000282 (2008).","journal-title":"PLoS Genet."},{"key":"7518_CR3","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/ng.837","volume":"43","author":"K Suhre","year":"2011","unstructured":"Suhre, K. et al. A genome-wide association study of metabolic traits in human urine. Nat. Genet. 43, 565\u2013569 (2011).","journal-title":"Nat. Genet."},{"key":"7518_CR4","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nrg3472","volume":"14","author":"E Evangelou","year":"2013","unstructured":"Evangelou, E. & Ioannidis, J. P. A. 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Dr Bahn reported grants from Stanley Medical Research Institute and Psyomics during the conduct of the study; is a founder and shareholder in Psyomics; is Director of Psynova Neuro-tech outside the submitted work; and has a patent pending for dried blood spot biomarkers for bipolar disorder. The other authors have no conflicts to declare.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"20375"}}