{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T16:22:54Z","timestamp":1780503774115,"version":"3.54.1"},"posted":{"date-parts":[[2025,10,7]]},"group-title":"Genetic and Genomic Medicine","reference-count":73,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T00:00:00Z","timestamp":1759795200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.medrxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Protein quantitative trait loci (pQTLs) provide insight into the genetic regulation of protein expression and disease biology. We performed a large-scale cross-platform meta-analysis of plasma proteomics, integrating data from over 90,000 individuals across Olink and SomaScan platforms. This effort identified &gt;30,000 sentinel pQTLs, with multi-trait approach (MTAG) markedly boosting both discovery and replication, despite the potential differences in the protein measurements of the two platforms. While both platforms captured well-known pleiotropic loci (\n                  <jats:italic>HLA, ABO, SH2B3<\/jats:italic>\n                  ), we also uncovered platform-specific associations, reflecting unique assay designs. We further established a comprehensive resource for transcriptome- and proteome-wide association studies (TWAS, PWAS), identifying &gt;100,000 upstream regulators with strong replication. As a proof of concept, we applied this framework to inflammatory bowel disease (IBD), generating the largest to date GWAS directly comparing Crohn\u2019s disease (CD) and ulcerative colitis (UC). Integrative multi-omics analyses revealed divergent loci enriched in the NF-\n                  <jats:italic>\u03ba<\/jats:italic>\n                  B signaling pathway and improved CD vs. UC classification when proteomic features were combined with polygenic risk scores (PRS). Our findings provide a comprehensive resource for plasma protein genetics and demonstrate the value of integrative multi-omics for disease subtype classification, with broad implications for precision medicine.\n                <\/jats:p>","DOI":"10.1101\/2025.10.06.25336803","type":"posted-content","created":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T01:15:21Z","timestamp":1759886121000},"source":"Crossref","is-referenced-by-count":2,"title":["An Integrated Large-Scale Atlas of Protein Quantitative Trait Loci across Olink and SomaScan 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