PuSH - Publication Server of Helmholtz Zentrum München: Identification of novel type 1 and type 2 diabetes genes by co-localization of human islet eQTL and GWAS variants with <em>colocRedRibbon</em>.

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Piron, A.* ; Szymczak, F.* ; Folon, L.* ; Crouch, D.J.M.* ; Papadopoulou, T.* ; Lytrivi, M.* ; Tong, Y.* ; Alvelos, M.I.* ; Colli, M.L.* ; Yi, X.* ; Pekalski, M.L.* ; Hatzikotoulas, K. ; Huerta-Chagoya, A.* ; Taylor, H.J.* ; Defrance, M.* ; Todd, J.A.* ; Eizirik, D.L.* ; Mercader, J.M.* ; Cnop, M.*

Identification of novel type 1 and type 2 diabetes genes by co-localization of human islet eQTL and GWAS variants with colocRedRibbon.

Cell Genom., DOI: 10.1016/j.xgen.2025.101004:101004 (2025)

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Over 1,000 genetic variants have been associated with diabetes by genome-wide association studies (GWASs), but for most, their functional impact is unknown; only 7% alter gene expression in pancreatic islets in expression quantitative trait locus (eQTL) studies. To fill this gap, we developed a co-localization pipeline, colocRedRibbon, that prefilters eQTLs by the direction of effect on gene expression and shortlists overlapping eQTL and GWAS variants prior to co-localization. Applying colocRedRibbon to recent diabetes and glycemic trait GWASs, we identified 292 co-localizing gene regions, including 24 co-localizations for type 1 diabetes and 268 for type 2 diabetes and glycemic traits, representing a 4-fold increase. A low-frequency type 2 diabetes protective variant increases islet MYO5C expression, and a type 1 diabetes protective variant increases FUT2 expression. These novel co-localizations advance the understanding of diabetes genetics and its impact on human islet biology. colocRedRibbon has broad applicability to co-localize GWASs and various QTLs.

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