Pancreatic islets PISA RNA-seq samples

GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 4 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001007990	The TIGER samples dataset contains PISA cohort samples which consist of paired RNA-seq and genotyping array data. It contains 127 RNA-seq pair-end samples in fastq format and 127 individuals genotypes in PLINK format.	unspecified	127
EGAD00010002218	TIGER samples PISA genotyping array data	Illumina	127

Publications	Citations
TIGER: The gene expression regulatory variation landscape of human pancreatic islets. Alonso L, Piron A, Morán I, Guindo-Martínez M, Bonàs-Guarch S, Atla G, Miguel-Escalada I, Royo R, Puiggròs M, Garcia-Hurtado X, Suleiman M, Marselli L, Esguerra JLS, Turatsinze JV, Torres JM, Nylander V, Chen J, Eliasson L, Defrance M, Amela R, MAGIC, Mulder H, Gloyn AL, Groop L, Marchetti P, Eizirik DL, Ferrer J, Mercader JM, Cnop M, Torrents D. Cell Rep 37: 2021 109807	42
Genetic regulation of RNA splicing in human pancreatic islets. Atla G, Bonàs-Guarch S, Cuenca-Ardura M, Beucher A, Crouch DJM, Garcia-Hurtado J, Moran I, T2DSystems Consortium, Irimia M, Prasad RB, Gloyn AL, Marselli L, Suleiman M, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Todd JA, Piemonti L, Ferrer J. Genome Biol 23: 2022 196	15
Mining the transcriptome of target tissues of autoimmune and degenerative pancreatic β-cell and brain diseases to discover therapies. Yi X, Marmontel de Souza B, Sawatani T, Szymczak F, Marselli L, Marchetti P, Cnop M, Eizirik DL. iScience 25: 2022 105376	3
Functional genetics reveals the contribution of delta opioid receptor to type 2 diabetes and beta-cell function. Meulebrouck S, Merrheim J, Queniat G, Bourouh C, Derhourhi M, Boissel M, Yi X, Badreddine A, Boutry R, Leloire A, Toussaint B, Amanzougarene S, Vaillant E, Durand E, Loiselle H, Huyvaert M, Dechaume A, Scherrer V, Marchetti P, Balkau B, Charpentier G, Franc S, Marre M, Roussel R, Scharfmann R, Cnop M, Canouil M, Baron M, Froguel P, Bonnefond A. Nat Commun 15: 2024 6627	0