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Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues

TitleCharacterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues
Publication TypeJournal Article
Year of Publication2018
AuthorsZhang, M, Lykke-Andersen, S, Zhu, B, Xiao, W, Hoskins, JW, Zhang, X, Rost, LM, Collins, I, Bunt, MV, Jia, J, Parikh, H, Zhang, T, Song, L, Jermusyk, A, Chung, CC, Zhu, B, Zhou, W, Matters, GL, Kurtz, RC, Yeager, M, Jensen, TH, Brown, KM, Ongen, H, Bamlet, WR, Murray, BA, McCarthy, MI, Chanock, SJ, Chatterjee, N, Wolpin, BM, Smith, JP, Olson, SH, Petersen, GM, Shi, J, Amundadottir, L
JournalGut
Volume67
Pagination521-533
Date PublishedMar
ISBN Number0017-5749
Accession Number28634199
Keywords*allele specific expression., *eQTL, *Gene Expression, *Pancreas, *Quantitative Trait Loci, *RNA-seq, *Transcriptome, ABO Blood-Group System/*genetics, Alleles, Chromosomes, Human, Pair 9, genome-wide association study, Genotype, Humans, Nonsense Mediated mRNA Decay, Pancreatic Neoplasms/*genetics, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, RNA, Neoplasm/*analysis, Sequence Analysis, RNA
Abstract

OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis-eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p

PMCID

PMC5762429