An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set

Melissa S. DeRycke, Melissa C. Larson, Asha A. Nair, Shannon K. McDonnell, Amy J. French, Lori S. Tillmans, Shaun M. Riska, Saurabh Baheti, Zachary C. Fogarty, Nicholas Larson, Daniel R. O'Brien, John Cheville, Liang Wang, Daniel J Schaid, Stephen N Thibodeau

Research output: Contribution to journalArticle

Abstract

Prostate cancer (PrCa) is highly heritable; 284 variants have been identified to date that are associated with increased prostate cancer risk, yet few genes contributing to its development are known. Expression quantitative trait loci (eQTL) studies link variants with affected genes, helping to determine how these variants might regulate gene expression and may influence prostate cancer risk. In the current study, we performed eQTL analysis on 471 normal prostate epithelium samples and 249 PrCa-risk variants in 196 risk loci, utilizing RNA sequencing transcriptome data based on ENSEMBL gene definition and genome-wide variant data. We identified a total of 213 genes associated with known PrCa-risk variants, including 141 protein-coding genes, 16 lncRNAs, and 56 other non-coding RNA species with differential expression. Compared to our previous analysis, where RefSeq was used for gene annotation, we identified an additional 130 expressed genes associated with known PrCa-risk variants. We detected an eQTL signal for more than half (n = 102, 52%) of the 196 loci tested; 52 (51%) of which were a Group 1 signal, indicating high linkage disequilibrium (LD) between the peak eQTL variant and the PrCa-risk variant (r 2 >0.5) and may help explain how risk variants influence the development of prostate cancer.

Original languageEnglish (US)
Article numbere0214588
JournalPloS one
Volume14
Issue number4
DOIs
StatePublished - Apr 1 2019

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Quantitative Trait Loci
prostatic neoplasms
Prostate
quantitative trait loci
Prostatic Neoplasms
Genes
Tissue
genes
Long Noncoding RNA
RNA Sequence Analysis
Molecular Sequence Annotation
Untranslated RNA
loci
Datasets
tissues
Linkage Disequilibrium
linkage disequilibrium
Transcriptome
Gene expression
transcriptome

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set. / DeRycke, Melissa S.; Larson, Melissa C.; Nair, Asha A.; McDonnell, Shannon K.; French, Amy J.; Tillmans, Lori S.; Riska, Shaun M.; Baheti, Saurabh; Fogarty, Zachary C.; Larson, Nicholas; O'Brien, Daniel R.; Cheville, John; Wang, Liang; Schaid, Daniel J; Thibodeau, Stephen N.

In: PloS one, Vol. 14, No. 4, e0214588, 01.04.2019.

Research output: Contribution to journalArticle

DeRycke, MS, Larson, MC, Nair, AA, McDonnell, SK, French, AJ, Tillmans, LS, Riska, SM, Baheti, S, Fogarty, ZC, Larson, N, O'Brien, DR, Cheville, J, Wang, L, Schaid, DJ & Thibodeau, SN 2019, 'An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set', PloS one, vol. 14, no. 4, e0214588. https://doi.org/10.1371/journal.pone.0214588
DeRycke, Melissa S. ; Larson, Melissa C. ; Nair, Asha A. ; McDonnell, Shannon K. ; French, Amy J. ; Tillmans, Lori S. ; Riska, Shaun M. ; Baheti, Saurabh ; Fogarty, Zachary C. ; Larson, Nicholas ; O'Brien, Daniel R. ; Cheville, John ; Wang, Liang ; Schaid, Daniel J ; Thibodeau, Stephen N. / An expanded variant list and assembly annotation identifies multiple novel coding and noncoding genes for prostate cancer risk using a normal prostate tissue eQTL data set. In: PloS one. 2019 ; Vol. 14, No. 4.
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