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Gene Set #270308 - GWAS Catalog Data for cancer biomarker measurement in 1,371 European ancestry individuals

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Description: List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies ( The disease/trait examined in this study, as reported by the authors, was PCA3 expression level. The EFO term cancer biomarker measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Uploaded: 02 May 2017
Species: Homo sapiens
Attribution: 6
Authors: Z Chen, J Sun, ST Kim, J Groskopf, J Feng, WB Isaacs, RS Rittmaster, LD Condreay, SL Zheng, J Xu
Title: Genome-wide association study identifies genetic determinants of urine PCA3 levels in men.
Journal: Neoplasia (New York, N.Y.) Apr 2013 , Vol 15 , pp. 448-53
Abstract: Prostate cancer gene 3 (PCA3) is a non-coding gene specifically overexpressed in prostate cancer (PCa) that has great potential as a clinical biomarker for predicting prostate biopsy outcome. However, genetic determinants of PCA3 expression level remain unknown. To investigate the association between genetic variants and PCA3 mRNA level, a genome-wide association study was conducted in 1371 men of European descent in the REduction by DUtasteride of prostate Cancer Events trial. First-voided urine specimens containing prostate cells were obtained after digital rectal examination. The PROGENSA PCA3 assay was used to determine PCA3 score in the urinary samples. A linear regression model was used to detect the associations between (single nucleotide polymorphisms) SNPs and PCA3 score under an additive genetic model, adjusting for age and population stratification. Two SNPs, rs10993994 in β-microseminoprotein at 10q11.23 and rs10424878 in kallikrein-related peptidase 2 at 19q13.33, were associated with PCA3 score at genome-wide significance level (P = 1.22 x 10(-9) and 1.06 x 10(-8), respectively). Men carrying the rs10993994 "T" allele or rs10424878 "A" allele had higher PCA3 score compared with men carrying rs10993994 "C" allele or rs10424878 "G" allele (β = 1.25 and 1.24, respectively). This is the first comprehensive search for genetic determinants of PCA3 score. The novel loci identified may provide insight into the molecular mechanisms of PCA3 expression as a potential marker of PCa.   PUBMED: 23555189
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Ontological Associations:
  • EFO:0005127: cancer biomarker measurement (GeneWeaver Primary Annotation)

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