Exome-based genome-wide association study and risk assessment using genetic risk score to prostate cancer in the Korean population

Oncotarget. 2017 Jul 4;8(27):43934-43943. doi: 10.18632/oncotarget.16540.

Abstract

Purpose: To investigate exome-wide genetic variants associated with prostate cancer (PCa) in Koreans and evaluate the discriminative ability by the genetic risk score (GRS).

Patients and methods: We prospectively recruited 1,001 PCa cases from a tertiary hospital and conducted a case-control study including 2,641 healthy men (Stage I). Participants were analyzed using HumanExome BeadChip. For the external validation, additionally enrolled 514 PCa cases and 548 controls (independent cohort) were analyzed for the identified single nucleotide polymorphisms (SNPs) of Stage I (Stage II). The GRS was calculated as a non-weighted sum of the risk allele counts and investigated for accuracy of prediction of PCa.

Results: the mean age was 66.3 years, and the median level of prostate specific antigen (PSA) was 9.19 ng/ml in PCa cases. In Stage I, 4 loci containing 5 variants (rs1512268 on 8p21.2; rs1016343 and rs7837688 on 8q24.21; rs7501939 on 17q12, and rs2735839 on 19q13.33) were confirmed to reach exome-wide significance (p<8.3x10-7). In Stage II, the mean GRS was 4.23 ± 1.44 for the controls and 4.78 ± 1.43 for the cases. As a reference to GRS 4, GRS 6, 7 and 8 showed a statistically significant risk of PCa (OR=1.85, 2.11 and 3.34, respectively).

Conclusions: The five variants were validated to associate with PCa in firstly performed exome-wide study in Koreans. The addition of individualized calculated GRS effectively enhanced the accuracy of prediction. These results need to be validated in future studies.

Keywords: Korean; exome; prostate; prostate cancer.

MeSH terms

  • Aged
  • Aged, 80 and over
  • Alleles
  • Asian Continental Ancestry Group
  • Exome*
  • Gene Frequency
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study*
  • Genotype
  • Humans
  • Male
  • Neoplasm Grading
  • Neoplasm Staging
  • Odds Ratio
  • Polymorphism, Single Nucleotide
  • Population Surveillance
  • Prognosis
  • Prostatic Neoplasms / epidemiology*
  • Prostatic Neoplasms / genetics*
  • Prostatic Neoplasms / mortality
  • Prostatic Neoplasms / pathology
  • Republic of Korea / epidemiology
  • Risk Assessment