Genetic variants and risk of prostate cancer using pathway analysis of a genome-wide association study

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

This study explored candidate causal single nucleotide polymorphisms (SNPs) to clarify the biological mechanism of prostate cancer (PCa). Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied using a PCa genome-wide association study (GWAS) dataset that included 473,736 SNPs in 1151 cases of PCa and 1156 controls of European ancestry. Five candidate causal SNPs, three candidate causal genes, and two candidate causal pathways were identified using integrating linkage disequilibrium analysis, functional SNP annotation, and pathway-based analysis. The ICSNPathway analysis suggested three hypothetical mechanisms of PCa. The first was rs13112390, rs13112358, rs2048074 to nei-like DNA glycosylase 3 (NEIL3) gene to damaged DNA binding. The second was rs3087386 to REV1, DNA directed polymerase (REV1) gene to damaged DNA binding. The third was rs1063134 to potassium channel, inwardly rectifying subfamily J, member 4 (KCNJ4) gene to inward rectifier potassium channel activity.

Original languageEnglish
Pages (from-to)629-634
Number of pages6
JournalNeoplasma
Volume63
Issue number4
DOIs
Publication statusPublished - 2016 Jan 1

Fingerprint

Genome-Wide Association Study
Single Nucleotide Polymorphism
Prostatic Neoplasms
Inwardly Rectifying Potassium Channel
Genes
DNA Glycosylases
DNA
Linkage Disequilibrium
DNA-Directed DNA Polymerase

Keywords

  • Genome-wide association study
  • Pathway-based analysis
  • Prostate cancer

ASJC Scopus subject areas

  • Cancer Research

Cite this

Genetic variants and risk of prostate cancer using pathway analysis of a genome-wide association study. / Kim, Young Sik; Kim, Y.; Choi, Jung-Woo; Oh, H. E.; Lee, Ju-Han.

In: Neoplasma, Vol. 63, No. 4, 01.01.2016, p. 629-634.

Research output: Contribution to journalArticle

@article{c68d56a3e7264b66b04cd1d9c8433fd2,
title = "Genetic variants and risk of prostate cancer using pathway analysis of a genome-wide association study",
abstract = "This study explored candidate causal single nucleotide polymorphisms (SNPs) to clarify the biological mechanism of prostate cancer (PCa). Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied using a PCa genome-wide association study (GWAS) dataset that included 473,736 SNPs in 1151 cases of PCa and 1156 controls of European ancestry. Five candidate causal SNPs, three candidate causal genes, and two candidate causal pathways were identified using integrating linkage disequilibrium analysis, functional SNP annotation, and pathway-based analysis. The ICSNPathway analysis suggested three hypothetical mechanisms of PCa. The first was rs13112390, rs13112358, rs2048074 to nei-like DNA glycosylase 3 (NEIL3) gene to damaged DNA binding. The second was rs3087386 to REV1, DNA directed polymerase (REV1) gene to damaged DNA binding. The third was rs1063134 to potassium channel, inwardly rectifying subfamily J, member 4 (KCNJ4) gene to inward rectifier potassium channel activity.",
keywords = "Genome-wide association study, Pathway-based analysis, Prostate cancer",
author = "Kim, {Young Sik} and Y. Kim and Jung-Woo Choi and Oh, {H. E.} and Ju-Han Lee",
year = "2016",
month = "1",
day = "1",
doi = "10.4149/neo_2016_418",
language = "English",
volume = "63",
pages = "629--634",
journal = "Neoplasma",
issn = "0028-2685",
publisher = "Vydavatel'stvo Slovenkej Akademie Vied/Veda Publishing House of the Slovak Academy of Sciences",
number = "4",

}

TY - JOUR

T1 - Genetic variants and risk of prostate cancer using pathway analysis of a genome-wide association study

AU - Kim, Young Sik

AU - Kim, Y.

AU - Choi, Jung-Woo

AU - Oh, H. E.

AU - Lee, Ju-Han

PY - 2016/1/1

Y1 - 2016/1/1

N2 - This study explored candidate causal single nucleotide polymorphisms (SNPs) to clarify the biological mechanism of prostate cancer (PCa). Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied using a PCa genome-wide association study (GWAS) dataset that included 473,736 SNPs in 1151 cases of PCa and 1156 controls of European ancestry. Five candidate causal SNPs, three candidate causal genes, and two candidate causal pathways were identified using integrating linkage disequilibrium analysis, functional SNP annotation, and pathway-based analysis. The ICSNPathway analysis suggested three hypothetical mechanisms of PCa. The first was rs13112390, rs13112358, rs2048074 to nei-like DNA glycosylase 3 (NEIL3) gene to damaged DNA binding. The second was rs3087386 to REV1, DNA directed polymerase (REV1) gene to damaged DNA binding. The third was rs1063134 to potassium channel, inwardly rectifying subfamily J, member 4 (KCNJ4) gene to inward rectifier potassium channel activity.

AB - This study explored candidate causal single nucleotide polymorphisms (SNPs) to clarify the biological mechanism of prostate cancer (PCa). Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied using a PCa genome-wide association study (GWAS) dataset that included 473,736 SNPs in 1151 cases of PCa and 1156 controls of European ancestry. Five candidate causal SNPs, three candidate causal genes, and two candidate causal pathways were identified using integrating linkage disequilibrium analysis, functional SNP annotation, and pathway-based analysis. The ICSNPathway analysis suggested three hypothetical mechanisms of PCa. The first was rs13112390, rs13112358, rs2048074 to nei-like DNA glycosylase 3 (NEIL3) gene to damaged DNA binding. The second was rs3087386 to REV1, DNA directed polymerase (REV1) gene to damaged DNA binding. The third was rs1063134 to potassium channel, inwardly rectifying subfamily J, member 4 (KCNJ4) gene to inward rectifier potassium channel activity.

KW - Genome-wide association study

KW - Pathway-based analysis

KW - Prostate cancer

UR - http://www.scopus.com/inward/record.url?scp=84978402775&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84978402775&partnerID=8YFLogxK

U2 - 10.4149/neo_2016_418

DO - 10.4149/neo_2016_418

M3 - Article

C2 - 27268928

AN - SCOPUS:84978402775

VL - 63

SP - 629

EP - 634

JO - Neoplasma

JF - Neoplasma

SN - 0028-2685

IS - 4

ER -