A replication study examining three common single-nucleotide polymorphisms and the risk of prostate cancer in a Japanese population

The Prostate ◽  
2010 ◽  
Vol 71 (10) ◽  
pp. 1023-1032 ◽  
Author(s):  
Miao Liu ◽  
Motofumi Suzuki ◽  
Tomio Arai ◽  
Motoji Sawabe ◽  
Yutaka Enomoto ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Japanese Population ◽  
Replication Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Single-Nucleotide Polymorphisms Sequencing Identifies Candidate Functional Variants at Prostate Cancer Risk Loci

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 547 ◽  
Author(s):  
Peng Zhang ◽  
Lori S. Tillmans ◽  
Stephen N. Thibodeau ◽  
Liang Wang
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Single Nucleotide Polymorphisms ◽  
Protein Binding ◽  
Prostate Cancer Risk ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Variants ◽  
Dependent Protein

Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding at 903 SNP sites covering 28 genomic regions. All selected SNPs have shown significant cis-association with at least one nearby gene. After preparing nuclear extract using LNCaP cell line, we first mixed the extract with dsDNA oligo pool for protein–DNA binding incubation. We then performed sequencing analysis on protein-bound oligos. SNPs-seq analysis showed protein-binding differences (>1.5-fold) between reference and variant alleles in 380 (42%) of 903 SNPs with androgen treatment and 403 (45%) of 903 SNPs without treatment. From these significant SNPs, we performed a database search and further narrowed down to 74 promising SNPs. To validate this initial finding, we performed electrophoretic mobility shift assay in two SNPs (rs12246440 and rs7077275) at CTBP2 locus and one SNP (rs113082846) at NCOA4 locus. This analysis showed that all three SNPs demonstrated allele-dependent protein-binding differences that were consistent with the SNPs-seq. Finally, clinical association analysis of the two candidate genes showed that CTBP2 was upregulated, while NCOA4 was downregulated in prostate cancer (p < 0.02). Lower expression of CTBP2 was associated with poor recurrence-free survival in prostate cancer. Utilizing our experimental data along with bioinformatic tools provides a strategy for identifying candidate functional elements at prostate cancer susceptibility loci to help guide subsequent laboratory studies.

A pilot replication study of two PER3 single nucleotide polymorphisms as potential genetic markers for morning and evening earliness-lateness

2017 ◽  
Vol 48 (4) ◽  
pp. 531-540 ◽  
Author(s):  
Vladimir B. Dorokhov ◽  
Alexandra N Puchkova ◽  
Anton O. Taranov ◽  
Petr A. Slominsky ◽  
Valentin A. Vavilin ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Markers ◽  
Replication Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Twenty­six Novel Single Nucleotide Polymorphisms and their Frequencies of the NR1I3(CAR) Gene in a Japanese Population

2003 ◽  
Vol 18 (6) ◽  
pp. 413-418 ◽  
Author(s):  
Shinobu Ikeda ◽  
Kouichi Kurose ◽  
Shogo Ozawa ◽  
Kimie Sai ◽  
Ryuichi Hasegawa ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Japanese Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
Sign in / Sign up

Export Citation Format

Share Document