Genome-Wide Association Study of Prostate Cancer

About 80 SNPs reached genome-wide significance in association with the risk of PCa in GWAS published (15 (link)-28 (link)) (http://www.genome.gov/gwastudies/). These SNPs were selected for the design of a GoldenGate VeraCode assay (Illumina). After score-based selection, 72 SNPs were retained for genotyping. All DNA samples were extracted from peripheral whole blood by using QIAamp DNA extraction kit (QIAGEN). Genotyping assay was then run on the Illumina BeadXpress Reader. Genotyping data were analyzed and exported using BeadStudio software. The genotyping call rate for the SNPs in this study was 99.86%.

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He Y., Gu J., Strom S., Logothetis C.J., Kim J, & Wu X. (2014). The Prostate Cancer Susceptibility Variant rs2735839 Near KLK3 Gene Is Associated with Aggressive Prostate Cancer and Can Stratify Gleason Score 7 Patients. Clinical cancer research : an official journal of the American Association for Cancer Research, 20(19), 5133-5139.

Publication 2014

GoldenGate VeraCode assay QIAamp DNA extraction kit BeadXpress Reader

Assay Blood Genome Gwas Snps

Corresponding Organization : The University of Texas MD Anderson Cancer Center

Other organizations : Ruijin Hospital, Shanghai Jiao Tong University

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Variable analysis

independent variables

SNPs (Single Nucleotide Polymorphisms)

dependent variables

Risk of Prostate Cancer (PCa)

control variables

DNA samples extracted from peripheral whole blood using QIAamp DNA extraction kit (QIAGEN)
Genotyping assay run on the Illumina BeadXpress Reader
Genotyping data analyzed and exported using BeadStudio software
Genotyping call rate for the SNPs in this study was 99.86%

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