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. 2017 May 3:6:621.
doi: 10.12688/f1000research.11027.1. eCollection 2017.

SNP-SNP interactions as risk factors for aggressive prostate cancer

Venkatesh Vaidyanathan  1   2 , Vijay Naidu  3 , Nishi Karunasinghe  2 , Anower Jabed  4 , Radha Pallati  1 , Gareth Marlow  5 , Lynnette R Ferguson  1   2
Affiliations

SNP-SNP interactions as risk factors for aggressive prostate cancer

Venkatesh Vaidyanathan et al. F1000Res. .

Abstract

Prostate cancer (PCa) is one of the most significant male health concerns worldwide. Single nucleotide polymorphisms (SNPs) are becoming increasingly strong candidate biomarkers for identifying susceptibility to PCa. We identified a number of SNPs reported in genome-wide association analyses (GWAS) as risk factors for aggressive PCa in various European populations, and then defined SNP-SNP interactions, using PLINK software, with nucleic acid samples from a New Zealand cohort. We used this approach to find a gene x environment marker for aggressive PCa, as although statistically gene x environment interactions can be adjusted for, it is highly impossible in practicality, and thus must be incorporated in the search for a reliable biomarker for PCa. We found two intronic SNPs statistically significantly interacting with each other as a risk for aggressive prostate cancer on being compared to healthy controls in a New Zealand population.

Keywords: SEQUENOM MassArray technology; SNP genotyping; SNP-SNP interaction; prostate cancer.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

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