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Genome-wide association study evaluating single-nucleotide polymorphisms and outcomes in patients with advanced stage serous ovarian or primary peritoneal cancer: An NRG Oncology/Gynecologic Oncology Group study

Published:September 19, 2017DOI:https://doi.org/10.1016/j.ygyno.2017.08.024

      Highlights

      • GWAS may identity single nucleotide polymorphisms (SNPs) associated with survival.
      • This GWAS study failed to identify SNPs associated with PFS or OS.
      • Larger GWAS analyses may prove more insightful.

      Abstract

      Objective

      This study evaluated single nucleotide polymorphisms (SNPs) associated with progression free (PFS) and overall survival (OS) in patients with advanced stage serous EOC.

      Methods

      Patients enrolled in GOG-172 and 182 who provided specimens for translational research and consent were included. Germline DNA was evaluated with the Illumina's HumanOMNI1-Quad beadchips and scanned using Illumina's iScan optical imaging system. SNPs with allele frequency > 0.05 and genotyping rate > 0.98 were included. Analysis of SNPs for PFS and OS was done using Cox regression. Statistical significance was determined using Bonferroni corrected p-values with genomic control adjustment.

      Results

      The initial GWAS analysis included 1,124,677 markers in 396 patients. To obtain the final data set, quality control checks were performed and limited to serous tumors and self-identified Caucasian race. In total 636,555 SNPs and 289 patients passed all the filters. The pre-specified statistical level of significance was 7.855e−08. No SNPs met this criteria for PFS or OS, however, two SNPs were close to significance (rs10899426 p-2.144e08) (rs6256 p-9.774e−07) for PFS and 2 different SNPs were identified (rs295315 p-7.536e07; rs17693104 p-7.734e07) which were close to significance for OS.

      Conclusions

      Using the pre-specified level of significance of 1 × 10−08, we did not identify any SNPs of statistical significance for OS or PFS, however several were close. The SNP's identified in this GWAS study will require validation and these preliminary findings may lead to identification of novel pathways and biomarkers.

      Keywords

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      1. Analysis and sample information courtesy of the Ovarian Cancer Association Consortium (OCAC).