OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets

Madden, Stephen F., Clarke, Colin, Stordal, Britta K. ORCID: https://orcid.org/0000-0002-7892-951X, Carey, Mark S., Broaddus, Russell, Gallagher, William M., Crown, John, Mills, Gordon B. and Hennessy, Bryan T. (2014) OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets. Molecular Cancer, 13 (1) , 241. pp. 1-11. ISSN 1476-4598 (doi:10.1186/1476-4598-13-241)

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Abstract

Background: Ovarian cancer has the lowest survival rate of all gynaecologic cancers and is characterised by a lack of early symptoms and frequent late stage diagnosis. There is a paucity of robust molecular markers that are independent of and complementary to clinical parameters such as disease stage and tumour grade.
METHODS: We have developed a user-friendly, web-based system to evaluate the association of genes/miRNAs with outcome in ovarian cancer. The OvMark algorithm combines data from multiple microarray platforms (including probesets targeting miRNAs) and correlates them with clinical parameters (e.g. tumour grade, stage) and outcomes (disease free survival (DFS), overall survival). In total, OvMark combines 14 datasets from 7 different array platforms measuring the expression of ~17,000 genes and 341 miRNAs across 2,129 ovarian cancer samples.
RESULTS: To demonstrate the utility of the system we confirmed the prognostic ability of 14 genes and 2 miRNAs known to play a role in ovarian cancer. Of these genes, CXCL12 was the most significant predictor of DFS (HR = 1.42, p-value = 2.42x10-6). Surprisingly, those genes found to have the greatest correlation with outcome have not been heavily studied in ovarian cancer, or in some cases in any cancer. For instance, the three genes with the greatest association with survival are SNAI3, VWA3A and DNAH12.
CONCLUSIONS/IMPACT:
OvMark is a powerful tool for examining putative gene/miRNA prognostic biomarkers in ovarian cancer (available at http://glados.ucd.ie/OvMark/index.html). The impact of this tool will be in the preliminary assessment of putative biomarkers in ovarian cancer, particularly for research groups with limited bioinformatics facilities.

Item Type: Article
Research Areas: A. > School of Science and Technology > Natural Sciences > Biomarkers for Cancer group
Item ID: 15466
Notes on copyright: © 2014 Madden et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
Useful Links:
Depositing User: Britta Stordal
Date Deposited: 28 Apr 2015 14:08
Last Modified: 23 Aug 2020 22:04
URI: https://eprints.mdx.ac.uk/id/eprint/15466

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