Journal article

Use of a Novel Nonparametric Version of DEPTH to Identify Genomic Regions Associated with Prostate Cancer Risk

Robert J MacInnis, Daniel F Schmidt, Enes Makalic, Gianluca Severi, Liesel M FitzGerald, Matthias Reumann, Miroslaw K Kapuscinski, Adam Kowalczyk, Zeyu Zhou, Benjamin Goudey, Guoqi Qian, Quang M Bui, Daniel J Park, Adam Freeman, Melissa C Southey, Ali Amin Al Olama, Zsofia Kote-Jarai, Rosalind A Eeles, John L Hopper, Graham G Giles

CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION | AMER ASSOC CANCER RESEARCH | Published : 2016

Abstract

BACKGROUND: We have developed a genome-wide association study analysis method called DEPTH (DEPendency of association on the number of Top Hits) to identify genomic regions potentially associated with disease by considering overlapping groups of contiguous markers (e.g., SNPs) across the genome. DEPTH is a machine learning algorithm for feature ranking of ultra-high dimensional datasets, built from well-established statistical tools such as bootstrapping, penalized regression, and decision trees. Unlike marginal regression, which considers each SNP individually, the key idea behind DEPTH is to rank groups of SNPs in terms of their joint strength of association with the outcome. Our aim was t..

View full abstract

Grants

Awarded by Victorian Life Sciences Computation Initiative (VLSCI)


Awarded by National Health and Medical Research Council Australia


Awarded by Cancer Research UK


Awarded by Prostate Cancer Research Program of Cancer Council Victoria from The National Health and Medical Research Council, Australia


Awarded by NATIONAL CANCER INSTITUTE


Funding Acknowledgements

This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0304 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government, Australia. J.L. Hopper, G. Severi, E. Makalic, D.F. Schmidt, Q.M. Bui, G. Qian, D.J. Park, and A. Kowalczyk received support from the National Health and Medical Research Council Australia project grant (1033452). R.A. Eeles and Z. Kote-Jarai received support from Cancer Research UK (grant numbers C5047/A7357, C1287/A10118, C1287/A5260, C5047/A3354, C5047/A10692, C16913/A6135, and C16913/A6835), Prostate Research Campaign UK (now Prostate Cancer UK), The Institute of Cancer Research and The Everyman Campaign, The National Cancer Research Network UK, The National Cancer Research Institute (NCRI) UK. R.A. Eeles and Z. Kote-Jarai are grateful for support of NIHR funding to the NIHR Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust. G.G. Giles, J.L. Hopper, M.C. Southey, and G. Severi received support for the Prostate Cancer Research Program of Cancer Council Victoria from The National Health and Medical Research Council, Australia (126402, 209057, 251533, 396414, 450104, 504700, 504702, 504715, 623204, 940394, and 614296), VicHealth, Cancer Council Victoria, The Prostate Cancer Foundation of Australia, The Whitten Foundation, PricewaterhouseCoopers, and Tattersall's. J.L. Hopper is a Senior Principal Research Fellow of the NationalHealth and Medical Research Council, Australia. M.C. Southey is a Senior Research Fellow of the National Health and Medical Research Council, Australia.