Prediction of individual genetic risk to prostate cancer using a polygenic score

Szulkin, Robert, Whitington, Thomas, Eklund, Martin, Aly, Markus, Eeles, Rosalind A., Easton, Douglas, Kote-Jarai, Z. Sofia, Amin Al Olama, Ali, Benlloch, Sara, Muir, Kenneth, Giles, Graham G., Southey, Melissa C., Fitzgerald, Liesel M., Henderson, Brian E., Schumacher, Fredrick, Haiman, Christopher A., Schleutker, Johanna, Wahlfors, Tiina, Tammela, Teuvo L.J., Nordestgaard, Børge G., Key, Tim J., Travis, Ruth C., Neal, David E., Donovan, Jenny L., Hamdy, Freddie C., Pharoah, Paul, Pashayan, Nora, Khaw, Kay-Tee, Stanford, Janet L., Thibodeau, Stephen N., McDonnell, Shannon K., Schaid, Daniel J., Maier, Christiane, Vogel, Walther, Luedeke, Manuel, Herkommer, Kathleen, Kibel, Adam S., Cybulski, Cezary, Lubiński, Jan, Kluźniak, Wojciech, Cannon-Albright, Lisa, Brenner, Hermann, Butterbach, Katja, Stegmaier, Christa, Park, Jong Y., Sellers, Thomas, Lim, Hui-Yi, Slavov, Chavdar, Kaneva, Radka, Mitev, Vanio, Batra, Jyotsna, Clements, Judith A., BioResource, The Australian Prostate Cancer, Spurdle, Amanda, Teixeira, Manuel R., Paulo, Paula, Maia, Sofia, Pandha, Hardev, Michael, Agnieszka, Kierzek, Andrzej, consortium, the PRACTICAL, Gronberg, Henrik, & Wiklund, Fredrik (2015) Prediction of individual genetic risk to prostate cancer using a polygenic score. The Prostate, 75(13), pp. 1467-1474.

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Polygenic risk scores comprising established susceptibility variants have shown to be informative classifiers for several complex diseases including prostate cancer. For prostate cancer it is unknown if inclusion of genetic markers that have so far not been associated with prostate cancer risk at a genome-wide significant level will improve disease prediction.


We built polygenic risk scores in a large training set comprising over 25,000 individuals. Initially 65 established prostate cancer susceptibility variants were selected. After LD pruning additional variants were prioritized based on their association with prostate cancer. Six-fold cross validation was performed to assess genetic risk scores and optimize the number of additional variants to be included. The final model was evaluated in an independent study population including 1,370 cases and 1,239 controls.


The polygenic risk score with 65 established susceptibility variants provided an area under the curve (AUC) of 0.67. Adding an additional 68 novel variants significantly increased the AUC to 0.68 (P = 0.0012) and the net reclassification index with 0.21 (P = 8.5E-08). All novel variants were located in genomic regions established as associated with prostate cancer risk.


Inclusion of additional genetic variants from established prostate cancer susceptibility regions improves disease prediction. Prostate 75:1467–1474, 2015. © 2015 Wiley Periodicals, Inc.

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ID Code: 94531
Item Type: Journal Article
Refereed: Yes
Keywords: prostate cancer;polygenic risk score;risk prediction
DOI: 10.1002/pros.23037
ISSN: 0270-4137
Subjects: Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > ONCOLOGY AND CARCINOGENESIS (111200)
Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > ONCOLOGY AND CARCINOGENESIS (111200) > Cancer Cell Biology (111201)
Divisions: Current > Schools > School of Biomedical Sciences
Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Deposited On: 07 Apr 2016 03:26
Last Modified: 07 Apr 2016 21:54

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