Karunamuni, RA;
Huynh-Le, M-P;
Fan, CC;
Thompson, W;
Eeles, RA;
Kote-Jarai, Z;
Muir, K;
... Seibert, TM; + view all
(2021)
Additional SNPs improve risk stratification of a polygenic hazard score for prostate cancer.
Prostate Cancer and Prostatic Diseases
, 24
pp. 532-541.
10.1038/s41391-020-00311-2.
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Pashayan_Karumanumi et al - 2021 -Additional SNP to improve risk stratification with PHS -Prostate Prostatic Dis - Accepted version.pdf - Accepted Version Download (167kB) | Preview |
Abstract
Background: Polygenic hazard scores (PHS) can identify individuals with increased risk of prostate cancer. We estimated the benefit of additional SNPs on performance of a previously validated PHS (PHS46). / Materials and method: 180 SNPs, shown to be previously associated with prostate cancer, were used to develop a PHS model in men with European ancestry. A machine-learning approach, LASSO-regularized Cox regression, was used to select SNPs and to estimate their coefficients in the training set (75,596 men). Performance of the resulting model was evaluated in the testing/validation set (6,411 men) with two metrics: (1) hazard ratios (HRs) and (2) positive predictive value (PPV) of prostate-specific antigen (PSA) testing. HRs were estimated between individuals with PHS in the top 5% to those in the middle 40% (HR95/50), top 20% to bottom 20% (HR80/20), and bottom 20% to middle 40% (HR20/50). PPV was calculated for the top 20% (PPV80) and top 5% (PPV95) of PHS as the fraction of individuals with elevated PSA that were diagnosed with clinically significant prostate cancer on biopsy. / Results: 166 SNPs had non-zero coefficients in the Cox model (PHS166). All HR metrics showed significant improvements for PHS166 compared to PHS46: HR95/50 increased from 3.72 to 5.09, HR80/20 increased from 6.12 to 9.45, and HR20/50 decreased from 0.41 to 0.34. By contrast, no significant differences were observed in PPV of PSA testing for clinically significant prostate cancer. / Conclusions: Incorporating 120 additional SNPs (PHS166 vs PHS46) significantly improved HRs for prostate cancer, while PPV of PSA testing remained the same.
| Type: | Article |
|---|---|
| Title: | Additional SNPs improve risk stratification of a polygenic hazard score for prostate cancer |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1038/s41391-020-00311-2 |
| Publisher version: | https://doi.org/10.1038/s41391-020-00311-2 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Epidemiology and Health UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Epidemiology and Health > Applied Health Research |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10122739 |
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