| Publication Information (EuropePMC) | |
| Title | Prediction of Breast and Prostate Cancer Risks in Male BRCA1 and BRCA2 Mutation Carriers Using Polygenic Risk Scores. |
| PubMed ID | 28448241(Europe PMC) |
| doi | 10.1200/JCO.2016.69.4935 |
| Publication Date | April 27, 2017 |
| Journal | J Clin Oncol |
| Author(s) | Lecarpentier J, Silvestri V, Kuchenbaecker KB, Barrowdale D, Dennis J, McGuffog L, Soucy P, Leslie G, Rizzolo P, Navazio AS, Valentini V, Zelli V, Lee A, Amin Al Olama A, Tyrer JP, Southey M, John EM, Conner TA, Goldgar DE, Buys SS, Janavicius R, Steele L, Ding YC, Neuhausen SL, Hansen TVO, Osorio A, Weitzel JN, Toss A, Medici V, Cortesi L, Zanna I, Palli D, Radice P, Manoukian S, Peissel B, Azzollini J, Viel A, Cini G, Damante G, Tommasi S, Peterlongo P, Fostira F, Hamann U, Evans DG, Henderson A, Brewer C, Eccles D, Cook J, Ong KR, Walker L, Side LE, Porteous ME, Davidson R, Hodgson S, Frost D, Adlard J, Izatt L, Eeles R, Ellis S, Tischkowitz M, EMBRACE, Godwin AK, Meindl A, Gehrig A, Dworniczak B, Sutter C, Engel C, Niederacher D, Steinemann D, Hahnen E, Hauke J, Rhiem K, Kast K, Arnold N, Ditsch N, Wang-Gohrke S, Wappenschmidt B, Wand D, Lasset C, Stoppa-Lyonnet D, Belotti M, Damiola F, Barjhoux L, Mazoyer S, GEMO Study Collaborators, Van Heetvelde M, Poppe B, De Leeneer K, Claes KBM, de la Hoya M, Garcia-Barberan V, Caldes T, Perez Segura P, Kiiski JI, Aittomäki K, Khan S, Nevanlinna H, van Asperen CJ, HEBON, Vaszko T, Kasler M, Olah E, Balmaña J, Gutiérrez-Enríquez S, Diez O, Teulé A, Izquierdo A, Darder E, Brunet J, Del Valle J, Feliubadalo L, Pujana MA, Lazaro C, Arason A, Agnarsson BA, Johannsson OT, Barkardottir RB, Alducci E, Tognazzo S, Montagna M, Teixeira MR, Pinto P, Spurdle AB, Holland H, KConFab Investigators, Lee JW, Lee MH, Lee J, Kim SW, Kang E, Kim Z, Sharma P, Rebbeck TR, Vijai J, Robson M, Lincoln A, Musinsky J, Gaddam P, Tan YY, Berger A, Singer CF, Loud JT, Greene MH, Mulligan AM, Glendon G, Andrulis IL, Toland AE, Senter L, Bojesen A, Nielsen HR, Skytte AB, Sunde L, Jensen UB, Pedersen IS, Krogh L, Kruse TA, Caligo MA, Yoon SY, Teo SH, von Wachenfeldt A, Huo D, Nielsen SM, Olopade OI, Nathanson KL, Domchek SM, Lorenchick C, Jankowitz RC, Campbell I, James P, Mitchell G, Orr N, Park SK, Thomassen M, Offit K, Couch FJ, Simard J, Easton DF, Chenevix-Trench G, Schmutzler RK, Antoniou AC, Ottini L. |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000049 (PRS103_PrCa) |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |
Prostate cancer | prostate carcinoma | 103 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000049/ScoringFiles/PGS000049.txt.gz |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000045 (BCPRS_Overall) |
PGP000033 | Kuchenbaecker KB et al. J Natl Cancer Inst (2017) |
Breast cancer | breast carcinoma | 88 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000045/ScoringFiles/PGS000045.txt.gz |
| PGS000046 (BCPRS_ER+) |
PGP000033 | Kuchenbaecker KB et al. J Natl Cancer Inst (2017) |
Estrogen receptor [ER]-positive breast cancer | estrogen-receptor positive breast cancer | 87 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000046/ScoringFiles/PGS000046.txt.gz |
| PGS000047 (BCPRS_ER-) |
PGP000033 | Kuchenbaecker KB et al. J Natl Cancer Inst (2017) |
Estrogen receptor [ER]-negative breast cancer | estrogen-receptor negative breast cancer | 53 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000047/ScoringFiles/PGS000047.txt.gz |
|
PGS Performance Metric ID (PPM) |
Evaluated Score |
PGS Sample Set ID (PSS) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
Classification Metrics | Other Metrics | Covariates Included in the Model |
PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|---|
| PPM000120 | PGS000045 (BCPRS_Overall) |
PSS000074| European Ancestry| 1,590 individuals |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |Ext. |
Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations | OR: 1.36 [1.19, 1.56] | AUROC: 0.59 [0.55, 0.63] | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS |
| PPM000121 | PGS000046 (BCPRS_ER+) |
PSS000074| European Ancestry| 1,590 individuals |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |Ext. |
Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations | OR: 1.36 [1.19, 1.56] | AUROC: 0.59 [0.55, 0.63] | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS |
| PPM000122 | PGS000047 (BCPRS_ER-) |
PSS000074| European Ancestry| 1,590 individuals |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |Ext. |
Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations | OR: 1.19 [1.05, 1.35] | AUROC: 0.55 [0.51, 0.59] | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS |
| PPM000123 | PGS000049 (PRS103_PrCa) |
PSS000075| European Ancestry| 1,525 individuals |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |
Reported Trait: Prostate cancer in male carriers of BRCA1/2 mutations | OR: 1.56 [1.35, 1.81] | AUROC: 0.62 [0.58, 0.66] | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | — |
| PPM000124 | PGS000049 (PRS103_PrCa) |
PSS000077| European Ancestry| 1,366 individuals |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |
Reported Trait: Low prostate cancer aggressiveness (Gleason score < 7) | OR: 1.44 [1.1, 1.87] | — | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | — |
| PPM000125 | PGS000049 (PRS103_PrCa) |
PSS000076| European Ancestry| 3,325 individuals |
PGP000034 | Lecarpentier J et al. J Clin Oncol (2017) |
Reported Trait: High prostate cancer aggressiveness (Gleason score ≥ 7) | OR: 1.67 [1.37, 2.04] | — | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | — |
|
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
| PSS000076 | — | — | [ ,
100.0 % Male samples |
— | European | Self-reported European ancestry | 37 cohorts
|
— |
| PSS000077 | — | — | [ ,
100.0 % Male samples |
— | European | Self-reported European ancestry | 37 cohorts
|
— |
| PSS000074 | Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. | — | [ ,
100.0 % Male samples |
— | European | Self-reported European ancestry | 37 cohorts
|
— |
| PSS000075 | Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. | — | [ ,
100.0 % Male samples |
— | European | Self-reported European ancestry | 37 cohorts
|
— |