| Publication Information (EuropePMC) | |
| Title | Polygenic risk scores and breast and epithelial ovarian cancer risks for carriers of BRCA1 and BRCA2 pathogenic variants. |
| PubMed ID | 32665703(Europe PMC) |
| doi | 10.1038/s41436-020-0862-x |
| Publication Date | July 15, 2020 |
| Journal | Genet Med |
| Author(s) | Barnes DR, Rookus MA, McGuffog L, Leslie G, Mooij TM, Dennis J, Mavaddat N, Adlard J, Ahmed M, Aittomäki K, Andrieu N, Andrulis IL, Arnold N, Arun BK, Azzollini J, Balmaña J, Barkardottir RB, Barrowdale D, Benitez J, Berthet P, Białkowska K, Blanco AM, Blok MJ, Bonanni B, Boonen SE, Borg Å, Bozsik A, Bradbury AR, Brennan P, Brewer C, Brunet J, Buys SS, Caldés T, Caligo MA, Campbell I, Christensen LL, Chung WK, Claes KBM, Colas C, GEMO Study Collaborators, EMBRACE Collaborators, Collonge-Rame MA, Cook J, Daly MB, Davidson R, de la Hoya M, de Putter R, Delnatte C, Devilee P, Diez O, Ding YC, Domchek SM, Dorfling CM, Dumont M, Eeles R, Ejlertsen B, Engel C, Evans DG, Faivre L, Foretova L, Fostira F, Friedlander M, Friedman E, Frost D, Ganz PA, Garber J, Gehrig A, Gerdes AM, Gesta P, Giraud S, Glendon G, Godwin AK, Goldgar DE, González-Neira A, Greene MH, Gschwantler-Kaulich D, Hahnen E, Hamann U, Hanson H, Hentschel J, Hogervorst FBL, Hooning MJ, Horvath J, Hu C, Hulick PJ, Imyanitov EN, kConFab Investigators, HEBON Investigators, GENEPSO Investigators, Isaacs C, Izatt L, Izquierdo A, Jakubowska A, James PA, Janavicius R, John EM, Joseph V, Karlan BY, Kast K, Koudijs M, Kruse TA, Kwong A, Laitman Y, Lasset C, Lazaro C, Lester J, Lesueur F, Liljegren A, Loud JT, Lubiński J, Mai PL, Manoukian S, Mari V, Mebirouk N, Meijers-Heijboer HEJ, Meindl A, Mensenkamp AR, Miller A, Montagna M, Mouret-Fourme E, Mukherjee S, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Niederacher D, Nielsen FC, Nikitina-Zake L, Noguès C, Olah E, Olopade OI, Ong KR, O'Shaughnessy-Kirwan A, Osorio A, Ott CE, Papi L, Park SK, Parsons MT, Pedersen IS, Peissel B, Peixoto A, Peterlongo P, Pfeiler G, Phillips KA, Prajzendanc K, Pujana MA, Radice P, Ramser J, Ramus SJ, Rantala J, Rennert G, Risch HA, Robson M, Rønlund K, Salani R, Schuster H, Senter L, Shah PD, Sharma P, Side LE, Singer CF, Slavin TP, Soucy P, Southey MC, Spurdle AB, Steinemann D, Steinsnyder Z, Stoppa-Lyonnet D, Sutter C, Tan YY, Teixeira MR, Teo SH, Thull DL, Tischkowitz M, Tognazzo S, Toland AE, Trainer AH, Tung N, van Engelen K, van Rensburg EJ, Vega A, Vierstraete J, Wagner G, Walker L, Wang-Gohrke S, Wappenschmidt B, Weitzel JN, Yadav S, Yang X, Yannoukakos D, Zimbalatti D, Offit K, Thomassen M, Couch FJ, Schmutzler RK, Simard J, Easton DF, Chenevix-Trench G, Antoniou AC, Consortium of Investigators of Modifiers of BRCA and BRCA2. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000351 (PRS_EOC) |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Invasive epithelial ovarian cancer | ovarian carcinoma | 30 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000351/ScoringFiles/PGS000351.txt.gz |
| PGS000352 (PRS_HGS) |
PGP000117 | Barnes DR et al. Genet Med (2020) |
High grade serous ovarian cancer | high grade ovarian serous adenocarcinoma | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000352/ScoringFiles/PGS000352.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) |
|---|---|---|---|---|---|---|
| PGS000004 (PRS313_BC) |
PGP000002 | Mavaddat N et al. Am J Hum Genet (2018) |
Breast cancer | breast carcinoma | 313 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz | |
| PGS000005 (PRS313_ERpos) |
PGP000002 | Mavaddat N et al. Am J Hum Genet (2018) |
ER-positive breast cancer | estrogen-receptor positive breast cancer | 313 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000005/ScoringFiles/PGS000005.txt.gz | |
| PGS000006 (PRS313_ERneg) |
PGP000002 | Mavaddat N et al. Am J Hum Genet (2018) |
ER-negative breast cancer | estrogen-receptor negative breast cancer | 313 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000006/ScoringFiles/PGS000006.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM001012 | PGS000004 (PRS313_BC) |
PSS000521| European Ancestry| 18,935 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Breast cancer in BRCA1 carriers | HR: 1.2 [1.17, 1.23] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001013 | PGS000004 (PRS313_BC) |
PSS000525| European Ancestry| 12,339 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Breast cancer in BRCA2 carriers | HR: 1.31 [1.26, 1.36] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001014 | PGS000004 (PRS313_BC) |
PSS000522| European Ancestry| 13,401 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER negative breast cancer in BRCA1 carriers | HR: 1.09 [1.05, 1.13] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001015 | PGS000004 (PRS313_BC) |
PSS000526| European Ancestry| 8,752 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER negative breast cancer in BRCA2 carriers | HR: 1.19 [1.1, 1.29] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001016 | PGS000004 (PRS313_BC) |
PSS000523| European Ancestry| 13,401 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER positive breast cancer in BRCA1 carriers | HR: 1.44 [1.35, 1.54] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001017 | PGS000004 (PRS313_BC) |
PSS000527| European Ancestry| 8,752 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER positive breast cancer in BRCA2 carriers | HR: 1.36 [1.3, 1.43] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001018 | PGS000005 (PRS313_ERpos) |
PSS000521| European Ancestry| 18,935 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Breast cancer in BRCA1 carriers | HR: 1.17 [1.14, 1.2] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001019 | PGS000005 (PRS313_ERpos) |
PSS000525| European Ancestry| 12,339 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Breast cancer in BRCA2 carriers | HR: 1.3 [1.26, 1.35] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001020 | PGS000005 (PRS313_ERpos) |
PSS000522| European Ancestry| 13,401 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER negative breast cancer in BRCA1 carriers | HR: 1.06 [1.02, 1.1] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001021 | PGS000005 (PRS313_ERpos) |
PSS000526| European Ancestry| 8,752 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER negative breast cancer in BRCA2 carriers | HR: 1.15 [1.07, 1.25] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001022 | PGS000005 (PRS313_ERpos) |
PSS000523| European Ancestry| 13,401 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER positive breast cancer in BRCA1 carriers | HR: 1.45 [1.35, 1.54] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001023 | PGS000005 (PRS313_ERpos) |
PSS000527| European Ancestry| 8,752 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER positive breast cancer in BRCA2 carriers | HR: 1.37 [1.31, 1.44] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001024 | PGS000006 (PRS313_ERneg) |
PSS000521| European Ancestry| 18,935 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Breast cancer in BRCA1 carriers | HR: 1.29 [1.25, 1.33] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001025 | PGS000006 (PRS313_ERneg) |
PSS000525| European Ancestry| 12,339 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Breast cancer in BRCA2 carriers | HR: 1.23 [1.18, 1.27] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001026 | PGS000006 (PRS313_ERneg) |
PSS000522| European Ancestry| 13,401 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER negative breast cancer in BRCA1 carriers | HR: 1.23 [1.18, 1.27] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001027 | PGS000006 (PRS313_ERneg) |
PSS000526| European Ancestry| 8,752 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER negative breast cancer in BRCA2 carriers | HR: 1.29 [1.19, 1.41] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001028 | PGS000006 (PRS313_ERneg) |
PSS000523| European Ancestry| 13,401 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER positive breast cancer in BRCA1 carriers | HR: 1.29 [1.21, 1.37] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001029 | PGS000006 (PRS313_ERneg) |
PSS000527| European Ancestry| 8,752 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: ER positive breast cancer in BRCA2 carriers | HR: 1.21 [1.15, 1.27] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001030 | PGS000351 (PRS_EOC) |
PSS000524| European Ancestry| 18,935 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Reported Trait: Ovarian cancer in BRCA1 carriers | HR: 1.31 [1.24, 1.39] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001031 | PGS000351 (PRS_EOC) |
PSS000528| European Ancestry| 12,339 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Reported Trait: Ovarian cancer in BRCA2 carriers | HR: 1.42 [1.28, 1.58] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001032 | PGS000352 (PRS_HGS) |
PSS000524| European Ancestry| 18,935 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Reported Trait: Ovarian cancer in BRCA1 carriers | HR: 1.32 [1.25, 1.4] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001033 | PGS000352 (PRS_HGS) |
PSS000528| European Ancestry| 12,339 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Reported Trait: Ovarian cancer in BRCA2 carriers | HR: 1.43 [1.29, 1.59] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
| PPM001034 | PGS000006 (PRS313_ERneg) |
PSS000529| European Ancestry| 2,088 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Incident breast cancer in BRCA1 carriers | HR: 1.28 [1.14, 1.44] | — | — | family history of the appropriate cancer in first- and second-degree relatives | — |
| PPM001035 | PGS000004 (PRS313_BC) |
PSS000531| European Ancestry| 1,757 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |Ext. |
Reported Trait: Incidient breast cancer in BRCA2 carriers | HR: 1.36 [1.17, 1.57] | — | — | family history of the appropriate cancer in first- and second-degree relatives | — |
| PPM001036 | PGS000352 (PRS_HGS) |
PSS000530| European Ancestry| 3,152 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Reported Trait: Incident ovarian cancer in BRCA1 carriers | HR: 1.28 [1.06, 1.55] | — | — | family history of the appropriate cancer in first- and second-degree relatives | — |
| PPM001037 | PGS000352 (PRS_HGS) |
PSS000532| European Ancestry| 2,495 individuals |
PGP000117 | Barnes DR et al. Genet Med (2020) |
Reported Trait: Incident ovarian cancer in BRCA2 carriers | HR: 1.45 [1.13, 1.86] | — | — | family history of the appropriate cancer in first- and second-degree relatives | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000521 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000522 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000523 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000524 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000525 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000526 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000527 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000528 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
| PSS000529 | Eligibility was restricted to female BRCA1 and BRCA2 carriers who at completion of the baseline questionnaire were free of any cancer diagnosis (excluding non-melanoma skin cancer) and had not undergone risk-reducing bilateral mastectomy. Participants diagosed with a first breast cancer were considered affected. | — | [ ,
0.0 % Male samples |
— | European | — | 61 cohorts
|
— |
| PSS000530 | To assess associationss between the PRS and ovarian cancer risk, eligibility was restricted to women who had not been diagnosed with ovarian cancer and had not had RRSO at the time of baselinne questionnaire completion. Carriers diagnosed with invasive ovarian, fallopian tube, or peritoneal cancer during the follow-up were considered affected. | — | [ ,
0.0 % Male samples |
— | European | — | 61 cohorts
|
— |
| PSS000531 | Eligibility was restricted to female BRCA1 and BRCA2 carriers who at completion of the baseline questionnaire were free of any cancer diagnosis (excluding non-melanoma skin cancer) and had not undergone risk-reducing bilateral mastectomy. Participants diagosed with a first breast cancer were considered affected. | — | [ ,
0.0 % Male samples |
— | European | — | 61 cohorts
|
— |
| PSS000532 | To assess associationss between the PRS and ovarian cancer risk, eligibility was restricted to women who had not been diagnosed with ovarian cancer and had not had RRSO at the time of baseline questionnaire completion. Carriers diagnosed with invasive ovarian, fallopian tbe, or peritoneal cancer during the follow-up were considered affected. | — | [ ,
0.0 % Male samples |
— | European | — | 61 cohorts
|
— |