| Publication Information (EuropePMC) | |
| Title | Prediction of breast cancer risk based on profiling with common genetic variants. |
| PubMed ID | 25855707(Europe PMC) |
| doi | 10.1093/jnci/djv036 |
| Publication Date | April 8, 2015 |
| Journal | J Natl Cancer Inst |
| Author(s) | Mavaddat N, Pharoah PD, Michailidou K, Tyrer J, Brook MN, Bolla MK, Wang Q, Dennis J, Dunning AM, Shah M, Luben R, Brown J, Bojesen SE, Nordestgaard BG, Nielsen SF, Flyger H, Czene K, Darabi H, Eriksson M, Peto J, Dos-Santos-Silva I, Dudbridge F, Johnson N, Schmidt MK, Broeks A, Verhoef S, Rutgers EJ, Swerdlow A, Ashworth A, Orr N, Schoemaker MJ, Figueroa J, Chanock SJ, Brinton L, Lissowska J, Couch FJ, Olson JE, Vachon C, Pankratz VS, Lambrechts D, Wildiers H, Van Ongeval C, van Limbergen E, Kristensen V, Grenaker Alnæs G, Nord S, Borresen-Dale AL, Nevanlinna H, Muranen TA, Aittomäki K, Blomqvist C, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Fasching PA, Haeberle L, Ekici AB, Beckmann MW, Burwinkel B, Marme F, Schneeweiss A, Sohn C, Trentham-Dietz A, Newcomb P, Titus L, Egan KM, Hunter DJ, Lindstrom S, Tamimi RM, Kraft P, Rahman N, Turnbull C, Renwick A, Seal S, Li J, Liu J, Humphreys K, Benitez J, Pilar Zamora M, Arias Perez JI, Menéndez P, Jakubowska A, Lubinski J, Jaworska-Bieniek K, Durda K, Bogdanova NV, Antonenkova NN, Dörk T, Anton-Culver H, Neuhausen SL, Ziogas A, Bernstein L, Devilee P, Tollenaar RA, Seynaeve C, van Asperen CJ, Cox A, Cross SS, Reed MW, Khusnutdinova E, Bermisheva M, Prokofyeva D, Takhirova Z, Meindl A, Schmutzler RK, Sutter C, Yang R, Schürmann P, Bremer M, Christiansen H, Park-Simon TW, Hillemanns P, Guénel P, Truong T, Menegaux F, Sanchez M, Radice P, Peterlongo P, Manoukian S, Pensotti V, Hopper JL, Tsimiklis H, Apicella C, Southey MC, Brauch H, Brüning T, Ko YD, Sigurdson AJ, Doody MM, Hamann U, Torres D, Ulmer HU, Försti A, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Andrulis IL, Knight JA, Glendon G, Marie Mulligan A, Chenevix-Trench G, Balleine R, Giles GG, Milne RL, McLean C, Lindblom A, Margolin S, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Eilber U, Wang-Gohrke S, Hooning MJ, Hollestelle A, van den Ouweland AM, Koppert LB, Carpenter J, Clarke C, Scott R, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Brenner H, Arndt V, Stegmaier C, Karina Dieffenbach A, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Offit K, Vijai J, Robson M, Rau-Murthy R, Dwek M, Swann R, Annie Perkins K, Goldberg MS, Labrèche F, Dumont M, Eccles DM, Tapper WJ, Rafiq S, John EM, Whittemore AS, Slager S, Yannoukakos D, Toland AE, Yao S, Zheng W, Halverson SL, González-Neira A, Pita G, Rosario Alonso M, Álvarez N, Herrero D, Tessier DC, Vincent D, Bacot F, Luccarini C, Baynes C, Ahmed S, Maranian M, Healey CS, Simard J, Hall P, Easton DF, Garcia-Closas M. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000001 (PRS77_BC) |
PGP000001 | Mavaddat N et al. J Natl Cancer Inst (2015) |
Breast cancer | breast carcinoma | 77 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz |
| PGS000002 (PRS77_ERpos) |
PGP000001 | Mavaddat N et al. J Natl Cancer Inst (2015) |
ER-positive breast cancer | estrogen-receptor positive breast cancer | 77 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000002/ScoringFiles/PGS000002.txt.gz |
| PGS000003 (PRS77_ERneg) |
PGP000001 | Mavaddat N et al. J Natl Cancer Inst (2015) |
ER-negative breast cancer | estrogen-receptor negative breast cancer | 77 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000003/ScoringFiles/PGS000003.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000002 | PGS000002 (PRS77_ERpos) |
PSS000003| European Ancestry| 53,923 individuals |
PGP000001 | Mavaddat N et al. J Natl Cancer Inst (2015) |
Reported Trait: ER-positive breast cancer | OR: 1.63 [1.6, 1.67] | — | — | — | — |
| PPM000001 | PGS000001 (PRS77_BC) |
PSS000001| European Ancestry| 67,054 individuals |
PGP000001 | Mavaddat N et al. J Natl Cancer Inst (2015) |
Reported Trait: All breast cancer | OR: 1.55 [1.52, 1.58] | C-index: 0.622 [0.619, 0.627] | — | — | — |
| PPM000003 | PGS000003 (PRS77_ERneg) |
PSS000002| European Ancestry| 38,722 individuals |
PGP000001 | Mavaddat N et al. J Natl Cancer Inst (2015) |
Reported Trait: ER-negative breast cancer | OR: 1.45 [1.4, 1.49] | — | — | — | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000001 | All breast cancer | — | [
|
— | European | — | 33 cohorts
|
iCOGS |
| PSS000002 | ER-negative breast cancer | — | [
|
— | European | — | 33 cohorts
|
iCOGS |
| PSS000003 | ER-positive breast cancer | — | [
|
— | European | — | 33 cohorts
|
iCOGS |