PGS Publication: PGP000001

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.
Released in PGS: Oct. 14, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000001 PRS77_BC PGP000001
Mavaddat N et al. J Natl Cancer Inst (2015)
Breast Cancer breast carcinoma 77 http://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 http://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 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000003/ScoringFiles/PGS000003.txt.gz

PGS Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID
(PPM ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000001 PGS000001 (PRS77_BC) PSS000001 PGP000001
Mavaddat N et al. (2015)
Reported Trait: All breast cancer OR: 1.55[1.52, 1.58] C-index: 0.622[0.619, 0.627]
PPM000002 PGS000002 (PRS77_ERpos) PSS000003 PGP000001
Mavaddat N et al. (2015)
Reported Trait: ER-positive breast cancer OR: 1.63[1.6, 1.67]
PPM000003 PGS000003 (PRS77_ERneg) PSS000002 PGP000001
Mavaddat N et al. (2015)
Reported Trait: ER-negative breast cancer OR: 1.45[1.4, 1.49]

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
[
  • 33,673 cases
  • , 33,381 controls
]
European 33 cohorts
  • ABCFS
  • ,ABCS
  • ,BBCC
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HMBCS
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBHS
  • ,NorBCS
  • ,OBCS
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,pKARMA
iCOGS
PSS000002 ER-negative breast cancer
[
  • 5,738 cases
  • , 32,984 controls
]
European 33 cohorts
  • ABCFS
  • ,ABCS
  • ,BBCC
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HMBCS
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBHS
  • ,NorBCS
  • ,OBCS
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,pKARMA
iCOGS
PSS000003 ER-positive breast cancer
[
  • 21,365 cases
  • , 32,558 controls
]
European 33 cohorts
  • ABCFS
  • ,ABCS
  • ,BBCC
  • ,BIGGS
  • ,BSUCH
  • ,CECILE
  • ,CGPS
  • ,CTS
  • ,DEMOKRITOS
  • ,ESTHER
  • ,GENICA
  • ,HMBCS
  • ,KBCP
  • ,LMBC
  • ,MARIE
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MTLGEBCS
  • ,NBHS
  • ,NorBCS
  • ,OBCS
  • ,ORIGO
  • ,OSU
  • ,PBCS
  • ,RPCI
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UKBGS
  • ,pKARMA
iCOGS