Publication: Prediction of breast cancer risk based on profiling with common genetic variants.

Information

PGS Catalog Publication (PGP) ID: PGP000001
PubMed ID: 25855707
doi: 10.1093/jnci/djv036

Publication Date: April 8, 2015

Journal: J Natl Cancer Inst

Authors: 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.

PGS Associated with PGP000001

PGS Developed By This Study

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 (PPM) ID Evaluated Score PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000001 PGS000001 (PRS77_BC) PSS000001 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 Mavaddat N et al. (2015) Reported Trait: ER-positive breast cancer OR: 1.63 [1.6 - 1.67]
PPM000003 PGS000003 (PRS77_ERneg) PSS000002 Mavaddat N et al. (2015) Reported Trait: ER-negative breast cancer OR: 1.45 [1.4 - 1.49]

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000001 All breast cancer 67,054 individuals
[ 33,673 cases, 33,381 controls]
European ABCS, ABCFS, BBCC, BIGGS, BSUCH, CECILE, CTS, CGPS, ESTHER, GENICA, HMBCS, SZBCS, pKARMA, KBCP, ORIGO, LMBC, MARIE, MCBCS, MCCS, MTLGEBCS, MEC, NBHS, NorBCS, OBCS, PBCS, RPCI, SBCS, SASBAC, SKKDKFZS, SEARCH, OSU, UKBGS, DEMOKRITOS iCOGS
PSS000002 ER-negative breast cancer 38,722 individuals
[ 5,738 cases, 32,984 controls]
European ABCS, ABCFS, BBCC, BIGGS, BSUCH, CECILE, CTS, CGPS, ESTHER, GENICA, HMBCS, SZBCS, pKARMA, KBCP, ORIGO, LMBC, MARIE, MCBCS, MCCS, MTLGEBCS, MEC, NBHS, NorBCS, OBCS, PBCS, RPCI, SBCS, SASBAC, SKKDKFZS, SEARCH, OSU, UKBGS, DEMOKRITOS iCOGS
PSS000003 ER-positive breast cancer 53,923 individuals
[ 21,365 cases, 32,558 controls]
European ABCS, ABCFS, BBCC, BIGGS, BSUCH, CECILE, CTS, CGPS, ESTHER, GENICA, HMBCS, SZBCS, pKARMA, KBCP, ORIGO, LMBC, MARIE, MCBCS, MCCS, MTLGEBCS, MEC, NBHS, NorBCS, OBCS, PBCS, RPCI, SBCS, SASBAC, SKKDKFZS, SEARCH, OSU, UKBGS, DEMOKRITOS iCOGS