PGS Publication: PGP000109

Publication Information (EuropePMC)
Title Breast Cancer Polygenic Risk Score and Contralateral Breast Cancer Risk.
PubMed ID 33022221(Europe PMC)
doi 10.1016/j.ajhg.2020.09.001
Publication Date Oct. 5, 2020
Journal Am J Hum Genet
Author(s) Kramer I, Hooning MJ, Mavaddat N, Hauptmann M, Keeman R, Steyerberg EW, Giardiello D, Antoniou AC, Pharoah PDP, Canisius S, Abu-Ful Z, Andrulis IL, Anton-Culver H, Aronson KJ, Augustinsson A, Becher H, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Brauch H, Bremer M, Brucker SY, Burwinkel B, Castelao JE, Chan TL, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Choi JY, Clarke CL, NBCS Collaborators, Collée JM, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Dörk T, Dos-Santos-Silva I, Dunning AM, Dwek M, Eccles DM, Evans DG, Fasching PA, Flyger H, Gago-Dominguez M, García-Closas M, García-Sáenz JA, Giles GG, Goldgar DE, González-Neira A, Haiman CA, Håkansson N, Hamann U, Hartman M, Heemskerk-Gerritsen BAM, Hollestelle A, Hopper JL, Hou MF, Howell A, ABCTB Investigators, kConFab Investigators, Ito H, Jakimovska M, Jakubowska A, Janni W, John EM, Jung A, Kang D, Kets CM, Khusnutdinova E, Ko YD, Kristensen VN, Kurian AW, Kwong A, Lambrechts D, Le Marchand L, Li J, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Margolin S, Matsuo K, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Muranen TA, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Park-Simon TW, Peto J, Petridis C, Plaseska-Karanfilska D, Presneau N, Pylkäs K, Radice P, Rennert G, Romero A, Roylance R, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, See MH, Shah M, Shen CY, Shu XO, Siesling S, Slager S, Sohn C, Southey MC, Spinelli JJ, Stone J, Tapper WJ, Tengström M, Teo SH, Terry MB, Tollenaar RAEM, Tomlinson I, Troester MA, Vachon CM, van Ongeval C, van Veen EM, Winqvist R, Wolk A, Zheng W, Ziogas A, Easton DF, Hall P, Schmidt MK.
Released in PGS Catalog: Nov. 20, 2020

Associated Polygenic Score(s)

External PGS Evaluated 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
PGS000004 PRS313_BC PGP000002 Mavaddat N et al. Am J Hum Genet (2018) Breast Cancer breast carcinoma 313 http://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 http://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 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000006/ScoringFiles/PGS000006.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
PPM000965 PGS000005 (PRS313_ERpos) PSS000485 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Estrogen-receptor positive metachronous invasive contralateral breast cancer HR: 1.37[1.22, 1.54] Country
PPM000964 PGS000005 (PRS313_ERpos) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.22[1.15, 1.3] Country
PPM000963 PGS000005 (PRS313_ERpos) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.23[1.16, 1.31] Country
PPM000962 PGS000001 (PRS77_BC) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.21[1.13, 1.29] Country
PPM000961 PGS000001 (PRS77_BC) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.21[1.14, 1.29] Country
PPM000960 PGS000004 (PRS313_BC) PSS000480 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Unilateral breast cancer OR: 1.56[1.52, 1.6] Age, country
PPM000959 PGS000004 (PRS313_BC) PSS000481 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Contralateral breast cancer OR: 1.15[1.02, 1.29] Age, country
PPM000958 PGS000004 (PRS313_BC) PSS000483 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Unilateral breast cancer OR: 1.67[1.59, 1.76] Age, country, PCs (1-10)
PPM000957 PGS000004 (PRS313_BC) PSS000482 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Contralateral breast cancer OR: 1.39[1.13, 1.7] Age, country, PCs (1-10)
PPM000956 PGS000004 (PRS313_BC) PSS000483 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Unilateral breast cancer OR: 1.82[1.8, 1.84] Age, country
PPM000955 PGS000004 (PRS313_BC) PSS000482 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Contralateral breast cancer OR: 1.3[1.26, 1.35] Age, country
PPM000954 PGS000004 (PRS313_BC) PSS000485 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Estrogen-receptor positive metachronous invasive contralateral breast cancer HR: 1.38[1.23, 1.55] Country
PPM000953 PGS000004 (PRS313_BC) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.24[1.16, 1.32] Country
PPM000951 PGS000004 (PRS313_BC) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.25[1.18, 1.33] C-index: 0.563[0.547, 0.586] Country
PPM000950 PGS000006 (PRS313_ERneg) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.24[1.16, 1.33] Country
PPM000949 PGS000006 (PRS313_ERneg) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.25[1.17, 1.33] Country
PPM000948 PGS000005 (PRS313_ERpos) PSS000485 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Estrogen-receptor positive metachronous invasive contralateral breast cancer HR: 1.37[1.22, 1.54] Country
PPM000947 PGS000005 (PRS313_ERpos) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.22[1.15, 1.3] Country
PPM000946 PGS000005 (PRS313_ERpos) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.23[1.16, 1.31] Country
PPM000945 PGS000001 (PRS77_BC) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.21[1.13, 1.29] Country
PPM000944 PGS000001 (PRS77_BC) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.21[1.14, 1.29] Country
PPM000943 PGS000004 (PRS313_BC) PSS000480 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Unilateral breast cancer OR: 1.56[1.52, 1.6] Age, country
PPM000942 PGS000004 (PRS313_BC) PSS000481 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Contralateral breast cancer OR: 1.15[1.02, 1.29] Age, country
PPM000941 PGS000004 (PRS313_BC) PSS000483 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Unilateral breast cancer OR: 1.67[1.59, 1.76] Age, country, PCs (1-10)
PPM000940 PGS000004 (PRS313_BC) PSS000482 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Contralateral breast cancer OR: 1.39[1.13, 1.7] Age, country, PCs (1-10)
PPM000939 PGS000004 (PRS313_BC) PSS000483 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Unilateral breast cancer OR: 1.82[1.8, 1.84] Age, country
PPM000938 PGS000004 (PRS313_BC) PSS000482 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Contralateral breast cancer OR: 1.3[1.26, 1.35] Age, country
PPM000937 PGS000004 (PRS313_BC) PSS000485 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Estrogen-receptor positive metachronous invasive contralateral breast cancer HR: 1.38[1.23, 1.55] Country
PPM000936 PGS000004 (PRS313_BC) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.24[1.16, 1.32] Country
PPM000935 PGS000004 (PRS313_BC) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer C-index: 0.623[0.591, 0.629] Country, age at first diagnosis, year of first diagnosis, family history for breast cancer in a first degree relative, clinical characteristics of the first breast cancer (nodal status, tumor size, differentiation grade, morphology, estrogen receptor status, human epidermal growth factor receptor 2 status, chemotherapy, endocrine therapy, radiotherapy)
PPM000934 PGS000004 (PRS313_BC) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.25[1.18, 1.33] C-index: 0.563[0.547, 0.586] Country
PPM000967 PGS000006 (PRS313_ERneg) PSS000486 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Invasive metachronous contralateral breast cancer HR: 1.24[1.16, 1.33] Country
PPM000966 PGS000006 (PRS313_ERneg) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer HR: 1.25[1.17, 1.33] Country
PPM000952 PGS000004 (PRS313_BC) PSS000484 PGP000109
Kramer I et al. (2020)
Ext.
Reported Trait: Metachronous contralateral breast cancer C-index: 0.623[0.591, 0.629] Country, age at first diagnosis, year of first diagnosis, family history for breast cancer in a first degree relative, clinical characteristics of the first breast cancer (nodal status, tumor size, differentiation grade, morphology, estrogen receptor status, human epidermal growth factor receptor 2 status, chemotherapy, endocrine therapy, radiotherapy)

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
PSS000480 Women (European Ancestry) diagnosed with unilateral breast cancer
[
  • 12,133 cases
  • , 13,398 controls
]
,
0.0 % Male samples
Asian unspecified 8 cohorts
  • CBCS
  • ,HERPACC
  • ,HKBCS
  • ,MYBRCA
  • ,NC-BCFR
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
PSS000481 Women (Asian Ancestry) diagnosed with unilateral breast cancer or CBC. CBC was defined as breast cancer (in situ or invasive) in the contralateral breast irrespective of the time since the first breast cancer.
[
  • 340 cases
  • , 12,133 controls
]
,
0.0 % Male samples
Asian unspecified 8 cohorts
  • CBCS
  • ,HERPACC
  • ,HKBCS
  • ,MYBRCA
  • ,NC-BCFR
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
PSS000482 Women (European Ancestry) diagnosed with unilateral breast cancer or CBC. CBC was defined as breast cancer (in situ or invasive) in the contralateral breast irrespective of the time since the first breast cancer.
[
  • 3,607 cases
  • , 81,000 controls
]
,
0.0 % Male samples
European 63 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BBCS
  • ,BCEES
  • ,BCFR-NY
  • ,BCFR-PA
  • ,BCFR-UTAH
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CBCS
  • ,CCGP
  • ,CGPS
  • ,CNIO-BCS
  • ,DIETCOMPLYF
  • ,FHRISK
  • ,GC-HBOC
  • ,GENICA
  • ,GESBC
  • ,GLACIER
  • ,HABCS
  • ,HCSC
  • ,HEBCS
  • ,HMBCS
  • ,HUBCS
  • ,ICICLE
  • ,KARBAC
  • ,KARMA
  • ,KBCP
  • ,KCONFAB/AOCS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MISS
  • ,MMHS
  • ,NBCS
  • ,NC-BCFR
  • ,NCBRCS
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PREFACE
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
PSS000483 Women (European Ancestry) diagnosed with unilateral breast cancer
[
  • 81,000 cases
  • , 62,830 controls
]
,
0.0 % Male samples
European 63 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BBCS
  • ,BCEES
  • ,BCFR-NY
  • ,BCFR-PA
  • ,BCFR-UTAH
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CBCS
  • ,CCGP
  • ,CGPS
  • ,CNIO-BCS
  • ,DIETCOMPLYF
  • ,FHRISK
  • ,GC-HBOC
  • ,GENICA
  • ,GESBC
  • ,GLACIER
  • ,HABCS
  • ,HCSC
  • ,HEBCS
  • ,HMBCS
  • ,HUBCS
  • ,ICICLE
  • ,KARBAC
  • ,KARMA
  • ,KBCP
  • ,KCONFAB/AOCS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MISS
  • ,MMHS
  • ,NC-BCFR
  • ,NCBCS
  • ,NorBCS
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PREFACE
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
PSS000484 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 1,027 cases
  • , 55,041 controls
]
,
0.0 % Male samples
Median (Age At Diagnosis) = 56.0 years European 41 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,KCONFAB/AOCSS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS
PSS000485 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 275 cases
  • , 55,793 controls
]
,
0.0 % Male samples
Median (Age At Diagnosis) = 56.0 years European 41 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,KCONFAB/AOCSS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS
PSS000486 Women (European Ancestry) diagnosed with unilateral breast cancer or metachronous contralateral breast cancer (CBC). Metachronous contralateral breast cancer was defined as breast cancer in the contralateral breast (in situ or invasive) diagnosed at least 3 months after the first breast cancer. Median = 8.4 years
[
  • 923 cases
  • , 55,145 controls
]
,
0.0 % Male samples
Median (Age At Diagnosis) = 56.0 years European 41 cohorts
  • ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,BBCC
  • ,BCFR-PA
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CCGP
  • ,CGPS
  • ,GC-HBOC
  • ,GENICA
  • ,HCSC
  • ,HEBCS
  • ,KARBAC
  • ,KARMA
  • ,KCONFAB/AOCSS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MEC
  • ,MISS
  • ,NBCS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PKARMA
  • ,POSH
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SZBCS
  • ,UCIBCS