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. |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000940 | PGS000004 (PRS313_BC) |
PSS000482| European Ancestry| 84,607 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Contralateral breast cancer | OR: 1.39 [1.13, 1.7] | — | — | Age, country, PCs (1-10) | — |
PPM000938 | PGS000004 (PRS313_BC) |
PSS000482| European Ancestry| 84,607 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Contralateral breast cancer | OR: 1.3 [1.26, 1.35] | — | — | Age, country | — |
PPM000964 | PGS000005 (PRS313_ERpos) |
PSS000486| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.22 [1.15, 1.3] | — | — | Country | — |
PPM000963 | PGS000005 (PRS313_ERpos) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Metachronous contralateral breast cancer | HR: 1.23 [1.16, 1.31] | — | — | Country | — |
PPM000962 | PGS000001 (PRS77_BC) |
PSS000486| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.21 [1.13, 1.29] | — | — | Country | — |
PPM000947 | PGS000005 (PRS313_ERpos) |
PSS000486| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.22 [1.15, 1.3] | — | — | Country | — |
PPM000946 | PGS000005 (PRS313_ERpos) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Metachronous contralateral breast cancer | HR: 1.23 [1.16, 1.31] | — | — | Country | — |
PPM000945 | PGS000001 (PRS77_BC) |
PSS000486| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.21 [1.13, 1.29] | — | — | Country | — |
PPM000944 | PGS000001 (PRS77_BC) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Metachronous contralateral breast cancer | HR: 1.21 [1.14, 1.29] | — | — | Country | — |
PPM000941 | PGS000004 (PRS313_BC) |
PSS000483| European Ancestry| 143,830 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Unilateral breast cancer | OR: 1.67 [1.59, 1.76] | — | — | Age, country, PCs (1-10) | — |
PPM000957 | PGS000004 (PRS313_BC) |
PSS000482| European Ancestry| 84,607 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Contralateral breast cancer | OR: 1.39 [1.13, 1.7] | — | — | Age, country, PCs (1-10) | — |
PPM000959 | PGS000004 (PRS313_BC) |
PSS000481| Additional Asian Ancestries| 12,473 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Contralateral breast cancer | OR: 1.15 [1.02, 1.29] | — | — | Age, country | — |
PPM000955 | PGS000004 (PRS313_BC) |
PSS000482| European Ancestry| 84,607 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Contralateral breast cancer | OR: 1.3 [1.26, 1.35] | — | — | Age, country | — |
PPM000965 | PGS000005 (PRS313_ERpos) |
PSS000485| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Estrogen-receptor positive metachronous invasive contralateral breast cancer | HR: 1.37 [1.22, 1.54] | — | — | Country | — |
PPM000961 | PGS000001 (PRS77_BC) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Metachronous contralateral breast cancer | HR: 1.21 [1.14, 1.29] | — | — | Country | — |
PPM000958 | PGS000004 (PRS313_BC) |
PSS000483| European Ancestry| 143,830 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Unilateral breast cancer | OR: 1.67 [1.59, 1.76] | — | — | Age, country, PCs (1-10) | — |
PPM000954 | PGS000004 (PRS313_BC) |
PSS000485| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (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| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.24 [1.16, 1.32] | — | — | Country | — |
PPM000951 | PGS000004 (PRS313_BC) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (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| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.24 [1.16, 1.33] | — | — | Country | — |
PPM000949 | PGS000006 (PRS313_ERneg) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Metachronous contralateral breast cancer | HR: 1.25 [1.17, 1.33] | — | — | Country | — |
PPM000948 | PGS000005 (PRS313_ERpos) |
PSS000485| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Estrogen-receptor positive metachronous invasive contralateral breast cancer | HR: 1.37 [1.22, 1.54] | — | — | Country | — |
PPM000942 | PGS000004 (PRS313_BC) |
PSS000481| Additional Asian Ancestries| 12,473 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Contralateral breast cancer | OR: 1.15 [1.02, 1.29] | — | — | Age, country | — |
PPM000960 | PGS000004 (PRS313_BC) |
PSS000480| Additional Asian Ancestries| 25,531 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Unilateral breast cancer | OR: 1.56 [1.52, 1.6] | — | — | Age, country | — |
PPM000956 | PGS000004 (PRS313_BC) |
PSS000483| European Ancestry| 143,830 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Unilateral breast cancer | OR: 1.82 [1.8, 1.84] | — | — | Age, country | — |
PPM000943 | PGS000004 (PRS313_BC) |
PSS000480| Additional Asian Ancestries| 25,531 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Unilateral breast cancer | OR: 1.56 [1.52, 1.6] | — | — | Age, country | — |
PPM000937 | PGS000004 (PRS313_BC) |
PSS000485| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (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| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.24 [1.16, 1.32] | — | — | Country | — |
PPM000935 | PGS000004 (PRS313_BC) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (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| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (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| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.24 [1.16, 1.33] | — | — | Country | — |
PPM000966 | PGS000006 (PRS313_ERneg) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Metachronous contralateral breast cancer | HR: 1.25 [1.17, 1.33] | — | — | Country | — |
PPM000952 | PGS000004 (PRS313_BC) |
PSS000484| European Ancestry| 56,068 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (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) | — |
PPM000939 | PGS000004 (PRS313_BC) |
PSS000483| European Ancestry| 143,830 individuals |
PGP000109 | Kramer I et al. Am J Hum Genet (2020) |Ext. |
Reported Trait: Unilateral breast cancer | OR: 1.82 [1.8, 1.84] | — | — | Age, country | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000480 | Women (European Ancestry) diagnosed with unilateral breast cancer | — | [ ,
0.0 % Male samples |
— | Asian unspecified | — | 8 cohorts
|
— |
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. | — | [ ,
0.0 % Male samples |
— | Asian unspecified | — | 8 cohorts
|
— |
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. | — | [ ,
0.0 % Male samples |
— | European | — | 63 cohorts
|
— |
PSS000483 | Women (European Ancestry) diagnosed with unilateral breast cancer | — | [ ,
0.0 % Male samples |
— | European | — | 63 cohorts
|
— |
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 | [ ,
0.0 % Male samples |
Median (Age At Diagnosis) = 56.0 years | European | — | 42 cohorts
|
— |
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 | [ ,
0.0 % Male samples |
Median (Age At Diagnosis) = 56.0 years | European | — | 42 cohorts
|
— |
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 | [ ,
0.0 % Male samples |
Median (Age At Diagnosis) = 56.0 years | European | — | 42 cohorts
|
— |