Predicted Trait | |
Reported Trait | ER-negative Breast Cancer |
Mapped Trait(s) | estrogen-receptor negative breast cancer (EFO_1000650) |
Score Construction | |
PGS Name | PRS313_ERneg |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 313 |
Development Method | |
Name | Hard-Thresholding Stepwise Forward Regression |
Parameters | p < 10^-5 |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000002 |
Citation (link to publication) | Mavaddat N et al. Am J Hum Genet (2018) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
GWAS Catalog: GCST004988 EuropePMC: 29059683 |
139,274 individuals | European |
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 |
---|---|---|---|---|---|---|---|
ER-negative breast cancer cases | — | [ ,
0.0 % Male samples |
— | European | — | 68 cohorts
|
Training Cohort |
ER-negative breast cancer cases | — | [ ,
0.0 % Male samples |
— | European | — | 25 cohorts
|
Validation Cohort |
PGS Performance Metric ID (PPM ID) |
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 |
---|---|---|---|---|---|---|---|---|
PPM000007 | PSS000006 | PGP000002 Mavaddat N et al. (2018) | Reported Trait: ER-negative breast cancer | OR: 1.45 [1.37, 1.53] | AUROC: 0.601 | — | study, genetic PCs 1-15 | — |
PPM000950 | PSS000486 | PGP000109 Kramer I et al. (2020) Ext. | Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.24 [1.16, 1.33] | — | — | Country | — |
PPM000949 | PSS000484 | PGP000109 Kramer I et al. (2020) Ext. | Reported Trait: Metachronous contralateral breast cancer | HR: 1.25 [1.17, 1.33] | — | — | Country | — |
PPM000967 | PSS000486 | PGP000109 Kramer I et al. (2020) Ext. | Reported Trait: Invasive metachronous contralateral breast cancer | HR: 1.24 [1.16, 1.33] | — | — | Country | — |
PPM000966 | PSS000484 | PGP000109 Kramer I et al. (2020) Ext. | Reported Trait: Metachronous contralateral breast cancer | HR: 1.25 [1.17, 1.33] | — | — | Country | — |
PPM001024 | PSS000521 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: Breast cancer in BRCA1 carriers | HR: 1.29 [1.25, 1.33] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
PPM001025 | PSS000525 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: Breast cancer in BRCA2 carriers | HR: 1.23 [1.18, 1.27] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
PPM001026 | PSS000522 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: ER negative breast cancer in BRCA1 carriers | HR: 1.23 [1.18, 1.27] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
PPM001027 | PSS000526 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: ER negative breast cancer in BRCA2 carriers | HR: 1.29 [1.19, 1.41] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
PPM001028 | PSS000523 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: ER positive breast cancer in BRCA1 carriers | HR: 1.29 [1.21, 1.37] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
PPM001029 | PSS000527 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: ER positive breast cancer in BRCA2 carriers | HR: 1.21 [1.15, 1.27] | — | — | birth cohort, PCs(1-4) of ancestry, family history in first- and second-degree relatives | — |
PPM001034 | PSS000529 | PGP000117 Barnes DR et al. (2020) Ext. | Reported Trait: Incident breast cancer in BRCA1 carriers | HR: 1.28 [1.14, 1.44] | — | — | family history of the appropriate cancer in first- and second-degree relatives | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000529 | Eligibility was restricted to female BRCA1 and BRCA2 carriers who at completion of the baseline questionnaire were free of any cancer diagnosis (excluding non-melanoma skin cancer) and had not undergone risk-reducing bilateral mastectomy. Participants diagosed with a first breast cancer were considered affected. | — | [ ,
0.0 % Male samples |
— | European | — | 61 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
|
— |
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
|
— |
PSS000521 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
PSS000522 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
PSS000523 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
PSS000525 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
PSS000526 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
PSS000527 | — | — | [ ,
0.0 % Male samples |
— | European | — | 59 cohorts
|
— |
PSS000006 | ER-negative breast cancer cases | — | [ ,
0.0 % Male samples |
— | European | — | 10 cohorts
|
Prospective Test Set |