Predicted Trait | |
Reported Trait | Estrogen receptor [ER]-negative breast cancer |
Mapped Trait(s) | estrogen-receptor negative breast cancer (EFO_1000650) |
Score Construction | |
PGS Name | BCPRS_ER- |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 53 |
Development Method | |
Name | Known susceptibility loci (genome-wide significant SNPs) |
Parameters | p<5x10-8, included indpendent SNPs from fine-mapping studies (p < 10-4) |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000033 |
Citation (link to publication) | Kuchenbaecker KB et al. J Natl Cancer Inst (2017) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
GWAS Catalog: GCST001937 EuropePMC: 23535729 |
22,627 individuals | European |
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 |
---|---|---|---|---|---|---|---|---|
PPM000122 | PSS000074 | PGP000034 Lecarpentier J et al. (2017) Ext. | Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations | OR: 1.19 [1.05, 1.35] | AUROC: 0.55 [0.51, 0.59] | — | 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 | PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS |
PPM000110 | PSS000070 | PGP000033 Kuchenbaecker KB et al. (2017) | Reported Trait: Breast cancer in BRCA1 mutation carriers | HR: 1.27 [1.23, 1.31] | C-index: 0.581 [0.571, 0.592] | — | Country, birth year | — |
PPM000111 | PSS000071 | PGP000033 Kuchenbaecker KB et al. (2017) | Reported Trait: Breast cancer in BRCA2 mutation carriers | HR: 1.15 [1.1, 1.2] | C-index: 0.538 [0.523, 0.553] | — | Country, birth year | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000071 | BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. | — | [ ,
0.0 % Male samples |
— | European | Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry | CIMBA | Median censoring age (cases) = 43 |
PSS000074 | Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. | — | [ ,
100.0 % Male samples |
— | European | Self-reported European ancestry | 37 cohorts
|
— |
PSS000070 | BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. | — | [ ,
0.0 % Male samples |
— | European | Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry | CIMBA | Median censoring age (cases) = 40 |