Predicted Trait | |
Reported Trait | ER-positive Breast Cancer |
Mapped Trait(s) | estrogen-receptor positive breast cancer (EFO_1000649) |
Score Construction | |
PGS Name | PRS3820_ERpos |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 3,820 |
Development Method | |
Name | LASSO penalized regression |
Parameters | p < 0.001 |
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-positive breast cancer cases | — | [ ,
0.0 % Male samples |
— | European | — | 68 cohorts
|
Training Cohort |
ER-positive 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 |
---|---|---|---|---|---|---|---|---|
PPM000009 | PSS000005 | PGP000002 Mavaddat N et al. (2018) | Reported Trait: ER-positive breast cancer | OR: 1.73 [1.68, 1.78] | AUROC: 0.647 | — | study, genetic PCs 1-15 | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000005 | ER-positive breast cancer cases | — | [ ,
0.0 % Male samples |
— | European | — | 10 cohorts
|
Prospective Test Set |