Predicted Trait | |
Reported Trait | Breast cancer |
Mapped Trait(s) | breast carcinoma (EFO_0000305) |
Score Construction | |
PGS Name | GPS_BC |
Variants | |
Original Genome Build | hg19 |
Number of Variants | 5,218 |
Development Method | |
Name | Pruning and thresholding (P+T) |
Parameters | r2 < 0.2; P < 5e−4; LD panel = 503 100G Europeans |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000006 |
Citation (link to publication) | Khera AV et al. Nat 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 |
---|---|---|---|---|---|---|---|
Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. | — | [ ,
0.0 % Male samples |
— | European | — | UKB | UKB Phase 1 |
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 |
---|---|---|---|---|---|---|---|---|
PPM000024 | PSS000014 | PGP000006 Khera AV et al. (2018) | Reported Trait: Breast cancer | — | AUROC: 0.69 [0.68, 0.69] | Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.027 | age; sex; Ancestry PC 1-4; genotyping chip | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000014 | Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. | — | [ ,
0.0 % Male samples |
— | European | — | UKB | UKB Phase 2 |