| 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 |
| Detailed Phenotype Description | 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 |
Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.
|
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) |
Detailed Phenotype Description | 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 |