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breast cancer, glaucoma, BMI
, EFO_0001645 Examples: breast cancer, glaucoma, BMI
, EFO_0001645 Feedback
- PGS Catalog
- Polygenic Scores
- PGS000530
Polygenic Score (PGS) ID: PGS000530
| Predicted Trait |
| Reported Trait | Breast cancer (female) |
| Mapped Trait(s) | breast carcinoma (EFO_0000305) |
| Additional Trait Information | PheCode 174.1 |
Released in PGS Catalog: Dec. 15, 2020 Download Score FTP directory Terms and Licenses PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.
Score Details
| Score Construction |
| PGS Name | PRSWEB_PHECODE174.1_iCOGS-ER-positive-BRCA_PT_UKB_20200608 |
| Development Method |
| Name | Pruning and Thresholding (P+T) |
| Parameters | LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.98e-06 |
| Variants |
| Original Genome Build | GRCh37 |
| Number of Variants | 174 |
| Effect Weight Type | NR |
| PGS Source |
| PGS Catalog Publication (PGP) ID | PGP000118 |
| Citation (link to publication) | Fritsche LG et al. Am J Hum Genet (2020) |
| Ancestry Distribution |
| Source of VariantAssociations (GWAS) | European: 100%1,063,736 individuals (100%) |
| Score Development/Training | European: 100%68,451 individuals (100%) |
| PGS Evaluation | European: 100%1 Sample Sets |
Development Samples
Source of Variant Associations (GWAS)
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
| Europe PMC: 29059683 | 175,475 individuals[ - 69,501 cases
- , 105,974 controls
] | European | NR |
| Europe PMC: 29059683 | 127,442 individuals[ - 21,468 cases
- , 105,974 controls
] | European | NR |
| Europe PMC: 29059683 | 228,951 individuals[ - 122,977 cases
- , 105,974 controls
] | European | NR |
| Europe PMC: 29059683 | 175,475 individuals[ - 69,501 cases
- , 105,974 controls
] | European | NR |
| Europe PMC: 29059683 | 127,442 individuals[ - 21,468 cases
- , 105,974 controls
] | European | NR |
| Europe PMC: 29059683 | 228,951 individuals[ - 122,977 cases
- , 105,974 controls
] | European | NR |
Score Development/Training
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) | Phenotype Definitions & Methods | Age of Study Participants | Participant Follow-up Time | Additional Ancestry Description | Additional Sample/Cohort Information |
| Europe PMC: 32991828 | 68,451 individuals[ - 6,234 cases
- , 62,217 controls
] | European | UKB | PheCode:174.1; ICD9:233.0; ICD10:C50.0, C50.1, C50.2, C50.3, C50.4, C50.5, C50.6, C50.8, C50.9, D05.1, D05.7, D05.9, Z85.3 | — | — | — | — |
Performance Metrics
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.
Evaluated Samples
| PGS Sample Set ID(PSS) | 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 |
| PSS000570 | PheCode:174.1; ICD9:233.0; ICD10:C50.0, C50.1, C50.2, C50.3, C50.4, C50.5, C50.6, C50.8, C50.9, D05.1, D05.7, D05.9, Z85.3 | — | 68,531 individuals[ - 6,242 cases
- , 62,289 controls
] | — | European | — | UKB | — |