Polygenic Score (PGS) ID: PGS001337

Predicted Trait
Reported Trait Family history of breast cancer
Mapped Trait(s) family history of breast cancer (EFO_0005606)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1002
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_FH1002
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 195
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

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
—
[
  • 49,873 cases
  • , 219,831 controls
]
 European UKB — — — white British ancestry —

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.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM009171 PSS004034|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.57882 [0.5595, 0.59814] R²: 0.01774
Incremental AUROC (full-covars): 0.00262
PGS R2 (no covariates): 0.00016
PGS AUROC (no covariates): 0.50866 [0.48823, 0.52909]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009172 PSS004035|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.60865 [0.56929, 0.64801] R²: 0.03344
Incremental AUROC (full-covars): 0.01456
PGS R2 (no covariates): 0.0091
PGS AUROC (no covariates): 0.56734 [0.52563, 0.60905]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009173 PSS004036|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.57917 [0.56994, 0.5884] R²: 0.01887
Incremental AUROC (full-covars): 0.00313
PGS R2 (no covariates): 0.002
PGS AUROC (no covariates): 0.52353 [0.51419, 0.53286]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009174 PSS004037|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.60464 [0.58531, 0.62397] R²: 0.02766
Incremental AUROC (full-covars): 0.00261
PGS R2 (no covariates): 0.00157
PGS AUROC (no covariates): 0.52221 [0.5025, 0.54191]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009175 PSS004038|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.57389 [0.56837, 0.57941] R²: 0.01618
Incremental AUROC (full-covars): 0.00514
PGS R2 (no covariates): 0.0022
PGS AUROC (no covariates): 0.527 [0.52143, 0.53258]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004034 — —
[
  • 886 cases
  • , 5,611 controls
]
 — African unspecified — UKB —
PSS004035 — —
[
  • 205 cases
  • , 1,499 controls
]
 — East Asian — UKB —
PSS004036 — —
[
  • 4,521 cases
  • , 20,384 controls
]
 — European non-white British ancestry UKB —
PSS004037 — —
[
  • 966 cases
  • , 6,865 controls
]
 — South Asian — UKB —
PSS004038 — —
[
  • 12,512 cases
  • , 54,913 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)