Polygenic Score (PGS) ID: PGS001336

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1002
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_cancer1002
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 555
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
—
[
  • 9,895 cases
  • , 259,809 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
PPM009166 PSS007616|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer — AUROC: 0.79293 [0.76728, 0.81858] R²: 0.15047
Incremental AUROC (full-covars): 0.01474
PGS R2 (no covariates): 0.00598
PGS AUROC (no covariates): 0.56918 [0.51783, 0.62054]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009167 PSS007617|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer — AUROC: 0.7602 [0.71475, 0.80565] R²: 0.14344
Incremental AUROC (full-covars): 0.01509
PGS R2 (no covariates): 0.01507
PGS AUROC (no covariates): 0.59411 [0.51563, 0.67258]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009168 PSS007618|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer — AUROC: 0.80561 [0.79545, 0.81577] R²: 0.18447
Incremental AUROC (full-covars): 0.01345
PGS R2 (no covariates): 0.01264
PGS AUROC (no covariates): 0.58544 [0.56669, 0.6042]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009169 PSS007619|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer — AUROC: 0.83564 [0.81289, 0.85838] R²: 0.18535
Incremental AUROC (full-covars): 0.00869
PGS R2 (no covariates): 0.00739
PGS AUROC (no covariates): 0.5725 [0.52745, 0.61755]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009170 PSS007620|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer — AUROC: 0.80961 [0.80348, 0.81573] R²: 0.1894
Incremental AUROC (full-covars): 0.02139
PGS R2 (no covariates): 0.01602
PGS AUROC (no covariates): 0.59627 [0.58498, 0.60756]		 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
PSS007616 — —
[
  • 126 cases
  • , 6,371 controls
]
 — African unspecified — UKB —
PSS007617 — —
[
  • 53 cases
  • , 1,651 controls
]
 — East Asian — UKB —
PSS007618 — —
[
  • 954 cases
  • , 23,951 controls
]
 — European non-white British ancestry UKB —
PSS007619 — —
[
  • 161 cases
  • , 7,670 controls
]
 — South Asian — UKB —
PSS007620 — —
[
  • 2,471 cases
  • , 64,954 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)