Polygenic Score (PGS) ID: PGS000950

Predicted Trait
Reported Trait Skin changes due to chronic exposure to nonionising radiation (time-to-event)
Mapped Trait(s) response to radiation (GO_0009314)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1171
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_HC1171
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 169
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
—
[
  • 10,722 cases
  • , 258,982 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
PPM007574 PSS004163|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE skin changes due to chronic exposure to nonionising radiation — AUROC: 0.7986 [0.66831, 0.9289] R²: 0.07289
Incremental AUROC (full-covars): -0.00483
PGS R2 (no covariates): 0.0037
PGS AUROC (no covariates): 0.43607 [0.26599, 0.60615]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007575 PSS004164|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE skin changes due to chronic exposure to nonionising radiation — AUROC: 0.71374 [0.60185, 0.82563] R²: 0.03768
Incremental AUROC (full-covars): 0.00075
PGS R2 (no covariates): 0.00291
PGS AUROC (no covariates): 0.56978 [0.40767, 0.73189]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007576 PSS004165|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE skin changes due to chronic exposure to nonionising radiation — AUROC: 0.68867 [0.67287, 0.70447] R²: 0.05974
Incremental AUROC (full-covars): 0.01376
PGS R2 (no covariates): 0.01894
PGS AUROC (no covariates): 0.61159 [0.59382, 0.62937]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007577 PSS004166|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE skin changes due to chronic exposure to nonionising radiation — AUROC: 0.69762 [0.60805, 0.78718] R²: 0.0473
Incremental AUROC (full-covars): 0.0039
PGS R2 (no covariates): 7e-05
PGS AUROC (no covariates): 0.50078 [0.40515, 0.59641]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007578 PSS004167|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE skin changes due to chronic exposure to nonionising radiation — AUROC: 0.6853 [0.67565, 0.69495] R²: 0.06036
Incremental AUROC (full-covars): 0.01019
PGS R2 (no covariates): 0.00689
PGS AUROC (no covariates): 0.563 [0.55189, 0.57411]		 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
PSS004163 — —
[
  • 9 cases
  • , 6,488 controls
]
 — African unspecified — UKB —
PSS004164 — —
[
  • 11 cases
  • , 1,693 controls
]
 — East Asian — UKB —
PSS004165 — —
[
  • 964 cases
  • , 23,941 controls
]
 — European non-white British ancestry UKB —
PSS004166 — —
[
  • 32 cases
  • , 7,799 controls
]
 — South Asian — UKB —
PSS004167 — —
[
  • 2,714 cases
  • , 64,711 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)