Polygenic Score (PGS) ID: PGS001115

Predicted Trait
Reported Trait Paracetamol use self-reported
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC9006154
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_BIN_FC9006154
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,673
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%
209,995 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
—
[
  • 61,226 cases
  • , 148,769 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
PPM008313 PSS004024|
African Ancestry|
5,085 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Paracetamol use self-reported — AUROC: 0.61918 [0.60368, 0.63468] R²: 0.05618
Incremental AUROC (full-covars): -0.00248
PGS R2 (no covariates): 0.00088
PGS AUROC (no covariates): 0.514 [0.49793, 0.53008]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008314 PSS004025|
East Asian Ancestry|
1,387 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Paracetamol use self-reported — AUROC: 0.66023 [0.62475, 0.6957] R²: 0.10401
Incremental AUROC (full-covars): 0.00543
PGS R2 (no covariates): 0.00338
PGS AUROC (no covariates): 0.53113 [0.49267, 0.56958]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008315 PSS004026|
European Ancestry|
19,451 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Paracetamol use self-reported — AUROC: 0.58754 [0.57874, 0.59635] R²: 0.02785
Incremental AUROC (full-covars): 0.01048
PGS R2 (no covariates): 0.0066
PGS AUROC (no covariates): 0.54192 [0.53304, 0.5508]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008316 PSS004027|
South Asian Ancestry|
5,818 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Paracetamol use self-reported — AUROC: 0.62877 [0.61375, 0.6438] R²: 0.06084
Incremental AUROC (full-covars): 0.00451
PGS R2 (no covariates): 0.0045
PGS AUROC (no covariates): 0.53799 [0.52235, 0.55363]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008317 PSS004028|
European Ancestry|
52,582 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Paracetamol use self-reported — AUROC: 0.60087 [0.59559, 0.60615] R²: 0.03601
Incremental AUROC (full-covars): 0.01595
PGS R2 (no covariates): 0.01072
PGS AUROC (no covariates): 0.55514 [0.54977, 0.56051]		 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
PSS004028 — —
[
  • 15,397 cases
  • , 37,185 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004024 — —
[
  • 2,117 cases
  • , 2,968 controls
]
 — African unspecified — UKB —
PSS004025 — —
[
  • 278 cases
  • , 1,109 controls
]
 — East Asian — UKB —
PSS004026 — —
[
  • 5,524 cases
  • , 13,927 controls
]
 — European non-white British ancestry UKB —
PSS004027 — —
[
  • 1,958 cases
  • , 3,860 controls
]
 — South Asian — UKB —