Polygenic Score (PGS) ID: PGS001128

Predicted Trait
Reported Trait Previous smoker
Mapped Trait(s) smoking status measurement (EFO_0006527)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20020116
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_FC20020116
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,348
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%
268,823 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
—
[
  • 96,308 cases
  • , 172,515 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
PPM008368 PSS003844|
African Ancestry|
6,390 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Previous Smoker — AUROC: 0.62818 [0.61021, 0.64615] R²: 0.04625
Incremental AUROC (full-covars): -0.00333
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.49819 [0.47898, 0.5174]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008369 PSS003845|
East Asian Ancestry|
1,661 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Previous Smoker — AUROC: 0.70433 [0.66805, 0.74061] PGS R2 (no covariates): 0.00293
R²: 0.11247
Incremental AUROC (full-covars): -0.00189
PGS AUROC (no covariates): 0.5352 [0.49491, 0.57548]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008370 PSS003846|
European Ancestry|
24,816 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Previous Smoker — AUROC: 0.59213 [0.58495, 0.59931] R²: 0.03309
Incremental AUROC (full-covars): 0.00528
PGS R2 (no covariates): 0.0046
PGS AUROC (no covariates): 0.53522 [0.5279, 0.54253]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008371 PSS003847|
South Asian Ancestry|
7,615 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Previous Smoker — AUROC: 0.73887 [0.72262, 0.75511] R²: 0.14448
Incremental AUROC (full-covars): 0.00362
PGS R2 (no covariates): 0.00301
PGS AUROC (no covariates): 0.53352 [0.51394, 0.55311]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008372 PSS003848|
European Ancestry|
67,212 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Previous Smoker — AUROC: 0.61185 [0.60741, 0.61629] R²: 0.04715
Incremental AUROC (full-covars): 0.01019
PGS R2 (no covariates): 0.0091
PGS AUROC (no covariates): 0.5477 [0.54318, 0.55223]		 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
PSS003844 — —
[
  • 1,071 cases
  • , 5,319 controls
]
 — African unspecified — UKB —
PSS003845 — —
[
  • 237 cases
  • , 1,424 controls
]
 — East Asian — UKB —
PSS003846 — —
[
  • 9,959 cases
  • , 14,857 controls
]
 — European non-white British ancestry UKB —
PSS003847 — —
[
  • 962 cases
  • , 6,653 controls
]
 — South Asian — UKB —
PSS003848 — —
[
  • 23,931 cases
  • , 43,281 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)