Polygenic Score (PGS) ID: PGS001139

Predicted Trait
Reported Trait Light smokers, at least 100 smokes in lifetime
Mapped Trait(s) smoking behaviour measurement (EFO_0005671)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10002644
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_BIN_FC10002644
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 11
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%
74,920 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
—
[
  • 34,280 cases
  • , 40,640 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
PPM008422 PSS003726|
African Ancestry|
1,411 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Light smokers, at least 100 smokes in lifetime — AUROC: 0.60475 [0.57362, 0.63587] R²: 0.04431
Incremental AUROC (full-covars): -0.00017
PGS R2 (no covariates): 0.00387
PGS AUROC (no covariates): 0.52025 [0.48862, 0.55188]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008423 PSS003727|
East Asian Ancestry|
340 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Light smokers, at least 100 smokes in lifetime — AUROC: 0.72018 [0.66282, 0.77753] R²: 0.18473
Incremental AUROC (full-covars): 0.00217
PGS R2 (no covariates): 0.0059
PGS AUROC (no covariates): 0.50127 [0.43399, 0.56856]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008424 PSS003728|
European Ancestry|
7,260 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Light smokers, at least 100 smokes in lifetime — AUROC: 0.5677 [0.55413, 0.58127] R²: 0.01989
Incremental AUROC (full-covars): 0.00081
PGS R2 (no covariates): 0.00134
PGS AUROC (no covariates): 0.51767 [0.50394, 0.5314]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008425 PSS003729|
South Asian Ancestry|
1,269 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Light smokers, at least 100 smokes in lifetime — AUROC: 0.63663 [0.60494, 0.66832] R²: 0.07807
Incremental AUROC (full-covars): 0.00531
PGS R2 (no covariates): 0.00278
PGS AUROC (no covariates): 0.5327 [0.49921, 0.56619]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008426 PSS003730|
European Ancestry|
18,557 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Light smokers, at least 100 smokes in lifetime — AUROC: 0.57908 [0.57055, 0.58761] R²: 0.02444
Incremental AUROC (full-covars): 0.00325
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.52034 [0.51172, 0.52897]		 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
PSS003726 — —
[
  • 599 cases
  • , 812 controls
]
 — African unspecified — UKB —
PSS003727 — —
[
  • 124 cases
  • , 216 controls
]
 — East Asian — UKB —
PSS003728 — —
[
  • 3,751 cases
  • , 3,509 controls
]
 — European non-white British ancestry UKB —
PSS003729 — —
[
  • 567 cases
  • , 702 controls
]
 — South Asian — UKB —
PSS003730 — —
[
  • 8,496 cases
  • , 10,061 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)