Polygenic Score (PGS) ID: PGS001374

Predicted Trait
Reported Trait Age stopped smoking
Mapped Trait(s) smoking cessation (EFO_0004319)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI2897
Released in PGS Catalog: Nov. 25, 2021
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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_INI2897
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 663
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%
67,352 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
— 67,352 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM007025 PSS006876|
African Ancestry|
565 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.21854 [0.20078, 0.2363]
Incremental R2 (full-covars): 0.00162
PGS R2 (no covariates): 0.00424 [0.00109, 0.00739]		 age, sex, UKB array type, Genotype PCs —
PPM007026 PSS006877|
East Asian Ancestry|
128 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.19019 [0.15672, 0.22365]
Incremental R2 (full-covars): 0.00459
PGS R2 (no covariates): 0.00658 [-0.00106, 0.01421]		 age, sex, UKB array type, Genotype PCs —
PPM007027 PSS006878|
European Ancestry|
6,992 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.14667 [0.13855, 0.15479]
Incremental R2 (full-covars): -0.00089
PGS R2 (no covariates): 0.0003 [-0.00013, 0.00074]		 age, sex, UKB array type, Genotype PCs —
PPM007028 PSS006879|
South Asian Ancestry|
601 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.18218 [0.16673, 0.19764]
Incremental R2 (full-covars): -0.00589
PGS R2 (no covariates): 0.00251 [0.0003, 0.00472]		 age, sex, UKB array type, Genotype PCs —
PPM007029 PSS006880|
European Ancestry|
16,789 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.14537 [0.14045, 0.15029]
Incremental R2 (full-covars): 0.0003
PGS R2 (no covariates): 0.00121 [0.00068, 0.00173]		 age, sex, UKB array type, Genotype PCs —

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
PSS006876 — — 565 individuals — African unspecified — UKB —
PSS006877 — — 128 individuals — East Asian — UKB —
PSS006878 — — 6,992 individuals — European non-white British ancestry UKB —
PSS006879 — — 601 individuals — South Asian — UKB —
PSS006880 — — 16,789 individuals — European white British ancestry UKB Testing cohort (heldout set)