Polygenic Score (PGS) ID: PGS001532

Predicted Trait
Reported Trait Time from waking to first cigarette
Mapped Trait(s) smoking behavior trait (OBA_2050116)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC10003466
Released in PGS Catalog: Nov. 25, 2021
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Score Details

Score Construction
PGS Name GBE_QT_FC10003466
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 86
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%
18,841 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
— 18,841 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
PPM007235 PSS007511|
African Ancestry|
436 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Time from waking to first cigarette — — R²: 0.02268 [0.01552, 0.02983]
Incremental R2 (full-covars): -0.00073
PGS R2 (no covariates): 3e-05 [-0.00022, 0.00028]		 age, sex, UKB array type, Genotype PCs —
PPM007236 PSS007512|
East Asian Ancestry|
81 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Time from waking to first cigarette — — R²: 0.08524 [0.05993, 0.11055]
Incremental R2 (full-covars): -0.00086
PGS R2 (no covariates): 8e-05 [-0.00076, 0.00091]		 age, sex, UKB array type, Genotype PCs —
PPM007237 PSS007513|
European Ancestry|
2,322 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Time from waking to first cigarette — — R²: 0.06234 [0.05652, 0.06815]
Incremental R2 (full-covars): 0.00303
PGS R2 (no covariates): 0.004 [0.00244, 0.00557]		 age, sex, UKB array type, Genotype PCs —
PPM007238 PSS007514|
South Asian Ancestry|
400 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Time from waking to first cigarette — — R²: 0.05309 [0.04343, 0.06275]
Incremental R2 (full-covars): 0.00544
PGS R2 (no covariates): 0.0094 [0.00514, 0.01365]		 age, sex, UKB array type, Genotype PCs —
PPM007239 PSS007515|
European Ancestry|
4,577 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Time from waking to first cigarette — — R²: 0.03007 [0.02753, 0.03261]
Incremental R2 (full-covars): 0.0036
PGS R2 (no covariates): 0.00595 [0.00479, 0.00711]		 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
PSS007511 — — 436 individuals — African unspecified — UKB —
PSS007512 — — 81 individuals — East Asian — UKB —
PSS007513 — — 2,322 individuals — European non-white British ancestry UKB —
PSS007514 — — 400 individuals — South Asian — UKB —
PSS007515 — — 4,577 individuals — European white British ancestry UKB Testing cohort (heldout set)