PGS Catalog - PGS001532 / Time from waking to first cigarette (Polygenic Score)

Polygenic Score (PGS) ID: PGS001532

Predicted Trait
Reported Trait	Time from waking to first cigarette
Mapped Trait(s)	smoking behaviour measurement (EFO_0005671)
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)