Polygenic Score (PGS) ID: PGS001130

Predicted Trait
Reported Trait Number of cigarettes previously smoked per day
Mapped Trait(s) cigarettes per day measurement (EFO_0006525)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI2887
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_INI2887
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 725
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%
64,064 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
— 64,064 individuals 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
PPM008378 PSS006871|
African Ancestry|
553 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: # of cigarettes previously smoked daily — — R²: 0.05257 [0.04201, 0.06313]
Incremental R2 (full-covars): -0.00029
PGS R2 (no covariates): 0.00089 [-0.00056, 0.00234]		 age, sex, UKB array type, Genotype PCs —
PPM008379 PSS006872|
East Asian Ancestry|
122 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: # of cigarettes previously smoked daily — — R²: 0.20745 [0.17324, 0.24166]
Incremental R2 (full-covars): -0.00582
PGS R2 (no covariates): 0.00074 [-0.00184, 0.00332]		 age, sex, UKB array type, Genotype PCs —
PPM008380 PSS006873|
European Ancestry|
6,735 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: # of cigarettes previously smoked daily — — R²: 0.10992 [0.10259, 0.11725]
Incremental R2 (full-covars): 0.00885
PGS R2 (no covariates): 0.00973 [0.0073, 0.01215]		 age, sex, UKB array type, Genotype PCs —
PPM008381 PSS006874|
South Asian Ancestry|
585 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: # of cigarettes previously smoked daily — — R²: 0.0678 [0.05705, 0.07855]
Incremental R2 (full-covars): -0.00447
PGS R2 (no covariates): 0.00066 [-0.00048, 0.0018]		 age, sex, UKB array type, Genotype PCs —
PPM008382 PSS006875|
European Ancestry|
15,927 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: # of cigarettes previously smoked daily — — R²: 0.0979 [0.09364, 0.10216]
Incremental R2 (full-covars): 0.0054
PGS R2 (no covariates): 0.00613 [0.00496, 0.00731]		 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
PSS006871 — — 553 individuals — African unspecified — UKB —
PSS006872 — — 122 individuals — East Asian — UKB —
PSS006873 — — 6,735 individuals — European non-white British ancestry UKB —
PSS006874 — — 585 individuals — South Asian — UKB —
PSS006875 — — 15,927 individuals — European white British ancestry UKB Testing cohort (heldout set)