Polygenic Score (PGS) ID: PGS002665

Predicted Trait
Reported Trait Smoking status
Mapped Trait(s) smoking status measurement (EFO_0006527)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name cov_SMOKING_STATUS.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 340,836
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
336,312 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 336,312 individuals European UKB

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
PPM014381 PSS009835|
African Ancestry|
6,455 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Smoking status — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0052 age, sex, age*sex, assessment center, genotyping array, 10 PCs See cov_SMOKING_STATUS.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014430 PSS009836|
East Asian Ancestry|
920 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Smoking status — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0024 age, sex, age*sex, assessment center, genotyping array, 10 PCs See cov_SMOKING_STATUS.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014479 PSS009837|
European Ancestry|
43,338 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Smoking status — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0332 age, sex, age*sex, assessment center, genotyping array, 10 PCs See cov_SMOKING_STATUS.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014528 PSS009838|
South Asian Ancestry|
8,007 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Smoking status — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0093 age, sex, age*sex, assessment center, genotyping array, 10 PCs See cov_SMOKING_STATUS.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009836 — — 920 individuals — East Asian — UKB —
PSS009837 — — 43,338 individuals — European Non-British European UKB —
PSS009838 — — 8,007 individuals — South Asian — UKB —
PSS009835 — — 6,455 individuals — African unspecified — UKB —