Polygenic Score (PGS) ID: PGS001129

Predicted Trait
Reported Trait Smoking status (ever vs never smokers)
Mapped Trait(s) smoking status measurement (EFO_0006527)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC30022506
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_BIN_FC30022506
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 974
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%
68,516 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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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
—
[
  • 27,438 cases
  • , 41,078 controls
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM008373PSS003904|
African Ancestry|
511 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Tobacco smoking ever vs no—AUROC: 0.6456 [0.59467, 0.69652]R²: 0.08383
Incremental AUROC (full-covars): -0.01967
PGS R2 (no covariates): 0.01985
PGS AUROC (no covariates): 0.42965 [0.37629, 0.483]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008374PSS003905|
East Asian Ancestry|
243 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Tobacco smoking ever vs no—AUROC: 0.72543 [0.64779, 0.80307]R²: 0.18478
Incremental AUROC (full-covars): 0.00769
PGS R2 (no covariates): 0.02947
PGS AUROC (no covariates): 0.59444 [0.50179, 0.6871]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008375PSS003906|
European Ancestry|
5,929 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Tobacco smoking ever vs no—AUROC: 0.59066 [0.5762, 0.60512]R²: 0.03312
Incremental AUROC (full-covars): 0.00637
PGS R2 (no covariates): 0.00344
PGS AUROC (no covariates): 0.52696 [0.51226, 0.54167]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008376PSS003907|
South Asian Ancestry|
699 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Tobacco smoking ever vs no—AUROC: 0.69293 [0.64829, 0.73757]R²: 0.12848
Incremental AUROC (full-covars): 0.00403
PGS R2 (no covariates): 0.00894
PGS AUROC (no covariates): 0.55217 [0.50411, 0.60023]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008377PSS003908|
European Ancestry|
17,150 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Tobacco smoking ever vs no—AUROC: 0.59861 [0.58997, 0.60724]R²: 0.03796
Incremental AUROC (full-covars): 0.00411
PGS R2 (no covariates): 0.00371
PGS AUROC (no covariates): 0.52942 [0.52057, 0.53826]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS003904——
[
  • 150 cases
  • , 361 controls
]
—African unspecified—UKB—
PSS003905——
[
  • 48 cases
  • , 195 controls
]
—East Asian—UKB—
PSS003906——
[
  • 2,751 cases
  • , 3,178 controls
]
—Europeannon-white British ancestryUKB—
PSS003907——
[
  • 169 cases
  • , 530 controls
]
—South Asian—UKB—
PSS003908——
[
  • 6,855 cases
  • , 10,295 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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