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. medRxiv (2021) Preprint
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
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
[
  • 27,438 cases
  • , 41,078 controls
]
European white British ancestry 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
PPM008373 PSS003904|
African Ancestry|
511 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.6456 [0.59467, 0.69652] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008374 PSS003905|
East Asian Ancestry|
243 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.72543 [0.64779, 0.80307] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008375 PSS003906|
European Ancestry|
5,929 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.59066 [0.5762, 0.60512] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008376 PSS003907|
South Asian Ancestry|
699 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.69293 [0.64829, 0.73757] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008377 PSS003908|
European Ancestry|
17,150 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.59861 [0.58997, 0.60724] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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