Polygenic Score (PGS) ID: PGS001046

Predicted Trait
Reported Trait Past tobacco smoking (Smoked at least once)
Mapped Trait(s) tobacco smoke exposure measurement (EFO_0009115)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC40001249
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_BIN_FC40001249
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,169
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%
249,242 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
—
[
  • 143,862 cases
  • , 105,380 controls
]
 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
PPM007988 PSS003919|
African Ancestry|
5,926 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked at least once) — AUROC: 0.66013 [0.64587, 0.67439] R²: 0.09483
Incremental AUROC (full-covars): -0.00813
PGS R2 (no covariates): 0.00042
PGS AUROC (no covariates): 0.48937 [0.47391, 0.50483]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007989 PSS003920|
East Asian Ancestry|
1,577 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked at least once) — AUROC: 0.67494 [0.64523, 0.70464] R²: 0.12932
Incremental AUROC (full-covars): 0.00219
PGS R2 (no covariates): 0.00369
PGS AUROC (no covariates): 0.53021 [0.49937, 0.56105]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007990 PSS003921|
European Ancestry|
22,450 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked at least once) — AUROC: 0.59705 [0.58934, 0.60476] R²: 0.03706
Incremental AUROC (full-covars): 0.01391
PGS R2 (no covariates): 0.00997
PGS AUROC (no covariates): 0.55171 [0.54388, 0.55954]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007991 PSS003922|
South Asian Ancestry|
7,192 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked at least once) — AUROC: 0.74129 [0.72884, 0.75373] R²: 0.20316
Incremental AUROC (full-covars): 0.00744
PGS R2 (no covariates): 0.00794
PGS AUROC (no covariates): 0.54619 [0.53131, 0.56108]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007992 PSS003923|
European Ancestry|
62,410 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked at least once) — AUROC: 0.61588 [0.61146, 0.6203] R²: 0.05447
Incremental AUROC (full-covars): 0.01564
PGS R2 (no covariates): 0.01446
PGS AUROC (no covariates): 0.55938 [0.55485, 0.56391]		 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
PSS003919 — —
[
  • 2,092 cases
  • , 3,834 controls
]
 — African unspecified — UKB —
PSS003920 — —
[
  • 495 cases
  • , 1,082 controls
]
 — East Asian — UKB —
PSS003921 — —
[
  • 14,474 cases
  • , 7,976 controls
]
 — European non-white British ancestry UKB —
PSS003922 — —
[
  • 1,964 cases
  • , 5,228 controls
]
 — South Asian — UKB —
PSS003923 — —
[
  • 35,715 cases
  • , 26,695 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)