Polygenic Score (PGS) ID: PGS001047

Predicted Trait
Reported Trait Past tobacco smoking (Smoked occasionally)
Mapped Trait(s) tobacco smoke exposure measurement (EFO_0009115)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20001249
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_FC20001249
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,245
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
—
[
  • 36,666 cases
  • , 212,576 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
PPM007993 PSS003805|
African Ancestry|
5,926 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked occasionally) — AUROC: 0.58093 [0.55858, 0.60327] R²: 0.01829
Incremental AUROC (full-covars): -0.05921
PGS R2 (no covariates): 0.00064
PGS AUROC (no covariates): 0.49651 [0.47342, 0.51961]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007994 PSS003806|
East Asian Ancestry|
1,577 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked occasionally) — AUROC: 0.68329 [0.63933, 0.72724] R²: 0.07701
Incremental AUROC (full-covars): 0.00274
PGS R2 (no covariates): 0.00038
PGS AUROC (no covariates): 0.50548 [0.45563, 0.55533]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007995 PSS003807|
European Ancestry|
22,450 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked occasionally) — AUROC: 0.58823 [0.5791, 0.59736] R²: 0.0603
Incremental AUROC (full-covars): 0.00694
PGS R2 (no covariates): 0.00257
PGS AUROC (no covariates): 0.52958 [0.5197, 0.53945]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007996 PSS003808|
South Asian Ancestry|
7,192 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked occasionally) — AUROC: 0.70233 [0.68241, 0.72224] R²: 0.09047
Incremental AUROC (full-covars): 0.00461
PGS R2 (no covariates): 0.00302
PGS AUROC (no covariates): 0.53831 [0.51304, 0.56357]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007997 PSS003809|
European Ancestry|
62,410 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Past tobacco smoking (Smoked occasionally) — AUROC: 0.59787 [0.59205, 0.6037] R²: 0.06
Incremental AUROC (full-covars): 0.01786
PGS R2 (no covariates): 0.00491
PGS AUROC (no covariates): 0.54138 [0.53499, 0.54777]		 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
PSS003805 — —
[
  • 743 cases
  • , 5,183 controls
]
 — African unspecified — UKB —
PSS003806 — —
[
  • 152 cases
  • , 1,425 controls
]
 — East Asian — UKB —
PSS003807 — —
[
  • 4,013 cases
  • , 18,437 controls
]
 — European non-white British ancestry UKB —
PSS003808 — —
[
  • 570 cases
  • , 6,622 controls
]
 — South Asian — UKB —
PSS003809 — —
[
  • 9,036 cases
  • , 53,374 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)