Polygenic Score (PGS) ID: PGS001127

Predicted Trait
Reported Trait Never Smoker
Mapped Trait(s) smoking status measurement (EFO_0006527)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10020116
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_FC10020116
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 12,310
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%
268,823 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
[
  • 147,638 cases
  • , 121,185 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
PPM008363 PSS003750|
African Ancestry|
6,390 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never Smoker AUROC: 0.65929 [0.64485, 0.67373] : 0.08669
Incremental AUROC (full-covars): -0.00756
PGS R2 (no covariates): 0.00049
PGS AUROC (no covariates): 0.51037 [0.49458, 0.52616]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008364 PSS003751|
East Asian Ancestry|
1,661 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never Smoker AUROC: 0.71794 [0.68736, 0.74851] : 0.15281
Incremental AUROC (full-covars): 0.00859
PGS R2 (no covariates): 0.00367
PGS AUROC (no covariates): 0.53548 [0.50244, 0.56852]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008365 PSS003752|
European Ancestry|
24,816 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never Smoker AUROC: 0.60529 [0.5983, 0.61228] : 0.04529
Incremental AUROC (full-covars): 0.0311
PGS R2 (no covariates): 0.02383
PGS AUROC (no covariates): 0.57608 [0.56899, 0.58317]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008366 PSS003753|
South Asian Ancestry|
7,615 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never Smoker AUROC: 0.7532 [0.74067, 0.76574] : 0.20415
Incremental AUROC (full-covars): 0.01888
PGS R2 (no covariates): 0.01842
PGS AUROC (no covariates): 0.5755 [0.55967, 0.59134]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008367 PSS003754|
European Ancestry|
67,212 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Never Smoker AUROC: 0.62158 [0.61735, 0.62581] : 0.06047
Incremental AUROC (full-covars): 0.03481
PGS R2 (no covariates): 0.03106
PGS AUROC (no covariates): 0.58693 [0.58262, 0.59123]
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
PSS003750
[
  • 4,607 cases
  • , 1,783 controls
]
African unspecified UKB
PSS003751
[
  • 1,302 cases
  • , 359 controls
]
East Asian UKB
PSS003752
[
  • 11,638 cases
  • , 13,178 controls
]
European non-white British ancestry UKB
PSS003753
[
  • 6,019 cases
  • , 1,596 controls
]
South Asian UKB
PSS003754
[
  • 37,219 cases
  • , 29,993 controls
]
European white British ancestry UKB Testing cohort (heldout set)