Trait: smoking cessation

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004319
Description Discontinuation of the habit of smoking, the inhaling and exhaling of tobacco smoke.
Trait category
Biological process
Mapped terms 2 mapped terms
  • MeSH:D016540
  • NCIt:C17427

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001374
(GBE_INI2897)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Age stopped smoking smoking cessation 663
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001374/ScoringFiles/PGS001374.txt.gz
PGS003369
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AFR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking cessation smoking cessation 1,193,789
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003369/ScoringFiles/PGS003369.txt.gz
PGS003370
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AMR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking cessation smoking cessation 1,109,663
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003370/ScoringFiles/PGS003370.txt.gz
PGS003371
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EAS)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking cessation smoking cessation 859,229
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003371/ScoringFiles/PGS003371.txt.gz
PGS003372
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EUR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking cessation smoking cessation 1,055,802
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003372/ScoringFiles/PGS003372.txt.gz

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) 		Evaluated Score 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
PPM007025 PGS001374
(GBE_INI2897)
 PSS006876|
African Ancestry|
565 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.21854 [0.20078, 0.2363]
Incremental R2 (full-covars): 0.00162
PGS R2 (no covariates): 0.00424 [0.00109, 0.00739]		 age, sex, UKB array type, Genotype PCs —
PPM007026 PGS001374
(GBE_INI2897)
 PSS006877|
East Asian Ancestry|
128 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.19019 [0.15672, 0.22365]
Incremental R2 (full-covars): 0.00459
PGS R2 (no covariates): 0.00658 [-0.00106, 0.01421]		 age, sex, UKB array type, Genotype PCs —
PPM007027 PGS001374
(GBE_INI2897)
 PSS006878|
European Ancestry|
6,992 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.14667 [0.13855, 0.15479]
Incremental R2 (full-covars): -0.00089
PGS R2 (no covariates): 0.0003 [-0.00013, 0.00074]		 age, sex, UKB array type, Genotype PCs —
PPM007028 PGS001374
(GBE_INI2897)
 PSS006879|
South Asian Ancestry|
601 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.18218 [0.16673, 0.19764]
Incremental R2 (full-covars): -0.00589
PGS R2 (no covariates): 0.00251 [0.0003, 0.00472]		 age, sex, UKB array type, Genotype PCs —
PPM007029 PGS001374
(GBE_INI2897)
 PSS006880|
European Ancestry|
16,789 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age stopped smoking — — R²: 0.14537 [0.14045, 0.15029]
Incremental R2 (full-covars): 0.0003
PGS R2 (no covariates): 0.00121 [0.00068, 0.00173]		 age, sex, UKB array type, Genotype PCs —
PPM016225 PGS003369
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AFR)
 PSS010064|
African Ancestry|
2,199 individuals
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Reported Trait: Smoking cessation OR: 0.276 (0.206) — ∆ AUC: 0.005
∆ R^2: 0.005		 — —
PPM016226 PGS003370
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AMR)
 PSS010061|
Hispanic or Latin American Ancestry|
1,132 individuals
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Reported Trait: Smoking cessation OR: 0.767 (0.488) — ∆ R^2: 0.007
∆ AUC: 0.009		 — —
PPM016227 PGS003371
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EAS)
 PSS010062|
East Asian Ancestry|
525 individuals
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Reported Trait: Smoking cessation OR: 0.034 (0.166) — ∆ AUC: -0.001
∆ R^2: 0.00039		 — —
PPM016228 PGS003372
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EUR)
 PSS010063|
European Ancestry|
6,092 individuals
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Reported Trait: Smoking cessation OR: 1.02 (0.139) — ∆ AUC: 0.049
∆ R^2: 0.026		 — —

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
PSS006876 — — 565 individuals — African unspecified — UKB —
PSS006877 — — 128 individuals — East Asian — UKB —
PSS006878 — — 6,992 individuals — European non-white British ancestry UKB —
PSS006879 — — 601 individuals — South Asian — UKB —
PSS006880 — — 16,789 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS010061 — — 1,132 individuals — Hispanic or Latin American — Add Health —
PSS010062 — — 525 individuals — East Asian — Add Health —
PSS010063 — — 6,092 individuals — European — Add Health —
PSS010064 — — 2,199 individuals — African unspecified — Add Health —