Trait: tobacco smoke exposure measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009115
Description Quantification of some aspect of tobacco smoke exposure.
Trait category
Other measurement
Mapped term PMID:29535761

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)
PGS001046
(GBE_BIN_FC40001249)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Past tobacco smoking (Smoked at least once) tobacco smoke exposure measurement 6,169
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001046/ScoringFiles/PGS001046.txt.gz
PGS001047
(GBE_BIN_FC20001249)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Past tobacco smoking (Smoked occasionally) tobacco smoke exposure measurement 2,245
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001047/ScoringFiles/PGS001047.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
PPM007988 PGS001046
(GBE_BIN_FC40001249)
 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 PGS001046
(GBE_BIN_FC40001249)
 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 PGS001046
(GBE_BIN_FC40001249)
 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 PGS001046
(GBE_BIN_FC40001249)
 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 PGS001046
(GBE_BIN_FC40001249)
 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
PPM007993 PGS001047
(GBE_BIN_FC20001249)
 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 PGS001047
(GBE_BIN_FC20001249)
 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 PGS001047
(GBE_BIN_FC20001249)
 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 PGS001047
(GBE_BIN_FC20001249)
 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 PGS001047
(GBE_BIN_FC20001249)
 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)
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)