Trait: smoking status measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0006527
Description self-reported binary measure, used to denote whether an individual is currently or has ever been a smoker
Trait category
Other measurement

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 Scoring File (FTP Link)
PGS001127
(GBE_BIN_FC10020116)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Never Smoker smoking status measurement 12,310
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001127/ScoringFiles/PGS001127.txt.gz
PGS001128
(GBE_BIN_FC20020116)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Previous Smoker smoking status measurement 4,348
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001128/ScoringFiles/PGS001128.txt.gz
PGS001129
(GBE_BIN_FC30022506)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Smoking status (ever vs never smokers) smoking status measurement 974
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001129/ScoringFiles/PGS001129.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
PPM008363 PGS001127
(GBE_BIN_FC10020116)
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 PGS001127
(GBE_BIN_FC10020116)
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 PGS001127
(GBE_BIN_FC10020116)
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 PGS001127
(GBE_BIN_FC10020116)
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 PGS001127
(GBE_BIN_FC10020116)
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
PPM008368 PGS001128
(GBE_BIN_FC20020116)
PSS003844|
African Ancestry|
6,390 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Previous Smoker AUROC: 0.62818 [0.61021, 0.64615] : 0.04625
Incremental AUROC (full-covars): -0.00333
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.49819 [0.47898, 0.5174]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008369 PGS001128
(GBE_BIN_FC20020116)
PSS003845|
East Asian Ancestry|
1,661 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Previous Smoker AUROC: 0.70433 [0.66805, 0.74061] PGS R2 (no covariates): 0.00293
: 0.11247
Incremental AUROC (full-covars): -0.00189
PGS AUROC (no covariates): 0.5352 [0.49491, 0.57548]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008370 PGS001128
(GBE_BIN_FC20020116)
PSS003846|
European Ancestry|
24,816 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Previous Smoker AUROC: 0.59213 [0.58495, 0.59931] : 0.03309
Incremental AUROC (full-covars): 0.00528
PGS R2 (no covariates): 0.0046
PGS AUROC (no covariates): 0.53522 [0.5279, 0.54253]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008371 PGS001128
(GBE_BIN_FC20020116)
PSS003847|
South Asian Ancestry|
7,615 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Previous Smoker AUROC: 0.73887 [0.72262, 0.75511] : 0.14448
Incremental AUROC (full-covars): 0.00362
PGS R2 (no covariates): 0.00301
PGS AUROC (no covariates): 0.53352 [0.51394, 0.55311]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008372 PGS001128
(GBE_BIN_FC20020116)
PSS003848|
European Ancestry|
67,212 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Previous Smoker AUROC: 0.61185 [0.60741, 0.61629] : 0.04715
Incremental AUROC (full-covars): 0.01019
PGS R2 (no covariates): 0.0091
PGS AUROC (no covariates): 0.5477 [0.54318, 0.55223]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008373 PGS001129
(GBE_BIN_FC30022506)
PSS003904|
African Ancestry|
511 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.6456 [0.59467, 0.69652] : 0.08383
Incremental AUROC (full-covars): -0.01967
PGS R2 (no covariates): 0.01985
PGS AUROC (no covariates): 0.42965 [0.37629, 0.483]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008374 PGS001129
(GBE_BIN_FC30022506)
PSS003905|
East Asian Ancestry|
243 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.72543 [0.64779, 0.80307] : 0.18478
Incremental AUROC (full-covars): 0.00769
PGS R2 (no covariates): 0.02947
PGS AUROC (no covariates): 0.59444 [0.50179, 0.6871]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008375 PGS001129
(GBE_BIN_FC30022506)
PSS003906|
European Ancestry|
5,929 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.59066 [0.5762, 0.60512] : 0.03312
Incremental AUROC (full-covars): 0.00637
PGS R2 (no covariates): 0.00344
PGS AUROC (no covariates): 0.52696 [0.51226, 0.54167]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008376 PGS001129
(GBE_BIN_FC30022506)
PSS003907|
South Asian Ancestry|
699 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.69293 [0.64829, 0.73757] : 0.12848
Incremental AUROC (full-covars): 0.00403
PGS R2 (no covariates): 0.00894
PGS AUROC (no covariates): 0.55217 [0.50411, 0.60023]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008377 PGS001129
(GBE_BIN_FC30022506)
PSS003908|
European Ancestry|
17,150 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Tobacco smoking ever vs no AUROC: 0.59861 [0.58997, 0.60724] : 0.03796
Incremental AUROC (full-covars): 0.00411
PGS R2 (no covariates): 0.00371
PGS AUROC (no covariates): 0.52942 [0.52057, 0.53826]
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
PSS003908
[
  • 6,855 cases
  • , 10,295 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS003904
[
  • 150 cases
  • , 361 controls
]
African unspecified UKB
PSS003905
[
  • 48 cases
  • , 195 controls
]
East Asian UKB
PSS003906
[
  • 2,751 cases
  • , 3,178 controls
]
European non-white British ancestry UKB
PSS003907
[
  • 169 cases
  • , 530 controls
]
South Asian UKB
PSS003844
[
  • 1,071 cases
  • , 5,319 controls
]
African unspecified UKB
PSS003845
[
  • 237 cases
  • , 1,424 controls
]
East Asian UKB
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)
PSS003846
[
  • 9,959 cases
  • , 14,857 controls
]
European non-white British ancestry UKB
PSS003847
[
  • 962 cases
  • , 6,653 controls
]
South Asian UKB
PSS003848
[
  • 23,931 cases
  • , 43,281 controls
]
European white British ancestry UKB Testing cohort (heldout set)