Polygenic Score (PGS) ID: PGS001911

Predicted Trait
Reported Trait Ever smoked
Mapped Trait(s) smoking status measurement (EFO_0006527)
Additional Trait Information lifestyle and environment
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_ever_smoked
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 41,266
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
391,124 individuals European UK (+ Ireland) 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
PPM010171 PSS009403|
European Ancestry|
19,926 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.1289 [0.1152, 0.1426] sex, age, birth date, deprivation index, 16 PCs
PPM010172 PSS009177|
European Ancestry|
4,104 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.1244 [0.0941, 0.1545] sex, age, birth date, deprivation index, 16 PCs
PPM010173 PSS008731|
European Ancestry|
6,620 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.1351 [0.1114, 0.1587] sex, age, birth date, deprivation index, 16 PCs
PPM010175 PSS008283|
South Asian Ancestry|
6,176 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.089 [0.0642, 0.1138] sex, age, birth date, deprivation index, 16 PCs
PPM010176 PSS008060|
East Asian Ancestry|
1,787 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.0908 [0.0443, 0.1368] sex, age, birth date, deprivation index, 16 PCs
PPM010177 PSS007847|
African Ancestry|
2,443 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.0425 [0.0027, 0.0822] sex, age, birth date, deprivation index, 16 PCs
PPM010178 PSS008951|
African Ancestry|
3,854 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.0157 [-0.016, 0.0473] sex, age, birth date, deprivation index, 16 PCs
PPM010174 PSS008505|
Greater Middle Eastern Ancestry|
1,152 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ever smoked Partial Correlation (partial-r): 0.0944 [0.0363, 0.1518] sex, age, birth date, deprivation index, 16 PCs

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
PSS007847 2,443 individuals African American or Afro-Caribbean Carribean UKB
PSS008731 6,620 individuals European Italy (South Europe) UKB
PSS008951 3,854 individuals African unspecified Nigeria (West Africa) UKB
PSS009177 4,104 individuals European Poland (NE Europe) UKB
PSS008505 1,152 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008283 6,176 individuals South Asian India (South Asia) UKB
PSS008060 1,787 individuals East Asian China (East Asia) UKB
PSS009403 19,926 individuals European UK (+ Ireland) UKB