PGS Catalog - PGS001911 / Ever smoked (Polygenic Score)

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

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Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)	Phenotype Definitions & Methods	Age of Study Participants	Participant Follow-up Time	Additional Ancestry Description	Additional Sample/Cohort Information
—	391,124 individuals	European	UKB	—	—	—	UK (+ Ireland)	—

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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.

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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	—
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	—
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	—

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Evaluated Samples

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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	—
PSS008060	—	—	1,787 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008283	—	—	6,176 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008505	—	—	1,152 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	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	—
PSS009403	—	—	19,926 individuals	—	European	UK (+ Ireland)	UKB	—

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