Polygenic Score (PGS) ID: PGS002126

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-ldpred2_ever_smoked
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 931,635
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
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) —

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
PPM011863 PSS009403|
European Ancestry|
19,926 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever smoked — — Partial Correlation (partial-r): 0.1431 [0.1295, 0.1567] sex, age, birth date, deprivation index, 16 PCs —
PPM011870 PSS008951|
African Ancestry|
3,854 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever smoked — — Partial Correlation (partial-r): 0.0413 [0.0096, 0.0728] sex, age, birth date, deprivation index, 16 PCs —
PPM011864 PSS009177|
European Ancestry|
4,104 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever smoked — — Partial Correlation (partial-r): 0.1539 [0.1238, 0.1837] sex, age, birth date, deprivation index, 16 PCs —
PPM011865 PSS008731|
European Ancestry|
6,620 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever smoked — — Partial Correlation (partial-r): 0.1402 [0.1165, 0.1638] sex, age, birth date, deprivation index, 16 PCs —
PPM011866 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): 0.0972 [0.0392, 0.1546] sex, age, birth date, deprivation index, 16 PCs —
PPM011867 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): 0.0991 [0.0743, 0.1237] sex, age, birth date, deprivation index, 16 PCs —
PPM011868 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): 0.1148 [0.0685, 0.1606] sex, age, birth date, deprivation index, 16 PCs —
PPM011869 PSS007847|
African Ancestry|
2,443 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ever smoked — — Partial Correlation (partial-r): 0.0851 [0.0454, 0.1245] 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 —
PSS008951 — — 3,854 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008505 — — 1,152 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009177 — — 4,104 individuals — European Poland (NE Europe) UKB —
PSS008731 — — 6,620 individuals — European Italy (South Europe) 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 —