Polygenic Score (PGS) ID: PGS002037

Predicted Trait
Reported Trait Tobacco use disorder
Mapped Trait(s) nicotine dependence (EFO_0003768)
Additional Trait Information psychiatric disorders
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_318
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 847,691
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
PPM011163 PSS009300|
European Ancestry|
19,400 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.0741 [0.0601, 0.0881] sex, age, birth date, deprivation index, 16 PCs —
PPM011164 PSS009074|
European Ancestry|
4,022 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.0253 [-0.0056, 0.0563] sex, age, birth date, deprivation index, 16 PCs —
PPM011166 PSS008402|
Greater Middle Eastern Ancestry|
1,180 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.043 [-0.0146, 0.1003] sex, age, birth date, deprivation index, 16 PCs —
PPM011167 PSS008182|
South Asian Ancestry|
6,249 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.0598 [0.035, 0.0845] sex, age, birth date, deprivation index, 16 PCs —
PPM011168 PSS007967|
East Asian Ancestry|
1,800 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.0244 [-0.0221, 0.0708] sex, age, birth date, deprivation index, 16 PCs —
PPM011169 PSS007748|
African Ancestry|
2,445 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.0244 [-0.0154, 0.0642] sex, age, birth date, deprivation index, 16 PCs —
PPM011170 PSS008852|
African Ancestry|
3,876 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): -0.0199 [-0.0514, 0.0117] sex, age, birth date, deprivation index, 16 PCs —
PPM011165 PSS008628|
European Ancestry|
6,548 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Tobacco use disorder — — Partial Correlation (partial-r): 0.0812 [0.0571, 0.1053] 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
PSS007748 — — 2,445 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009074 — — 4,022 individuals — European Poland (NE Europe) UKB —
PSS008402 — — 1,180 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009300 — — 19,400 individuals — European UK (+ Ireland) UKB —
PSS008852 — — 3,876 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008182 — — 6,249 individuals — South Asian India (South Asia) UKB —
PSS008628 — — 6,548 individuals — European Italy (South Europe) UKB —
PSS007967 — — 1,800 individuals — East Asian China (East Asia) UKB —