Polygenic Score (PGS) ID: PGS001830

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-PLR_318
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 13,838
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
PPM009533 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): 0.0557 [0.0416, 0.0697] sex, age, birth date, deprivation index, 16 PCs
PPM009534 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): 0.0092 [-0.0218, 0.0401] sex, age, birth date, deprivation index, 16 PCs
PPM009535 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): 0.0603 [0.0361, 0.0845] sex, age, birth date, deprivation index, 16 PCs
PPM009536 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): 0.0076 [-0.05, 0.0651] sex, age, birth date, deprivation index, 16 PCs
PPM009537 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): 0.0361 [0.0113, 0.0609] sex, age, birth date, deprivation index, 16 PCs
PPM009538 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): 0.0404 [-0.0061, 0.0867] sex, age, birth date, deprivation index, 16 PCs
PPM009539 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): -0.0084 [-0.0482, 0.0314] sex, age, birth date, deprivation index, 16 PCs
PPM009540 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): 0.0032 [-0.0284, 0.0347] 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
PSS008402 1,180 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009074 4,022 individuals European Poland (NE Europe) UKB
PSS009300 19,400 individuals European UK (+ Ireland) UKB
PSS008628 6,548 individuals European Italy (South Europe) UKB
PSS008182 6,249 individuals South Asian India (South Asia) UKB
PSS008852 3,876 individuals African unspecified Nigeria (West Africa) UKB
PSS007967 1,800 individuals East Asian China (East Asia) UKB