PGS Publication: PGP000717

Publication Information (EuropePMC)
Title Polygenic scores for tobacco use provide insights into systemic health risks in a diverse EHR-linked biobank in Los Angeles.
PubMed ID 38238290(Europe PMC)
doi 10.1038/s41398-024-02743-z
Publication Date Jan. 18, 2024
Journal Transl Psychiatry
Author(s) Venkateswaran V, Boulier K, Ding Y, Johnson R, Bhattacharya A, Pasaniuc B.
Released in PGS Catalog: March 17, 2025

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003360
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EUR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking initiation smoking initiation 1,055,915
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003360/ScoringFiles/PGS003360.txt.gz
PGS003364
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_EUR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Age of smoking initiation age at initiation of smoking 1,055,960
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003364/ScoringFiles/PGS003364.txt.gz
PGS003368
(GSCAN_CigDay_2022_PRS_WEIGHTS_EUR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Cigarettes smoked per day cigarettes per day measurement 1,055,811
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003368/ScoringFiles/PGS003368.txt.gz
PGS003369
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AFR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking cessation smoking cessation 1,193,789
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003369/ScoringFiles/PGS003369.txt.gz
PGS003372
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EUR)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking cessation smoking cessation 1,055,802
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003372/ScoringFiles/PGS003372.txt.gz
PGS002037
(portability-ldpred2_318)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Tobacco use disorder nicotine dependence 847,691
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002037/ScoringFiles/PGS002037.txt.gz
PGS003359
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EAS)
 PGP000410 |
Saunders GRB et al. Nature (2022)
 Smoking initiation smoking initiation 859,206
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003359/ScoringFiles/PGS003359.txt.gz

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) 		Evaluated Score 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
PPM022466 PGS002037
(portability-ldpred2_318)
 PSS011952|
European Ancestry|
15,780 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder OR: 1.2 [1.16, 1.24] — — — —
PPM022467 PGS002037
(portability-ldpred2_318)
 PSS011953|
East Asian Ancestry|
2,377 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder OR: 1.19 [1.11, 1.28] — — — —
PPM022468 PGS002037
(portability-ldpred2_318)
 PSS011954|
Hispanic or Latin American Ancestry|
4,412 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder OR: 1.18 [1.06, 1.31] — — — —
PPM022469 PGS003360
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EUR)
 PSS011952|
European Ancestry|
15,780 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder β: -0.34 (0.02) — — — —
PPM022470 PGS003364
(GSCAN_AgeSmk_2022_PRS_WEIGHTS_EUR)
 PSS011952|
European Ancestry|
15,780 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder β: 0.14 (0.017) — — — —
PPM022471 PGS003368
(GSCAN_CigDay_2022_PRS_WEIGHTS_EUR)
 PSS011952|
European Ancestry|
15,780 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder β: -0.11 (0.018) — — — —
PPM022472 PGS003372
(GSCAN_SmkCes_2022_PRS_WEIGHTS_EUR)
 PSS011952|
European Ancestry|
15,780 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder β: -0.11 (0.019) — — — —
PPM022473 PGS003359
(GSCAN_SmkInit_2022_PRS_WEIGHTS_EAS)
 PSS011953|
East Asian Ancestry|
2,377 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder β: -0.22 (0.06) — — — —
PPM022474 PGS003369
(GSCAN_SmkCes_2022_PRS_WEIGHTS_AFR)
 PSS011951|
African Ancestry|
1,633 individuals
 PGP000717 |
Venkateswaran V et al. Transl Psychiatry (2024)
|Ext.		 Reported Trait: Tobacco use disorder β: -0.18 (0.06) — — — —

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
PSS011953 — — 2,377 individuals — East Asian — UCLA T1
PSS011954 — — 4,412 individuals — Hispanic or Latin American — UCLA T1
PSS011951 — — 1,633 individuals — African American or Afro-Caribbean — UCLA T1
PSS011952 — — 15,780 individuals — European — UCLA T1