Polygenic Score (PGS) ID: PGS004909

Predicted Trait
Reported Trait Nicotine metabolite ratio
Mapped Trait(s) nicotine metabolite ratio (EFO_0007794)
Released in PGS Catalog: May 22, 2024
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Score Details

Score Construction
PGS Name EUR_wGRS7
Development Method
Name Genome-wide significant SNPs, conditional analysis
Parameters NR
Variants
Original Genome Build NR
Number of Variants 8
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000641
Citation (link to publication) El-Boraie A et al. Addict Biol (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
2,451 individuals (100%)
PGS Evaluation
European: 50%
Multi-ancestry (including European): 50%
  • African
  • European
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30815984
 933 individuals European PNAT2
GWAS Catalog: GCST009922
Europe PMC: 26407342
 1,518 individuals European FINRISK, FinnTwin12, FinnTwin16, YFS

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
PPM021363 PSS011703|
European Ancestry|
196 individuals
 PGP000641 |
El-Boraie A et al. Addict Biol (2019)
 Reported Trait: Nicotine metabolite ratio in treatment-seeking smokers — — R²: 0.411 Sex, age, body mass index —
PPM021364 PSS011703|
European Ancestry|
196 individuals
 PGP000641 |
El-Boraie A et al. Addict Biol (2019)
 Reported Trait: Nicotine metabolism (slow vs normal) in treatment seeking smokers — AUROC: 0.78 [0.71, 0.85] — — Slow metabolisers with a nicotine metabolite ratio (NMR) <0.31 vs normal metabolisers with a NMR ≥0.31.
PPM021365 PSS011703|
European Ancestry|
196 individuals
 PGP000641 |
El-Boraie A et al. Addict Biol (2019)
 Reported Trait: Nicotine metabolism (slow vs normal) in treatment seeking smokers — AUROC: 0.78 [0.71, 0.86] — — Slow metabolisers with a nicotine metabolite ratio (NMR) <0.26 vs normal metabolisers with a NMR ≥0.26.
PPM021409 PSS011733|
Multi-ancestry (including European)|
1,187 individuals
 PGP000655 |
El-Boraie A et al. Clin Pharmacol Ther (2021)
|Ext.		 Reported Trait: Nicotine metabolite ratio — — R²: 0.261 — Log transformed nicotine metabolite ratio, 49.4% overlap with score development and testing samples

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
PSS011703 Participants were treatment seeking smokers. Using a nicotine metabolite ratio (NMR) cut-point of 0.31, individuals with slow nicotine metabolism were defined as having a NMR <0.31 whilst individuals with normal rates of nicotine metabolism were defined as having a NMR ≥0.31. Using a nicotine metabolite ratio (NMR) cut-point of 0.26, individuals with slow nicotine metabolism were defined as having a NMR <0.26 whilst individuals with normal rates of nicotine metabolism were defined as having a NMR ≥0.26. — 196 individuals — European — Q2L —
PSS011733 Participants were smokers. — 1,187 individuals — African American or Afro-Caribbean, Sub-Saharan African, European African American or Afro-Caribbean and Sub-Saharan African = 954, European = 933 KIS3, PNAT2 —