Polygenic Score (PGS) ID: PGS004922

Predicted Trait
Reported Trait Nicotine metabolite ratio
Mapped Trait(s) nicotine metabolite ratio (EFO_0007794)
Released in PGS Catalog: June 27, 2024
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Score Details

Score Construction
PGS Name wGRS_AFR
Development Method
Name Backward stepwise regression
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 12
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000655
Citation (link to publication) El-Boraie A et al. Clin Pharmacol Ther (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 88.8%
European: 5.8%
East Asian: 5.4%
2,667 individuals (100%)
Score Development/Training
African: 100%
940 individuals (100%)
PGS Evaluation
African: 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)
GWAS Catalog: GCST004976
Europe PMC: 28921760
 954 individuals African American or Afro-Caribbean KIS3, PNAT2
Europe PMC: 16041240
 45 individuals African American or Afro-Caribbean NR
Europe PMC: 16041240
 156 individuals European NR
Europe PMC: 16041240
 144 individuals East Asian
(Chinese, Japanese, Korean)		 NR
Europe PMC: 15592323
 96 individuals African unspecified NR
Europe PMC: 15993850
 96 individuals African American or Afro-Caribbean NR
Europe PMC: 18360915
 280 individuals African unspecified NR
Europe PMC: 19365400
 896 individuals African American or Afro-Caribbean NR
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
—
[
  • 940 cases
]
,
41.81 % Male samples
 African American or Afro-Caribbean, Sub-Saharan African KIS3, PNAT2 PNAT2 included heavy smokers (≥10 Cigarettes per day). KIS3 participants included light smokers (≤10 cigarettes per day). — — African American or Afro-Caribbean, Sub-Saharan African —

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
PPM021405 PSS011734|
African Ancestry|
216 individuals
 PGP000655 |
El-Boraie A et al. Clin Pharmacol Ther (2021)
 Reported Trait: Nicotine metabolite ratio — — R²: 0.343 — Log transformed nicotine metabolite ratio
PPM021406 PSS011734|
African Ancestry|
216 individuals
 PGP000655 |
El-Boraie A et al. Clin Pharmacol Ther (2021)
 Reported Trait: Nicotine metabolite ratio — — R²: 0.393 Sex, age, body mass index Log transformed nicotine metabolite ratio
PPM021407 PSS011734|
African Ancestry|
216 individuals
 PGP000655 |
El-Boraie A et al. Clin Pharmacol Ther (2021)
 Reported Trait: Nicotine metabolism (slow vs normal) — AUROC: 0.77 [0.71, 0.84] — — CYP2A6 Slow metabolisers = NMR <0.31, CYP2A6 normal metabolisers = NMR ≥0.31
PPM021408 PSS011733|
Multi-ancestry (including European)|
1,187 individuals
 PGP000655 |
El-Boraie A et al. Clin Pharmacol Ther (2021)
 Reported Trait: Nicotine metabolite ratio — — R²: 0.3 — Log transformed nicotine metabolite ratio, 50.6% 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
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 —
PSS011734 Combination of heavy and light smokers. —
[
  • 216 cases
]
 — African unspecified — Q2L —