Polygenic Score (PGS) ID: PGS002233

Predicted Trait
Reported Trait Nicotine metabolite ratio
Mapped Trait(s) nicotine metabolite ratio (EFO_0007794)
Released in PGS Catalog: Dec. 10, 2021
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Score Details

Score Construction
PGS Name PRS27_NMR
Development Method
Name PRSice
Parameters P < 5e-8, r^2 < 0.10, minor allele frequency filter = 0.02
Variants
Original Genome Build NR
Number of Variants 27
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000266
Citation (link to publication) Chen LS et al. Pharmacogenomics (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,518 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST009922
Europe PMC: 26407342
 1,518 individuals European FINRISK, FinnTwin12, 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
PPM012703 PSS009499|
European Ancestry|
186 individuals
 PGP000266 |
Chen LS et al. Pharmacogenomics (2018)
 Reported Trait: Log nicotine metabolite ratio (ratio of 3-hydroxycotinine:cotinine) β: 8.04 [3.8, 12.3] — R²: 0.15 — —
PPM012704 PSS009499|
European Ancestry|
186 individuals
 PGP000266 |
Chen LS et al. Pharmacogenomics (2018)
 Reported Trait: Log experimental nicotine metabolite ratio (D2-3-hydroxycotinine:D2-cotinine 4 hours after ingestion of deuterated nicotine) β: 10.9 [7.2, 14.5] — R²: 0.15 — —
PPM012705 PSS009499|
European Ancestry|
186 individuals
 PGP000266 |
Chen LS et al. Pharmacogenomics (2018)
 Reported Trait: Log nicotine metabolism proportion experimental (D2-cotinine/ [D2-nicotine + D2-cotinine] 30 min after ingestion of deuterated nicotine) β: 2.0 [1.22, 2.78] — R²: 0.12 — —

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
PSS009499 — — 186 individuals,
45.7 % Male samples
 Mean = 35.9 years
Sd = 0.37 years		 European — COGEND —