Trait: nicotine metabolite ratio

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007794
Description quantification of the ratio of 3’-trans-hydroxycotinine to cotinine in a sample, typically in a urine or blood sample
Trait category
Other measurement
Mapped term PMID:26921259

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
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)
PGS002233
(PRS27_NMR)
 PGP000266 |
Chen LS et al. Pharmacogenomics (2018)
 Nicotine metabolite ratio nicotine metabolite ratio 27
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002233/ScoringFiles/PGS002233.txt.gz
PGS002234
(PRS10_NMR)
 PGP000266 |
Chen LS et al. Pharmacogenomics (2018)
 Nicotine metabolite ratio nicotine metabolite ratio 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002234/ScoringFiles/PGS002234.txt.gz
PGS004909
(EUR_wGRS7)
 PGP000641 |
El-Boraie A et al. Addict Biol (2019)
 Nicotine metabolite ratio nicotine metabolite ratio 7
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004909/ScoringFiles/PGS004909.txt.gz
PGS004922
(wGRS_AFR)
 PGP000655 |
El-Boraie A et al. Clin Pharmacol Ther (2021)
 Nicotine metabolite ratio nicotine metabolite ratio 14
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004922/ScoringFiles/PGS004922.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
PPM012703 PGS002233
(PRS27_NMR)
 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 PGS002233
(PRS27_NMR)
 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 PGS002233
(PRS27_NMR)
 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 — —
PPM012706 PGS002234
(PRS10_NMR)
 PSS009499|
European Ancestry|
186 individuals
 PGP000266 |
Chen LS et al. Pharmacogenomics (2018)
 Reported Trait: Log nicotine metabolite ratio (ratio of 3-hydroxycotinine:cotinine) β: 2.38 [0.93, 3.83] — R²: 0.12 — —
PPM012707 PGS002234
(PRS10_NMR)
 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: 2.77 [1.53, 4.0] — R²: 0.093 — —
PPM012708 PGS002234
(PRS10_NMR)
 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: 0.49 [0.22, 0.76] — R²: 0.068 — —
PPM021363 PGS004909
(EUR_wGRS7)
 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 PGS004909
(EUR_wGRS7)
 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 PGS004909
(EUR_wGRS7)
 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 PGS004909
(EUR_wGRS7)
 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
PPM021405 PGS004922
(wGRS_AFR)
 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 PGS004922
(wGRS_AFR)
 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 PGS004922
(wGRS_AFR)
 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 PGS004922
(wGRS_AFR)
 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
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 —
PSS009499 — — 186 individuals,
45.7 % Male samples
 Mean = 35.9 years
Sd = 0.37 years		 European — COGEND —
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 —