Genome-Wide Association of the Laboratory-Based Nicotine Metabolite Ratio in Three Ancestries.
Metabolic enzyme variation and other patient and environmental characteristics influence smoking behaviors, treatment success, and risk of related disease. Population-specific variation in metabolic genes contributes to challenges in developing and optimizing pharmacogenetic interventions. We applied a custom genome-wide genotyping array for addiction research (Smokescreen), to three laboratory-based studies of nicotine metabolism with oral or venous administration of labeled nicotine and cotinine, to model nicotine metabolism in multiple populations. The trans-3'-hydroxycotinine/cotinine ratio, the nicotine metabolite ratio (NMR), was the nicotine metabolism measure analyzed.



Three hundred twelve individuals of self-identified European, African, and Asian American ancestry were genotyped and included in ancestry-specific genome-wide association scans (GWAS) and a meta-GWAS analysis of the NMR. We modeled natural-log transformed NMR with covariates: principal components of genetic ancestry, age, sex, body mass index, and smoking status.



African and Asian American NMRs were statistically significantly (P values ≤ 5E-5) lower than European American NMRs. Meta-GWAS analysis identified 36 genome-wide significant variants over a 43 kilobase pair region at CYP2A6 with minimum P = 2.46E-18 at rs12459249, proximal to CYP2A6. Additional minima were located in intron 4 (rs56113850, P = 6.61E-18) and in the CYP2A6-CYP2A7 intergenic region (rs34226463, P = 1.45E-12). Most (34/36) genome-wide significant variants suggested reduced CYP2A6 activity; functional mechanisms were identified and tested in knowledge-bases. Conditional analysis resulted in intergenic variants of possible interest (P values < 5E-5).



This meta-GWAS of the NMR identifies CYP2A6 variants, replicates the top-ranked single nucleotide polymorphism from a recent Finnish meta-GWAS of the NMR, identifies functional mechanisms, and provides pan-continental population biomarkers for nicotine metabolism.



This multiple ancestry meta-GWAS of the laboratory study-based NMR provides novel evidence and replication for genome-wide association of CYP2A6 single nucleotide and insertion-deletion polymorphisms. We identify three regions of genome-wide significance: proximal, intronic, and distal to CYP2A6. We replicate the top-ranking single nucleotide polymorphism from a recent GWAS of the NMR in Finnish smokers, identify a functional mechanism for this intronic variant from in silico analyses of RNA-seq data that is consistent with CYP2A6 expression measured in postmortem lung and liver, and provide additional support for the intergenic region between CYP2A6 and CYP2A7.
BioRealm, LLC , Culver City , CA.
James W
JW
Baurley
BioRealm, LLC , Culver City , CA.
Christopher K
CK
Edlund
BioRealm, LLC , Culver City , CA.
Carissa I
CI
Pardamean
BioRealm, LLC , Culver City , CA.
David V
DV
Conti
SRI International , Menlo Park , CA.
Ruth
R
Krasnow
SRI International , Menlo Park , CA.
Harold S
HS
Javitz
Oregon Research Institute , Eugene , OR.
Hyman
H
Hops
Stanford University School of Medicine , Stanford , CA.
Gary E
GE
Swan
University of California, San Francisco School of Medicine , San Francisco , CA.
Neal L
NL
Benowitz
BioRealm, LLC , Culver City , CA.
Andrew W
AW
Bergen
D000328:Adult; D044466:Asian People / Q000235:genetics; D044383:Black People / Q000235:genetics; D065637:Cytochrome P-450 CYP2A6 / Q000235:genetics*; D005260:Female; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D008875:Middle Aged; D009538:Nicotine / Q000235:genetics* / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D012907:Smoking / Q000235:genetics*; D014029:Tobacco Use Disorder / Q000235:genetics*; D044465:White People / Q000235:genetics; D055815:Young Adult
D009538:Nicotine; D065637:Cytochrome P-450 CYP2A6