Biology and Biomedical Sciences: Human and Statistical Genetics
Date of Award
Doctor of Philosophy (PhD)
Chair and Committee
Alison M Goate
Genome-wide association studies: GWAS) have identified common variation in the CHRNA5-CHRNA3-CHRNB4 and CHRNA6-CHRNB3 gene clusters that contribute to nicotine dependence. However, the role of rare variation in risk for substance dependence in these nicotinic receptor genes has not been studied.
In order to investigate the role rare variants play in the development of nicotine dependence, we undertook pooled sequencing of the coding regions and flanking sequence of the CHRNA5, CHRNA3, CHRNB4, CHRNA6 and CHRNB3 genes in 710 African Americans: 461 nicotine dependent: ND) cases and 249 smokers with no symptoms of dependence: controls)) and 2055 European Americans: 1062 ND cases and 993 controls) from the Collaborative Study of the Genetics of Nicotine Dependence: COGEND). Carrier status of individuals harboring rare non-synonymous variants at conserved sites in each of these genes was then compared in cases and controls to test for an association with nicotine dependence. We find a reduced risk for nicotine dependence among carriers of missense variants at conserved residues in CHRNB4 in African Americans and European Americans.
We next aimed to determine whether rare genetic variation in these genes influence risk for developing alcohol or cocaine dependence, two conditions highly comorbid with nicotine dependence. We undertook pooled sequencing of the coding regions and flanking sequence of the CHRNA5, CHRNA3, CHRNB4, CHRNA6 and CHRNB3 genes in 287 African Americans: 147 DSM-IV alcohol dependent cases and 140 controls) and 1028 European Americans: 480 DSM-IV alcohol dependent cases and 548 controls) individuals from the Collaborative Study of the Genetics of Alcoholism: COGA). For European Americans, we find increased DSM-IV cocaine dependence symptoms: famSKAT p= 2x10-4) and increased DSM-IV alcohol dependence symptoms: famSKAT p= 5x10-4) among carriers of missense variants in CHRNB3. For African Americans, we find decreased cocaine dependence symptoms among carriers of missense variants in CHRNA3: famSKAT p= 0.006).
Finally, we sought to determine the functional impact of rare variants in CHRNB4 harbored by individuals in these two cohorts. A total of 10 variants in CHRNB4 observed in the COGEND cohort were investigated. One variant in CHRNA3 was also functionally tested as it is high linkage disequilibrium with another rare missense variant in CHRNB4. We find several variants that alter cellular response either to nicotine or acetylcholine as well as many variants that alter cell-surface protein expression as measured by cell-surface ELISA without altering either CHRNB4 mRNA or total β4 protein as measured by western blot. Further, when we integrate these in vitro findings into a model of association with nicotine dependence related traits, we improve the association, suggesting that the success of future association analyses in these and potentially many other genes across the genome, may depend greatly on functional assessment of observed genetic variation.
Haller, Gabriel Emanuel, "Identification and Characterization of Rare Variants in Cholinergic Nicotinic Receptor Genes and their Contribution to Substance Dependence" (2013). All Theses and Dissertations (ETDs). 1133.