A Systematic single nucleotide polymorphism screen to fine-map alcohol dependence genes on chromosome 7 identifies association with a novel susceptibility gene ACN9.
BACKGROUND
Chromosome 7 has shown consistent evidence of linkage with a variety of phenotypes related to alcohol dependence in the Collaborative Study on the Genetics of Alcoholism (COGA) project. With a sample of 262 densely affected families, a peak logarithm of odds (LOD) score for alcohol dependence of 2.9 was observed at D7S1799. The LOD score in the region increased to 4.1 when a subset of the sample was genotyped with the Illumina Linkage III panel for the Genetic Analysis Workshop 14 (GAW14). To follow up on this linkage region, we systematically screened single nucleotide polymorphisms (SNPs) across a 2 LOD support interval surrounding the alcohol dependence peak.


METHODS
The SNPs were selected from the HapMap Phase I CEPH data to tag linkage disequilibrium bins across the region. Across the 18-Mb region, genotyped by the Center for Inherited Disease Research (CIDR), 1340 SNPs were analyzed. Family-based association analyses were performed on a sample of 1172 individuals from 217 Caucasian families.


RESULTS
Eight SNPs showed association with alcohol dependence at p < .01. Four of the eight most significant SNPs were located in or very near the ACN9 gene. We conducted additional genotyping across ACN9 and identified multiple variants with significant evidence of association with alcohol dependence.


CONCLUSIONS
These analyses suggest that ACN9 is involved in the predisposition to alcohol dependence. Data from yeast suggest that ACN9 is involved in gluconeogenesis and the assimilation of ethanol or acetate into carbohydrate.
Dick
Danielle M
DM
Washington University in St. Louis, St. Louis, Missouri, USA. ddick@vcu.edu
Aliev
Fazil
F
Wang
Jen C
JC
Saccone
Scott
S
Hinrichs
Anthony
A
Bertelsen
Sarah
S
Budde
John
J
Saccone
Nancy
N
Foroud
Tatiana
T
Nurnberger
John
J
Xuei
Xiaoling
X
Conneally
P M
PM
Schuckit
Marc
M
Almasy
Laura
L
Crowe
Raymond
R
Kuperman
Samuel
S
Kramer
John
J
Tischfield
Jay A
JA
Hesselbrock
Victor
V
Edenberg
Howard J
HJ
Porjesz
Bernice
B
Rice
John P
JP
Bierut
Laura
L
Goate
Alison
A
D000328:Adult; D000437:Alcoholism / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D002897:Chromosomes, Human, Pair 7; D005192:Family Health; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*