We are searching for genetic loci that contribute to the predisposition to alcoholism and related behaviors by conducting genetic linkage and mapping analyses using both whole genome scanning [positional cloning] as well as the candidate gene approach. This report describes positional cloning activities. A marker panel was used consisting of >500 STR loci spanning all of the non-sex chromosomes at an average interval less than 10 centimorgans. Linkage was performed in SW American Indians and Finns, and a whole genome scan on a Plains Indian dataset is under way in collaboration with Peter Nurnberg. In Southwestern American Indians, the best evidence for linkage was seen with D11S1984 on chromosome 11p, in close proximity to several candidate genes with neurobiological functions. These candidate genes include the DRD4 dopamine receptor gene, the tyrosine hydroxylase gene, and the tryptophan hydroxylase gene. Good evidence for linkage was also seen with D4S3242 on chromosome 4p, nearby the beta1 GABA receptor gene. The chromosome 11 findings were followed up by genotyping a high resolution map on an expanded sample of subjects from the same Southwestern Indian population. The high resolution genetic map includes polymorphisms within the DRD4 and tyrosine hydroxylase genes as well as STR markers closely linked to these candidate genes. In Finns, association between alcohol dependence and Y-chromosomes was statistically significant. Interestingly, there is no association between Y- chromosomes and antisocial personality disorder after the comorbid effects of alcohol dependence were removed. However, we find evidence for genetic linkage and association between antisocial personality disorder (ASPD) occurring with alcoholism and the chromosome 6 serotonin receptor gene HTR1B. We also find evidence for linkage and association between ASPD with alcoholism and a polymorphism in the closely linked marker locus D6S286. These findings are confirmed by multipoint linkage analyses and by independent observations in the Southwestern Indian sample. In a two-stage full autosomal genome linkage scan on Finnish families, two hundred eighty two individuals are being genotyped for a panel of 256 microsatellite loci. These marker loci span the autosomal genome at an average density of 13.2 cM (largest gap = 25 cM). The 282 individuals belong to 112 informative full sibships from 89 pedigrees. Most loci in this panel segregate tetra-nucleotide repeat alleles. Two-point and multi-point linkage analyses are being performed on these data using a linkage method that simultaneously utilizes information from unaffected, discordant, and affected sib-pairs. Preliminary analyses indicate that the genomic region most likely to harbor a gene for alcohol dependence resides on chromosome 11p, and there are also linkage signal on chromosomes 4 and 5, at the location of GABAA receptor clusters. Several human and mouse QTLs implicate GABAA receptors. For example, a QTL for an alcoholism-related EEG variant was mapped by the COGA group to the same GABAA gene cluster on Chromosome 4. To isolate gene variants responsible for these signals in the human, we are using hih resolution SBP haplotyping and identifying structural variants in GANAA receptor genes. For chromosome 5, a panel of 50 SNPs is being genotyped, and for chromosome 4, 30. Haplotype localization on the chr5 cluster indicates maximum likelihood at the GABAA alpha6 gene or between this gene and the gene for the gamma 2 subunit, known to be required for alcohol?s action on the GABAA receptor. An Asn385Ser variant was detected at alpha 6 and this variant was shown to be associated with both alcohol and benzodiazepine response.
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