Next Generation Rare Variant Discovery in Multiplex AD Families

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 DESCRIPTION (provided by applicant): Despite the recognition that genetic factors play an important role in susceptibility to alcohol dependence (AD), few genes have been identified to date that have been replicated across studies. Because alcohol dependence is a common disorder affecting one in five men and one in twelve women, the prevailing thought has been that common genetic variants (those with minor allele frequency over 3% in the population) would be the appropriate place to look for susceptibility variants. The common disease/common variant hypothesis has provided the impetus for a large number of genome-wide association studies (GWAS) where a large number of common variants have been assessed. While some studies have reported findings meeting genome-wide significance, often the findings for AD cannot be replicated in other studies. Also, across a wide variety of diseases, it is now recognized that only 2-4% of the variance in disease outcome is explained by these common variants. Recent evidence suggests that variants that are rarer may be more penetrant and potentially explain a greater proportion of disease outcome. Members of families in which multiple cases of AD are seen are most likely to carry a burden of rare and highly penetrant risk variants. Using existing DNA collected from members of high density AD pedigrees, we will use next generation exome sequencing and novel bioinformatics tools to identify rare variation in these high risk individuals and examine the distribution of variants in the families in collaboratin with the Center for Human Genetic Variation at Duke. Aim 1 provides a discovery stage and is facilitated by the use of a subset of pedigrees in which DNA is available for parents and affected offspring. Aim 2 provides confirmation of the discovered variation using a larger set of pedigrees in which the existence of the variants and their distribution within the full pedigree will be determined. By focusing on individuals with a strong genetic burden with multigenerational involvement and including the entire exome, we expect to find rare highly penetrant variants that would be undetectable with other approaches. A search for early developmental indicators of AD susceptibility has revealed both clinical (e.g., presence of childhood conduct disorder) and biological endophenotypes (e.g., reduced amplitude of the P300 component of the event-related potential). In Aim 3,we will examine our newly discovered rare variants in a third generation sample of individuals followed from childhood through young adulthood and for whom developmental trajectories of P300 amplitude are available. This sample includes both high-risk offspring from multiplex for AD families and low-risk controls providing an opportunity to find variants associated with P300 trajectories, an endophenotype that is highly associated with AD.