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Chunk #6 — Methods

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Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data.
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The dataset includes a total of 143 nuclear and multigenerational families with 1,614 individuals. There are two kinds of diagnostic definitions of alcohol dependence, labelled in the data set as ALDX1 and ALDX2. ALDX1 alcohol-dependent subjects were defined as those individuals who met both the DSM-III-R (Diagnostic and Statistical Manual of the American Psychiatric Association-Revised) criteria for alcohol dependence and the Feighner criteria for alcoholism. ALDX2 alcohol-dependent subjects were defined as those who met the DSM-IV criteria. Both ALDX1 and ALDX2 alcohol dependence phenotypes are coded in four levels: pure unaffected, never drank, unaffected with some symptoms, and affected. We combined the first three codings as unaffected. We extracted genotyped affected sib pairs with their parents from each pedigree to ensure independence between nuclear families. This yielded 142 affected sib pairs with their parents for a total of 568 individuals for the ALDX1 phenotype for alcoholism. For the ALDX2 phenotype, this yielded 117 affected sib pairs with their parents for a total of 468 individuals. We utilized MAPMAKER/SIBS linkage program [6] to estimate the full multipoint probability of each pair