Even when all three programs detect a CNV, they often report different starting and ending points for the same CNV segment, which leads to computational challenges in combining CNV reports. There is a lack of consensus in the research community regarding this issue and therefore, in addition to studying the CNV as a deletion or duplication, we adopted an additional straightforward approach for association. First, SNP probes and intensity-only probes were used to detect CNVs by multiple programs. Second, a change of copy number at a particular probe was considered detected when all CNV programs reported CNV segments that cover the probe. Third, association between alcohol dependence and each probe (assigned the same copy number as the CNV) was examined. For instance, if a CNV (duplication or deletion) was detected in region X, using probes (SNP or intensity probes) A, B C, D, E, F and G by three different programs, then the results from the three programs for each probe were compared against each other (See Supplementary Figure 1). If agreement was reached among three programs, then the CNV
