A recently submitted manuscript (Bierut et al., in press) describes results from the Study of Addiction: Genetics and Environment consortium, which has performed a GWAS using the phenotype of alcohol dependence in a sample of cases and controls ascertained through three different studies (dbGaP accession phs000092.v1.p1). One of the three studies was COGA, with 612 EA alcohol dependent individuals and 413 EA controls included in both our analysis and the SAGE analyses. Two other studies also provided EA cases: one recruited cases with nicotine dependence through a population screening design (n=343 alcohol dependent EA cases) and the other recruited cases with cocaine dependence through treatment centers (n=278 alcohol dependent EA cases). While 52% of EA COGA subjects also reported another substance dependence, the inclusion of cases in the SAGE analysis recruited for different primary diagnoses will likely introduce a number of novel genes contributing to alcohol dependence and another comorbid condition, either nicotine dependence or cocaine dependence. For this reason, while we might hope for some commonality between the results from the COGA and SAGE studies due to the overlapping samples, it is not surprising that in practice results of GWAS from each study are quite different.
