Alterations in the number of copies of genomic DNA that are common or recurrent among diseased individuals are likely to contain disease-critical genes. Unfortunately, defining common or recurrent copy number alteration (CNA) regions remains a challenge. Moreover, the heterogeneous nature of many diseases requires that we search for common or recurrent CNA regions that affect only some subsets of the samples (without knowledge of the regions and subsets affected), but this is neglected by most methods.