Copy number differences between groups

Analogous to differential expression with RNA data, is there a statistic or tool to analyze the frequency of copy number alterations between two groups?

I had imagined this to be a Chi-square performed like 20,000 times (each gene) to see if that particular gene is deleted more than one would expect by chance. However, one cannot assume independence of the events since genes are often recurrently deleted together owing to deletion of large regions.

Any suggestions?