Across the genome, only four regions with copy number (CN) alterations were determined to be preferentially enriched in recurrent, compared to primary, tumors, including preferential CN loss of the tumor suppressors STK11/LKB1 and CDKN2A, and preferential CN gain of PTK6. A fourth focal 78 kbp region on chromosome 6p12.2 exhibited preferential CN gain in recurrent tumors and contained the entire coding sequence of only a single gene, PAQR8. To date, an in vivo role for PAQR8 in cancer has not been reported, and little is known about its function or mechanism of action. Here, CDKN2A is linked to cancer.