MSI status of SCCA in HIV-positive patients has never been investigated, but we have performed a CIN analysis of tumor specimens from 18 HIV- and 10 HIV+ patients diagnosed with SCCA in two US institutions [10]. Tumors in HIV-negative patients were more likely to present CIN than were tumors in HIV-positive patients (24.1% versus 6.6%, P<0.001). Consistent loss of heterozygosity (LOH) on chromosomes 17p, 18q, 5q, and 11q was observed in HIV-negative patients with SCCA. By contrast, allelic loss at 17p, 5q, and 18q was virtually absent in tumors of HIV-positive individuals, indicating that immune suppression promote SCCA progression through an alternate pathway to CIN.