Affymetrix SNP array data for Primary Effusion Lymphoma samples

Primary Effusion Lymphoma (PEL) is a Diffuse-Large B-cell Lymphoma (DLBCL) with poor prognosis. 100% of PEL carry the genome of Kaposi's Sarcoma-associated herpesvirus (KSHV) and approximately half are co-infected with Epstein-Barr virus (EBV). We profiled genomic aberrations in PEL using the Affymetrix 6.0 SNP array. This identified for the first time individual genes that are altered in PEL. 10/13 (76%) samples were deleted for both the fragile site tumor suppressors WWOX and FHIT. Alterations were also observed in: DERL1, ETV1, RASA4, TPK1, TRIM56 and VPS41 genes, which are yet to be characterized for their roles in cancer. Co-infection with EBV was associated with significantly fewer gross genomic aberrations. PEL could be segregated into EBV positive and EBV negative clusters on the basis of host chromosome alterations. The genomic signature of PEL cells in culture was analogous to those explanted from xenograft tumors. This suggests a model in which both host and virus contribute to the PEL phenotype. 17 samples (no replicates) were analyzed using Partek Genomic Suite software