- HIV-BL exhibited lower copy number (CN) alterations than HIV-DLBCL cases.- The overall genomic complexity was similar between IC-DLBCL and HIV-DLBCL, however the distribution of genomic alterations was significantly different.- HIV-DLBCL showed more frequently 3p14.3 deletion (containing FHIT and the fragile site FRA3B) and 12q21.31 gains.- IC-DLBCL exhibited more often 18q gains (containing BCL2, NFATC1 and others).- The tumor suppressor genes FHIT and WWOX were downregulated among HIV-NHL samples that carried either gene deletion or abnormal methylation patterns. Here, WWOX is linked to non-Hodgkin lymphoma.