Fig. 6

WGS revealed the complexity of the HPV16 sequences present in HPV positive OPSCCs. a). OPSCC tumors appeared to have the intact HPV16 sequence across the entire 7.9 kb genome, independent of HPV copy number. Tumor 543 has one HPV copy and tumor 670 has ~ 12 HPV copy. b). OPSCC tumors appeared to have at least two HPV populations present in them, independent of HPV copy number. Tumor 518 has ~ 2 HPV copy, tumor 568 has ~ 20 HPV copy and tumor 601 has ~ 100 HPV copy. c). OPSCC tumors contains either a small or a very large deletion, independent of HPV copy number. Tumor 669 has ~ 1 HPV copy, tumor 680 has ~ 2 HPV copy and tumor 522 has ~ 150 HPV copy. d). OPSCC tumors showed HPV copy number variation with peaks at different regions of the viral genome, mostly seen in the tumors with high HPV copy number