Background  Tonsil carcinoma is one of the common malignant tumors of the head and neck in China. In recent years, HPV-related tonsil carcinoma has been classified as an independent disease.

  Objective  To analyze the HPV infection of tonsil squamous cell carcinoma patients and the site of HPV DNA integration into the human genome by HPV capture and next generation sequencing.

  Methods  Tumor tissue samples (fresh frozen samples or paraffin-embedded tissue samples) of tonsil squamous cell carcinoma patients who admitted to Chinese PLA General Hospital from October 2015 to July 2020 were collected. CTAB method was used to extract DNA from tumor tissue samples, and Covaris interruption method, PCR amplification and product purification were applied to make a DNA whole genome library. The target genes were captured by HPV probe, which was designed according to whole genome of 17 HPV types (6, 11, 16, 18, 31, 33, 35, 39, 45, 52, 56, 58, 59, 66, 68, 69, 82). Then the Illumina HiSeq 2000 was used for sequencing, and finally bioinformatics analysis was conducted.

  Results  Five major HPV types (HPV16, 18, 33, 53 and 67) were detected in 32 samples; and 81.3% (26/32) of the samples were positive for HPV DNA; HPV integration occurred in 90.9% of HPV16 DNA positive samples. Furthermore, MIPOL1 and CDK12 were also discovered.

  Conclusion  In this study, the HPV positive rate in tonsil carcinoma patients is generally high. It is found that the two hot spots of MIPOL1 and CDK12 may be related to the occurrence of HPV-positive tonsil carcinoma.