Multiplex identification of HPV16 DNA integration sites in cervical carcinomas

We obtained fully consented and anonymized clinical cervical carcinoma samples from patients. Human papillomavirus type 16 (HPV16) had infected these patients, which then eventually caused these patients to develop cervical carcinomas. The HPV16 DNA, in most cases, stay inside carcinoma cells by integrating itself into the patients' cellular DNA. Since we are only interested in the HPV16 integration sites, we used HPV16-specific primers to amplify HPV-containing targets from the total cellular DNA. This resulted in HPV-enriched PCR products (PCR amplicons), which were then sequenced. The sequence reads contain not only the targetted HPV16 DNA (including pure HPV16 part and fused HPV16-human part, i.e. integration junctions), but also the unspecifically amplified products that do not have HPV16 DNA, i.e. purely human. However, all HPV16 DNA that have been sequenced are actually parts of the patients' cellular DNA. The manuscript has been submitted to PLOS ONE. It is in revision, and will be published soon.