Our study will have 3 main goals. 1) Through our novel approach utilizing the latest in NGS techniques, we will extensively map all HPV integration events across the human genome for each cancer and pre-cancer patients in our initial cohorts. 2) Using in-house developed analytic software, we will combine each patient’s integration maps and identify integration patterns that could be used for future targeted approaches, and 3) the whole genome human data will also be used to identify all chromosomal rearrangements within the tumors and the proximity of these events to the cataloged integration sites.
For this study we have chosen to use 10X Genomics Technology in combination with Illumina whole genome sequencing to provide us with the most accurate, phased human genomes. Our pilot study consists of 16 HPV16+ women (8 cancers, 4 pre-cancers (CIN3) and 4 control HPV16+ non-cancer samples (CIN2)).
We have performed whole genome seqeuncing on all 16 women from our pilot study. All 16 of the pilot samples have been processed through our cloud based analytic pipeline that aligned each sample to an HG19-HPV16 hybrid reference, for each sample their HPV16 integration sites have been recorded as well as all other chromosomal abnormalities have been identified and recorded.
We have developed a method that combines the latest in NGS technology to create a comprehensive list of HPV integration and chromosomal abnormalities for each of the 16 women in our first pilot study. This data will be used for potential development of targeted assays.We have developed a method that combines the latest in NGS technology to create a comprehensive list of HPV integration and chromosomal abnormalities for each of the 16 women in our first pilot study. This data will be used for potential development of targeted assays.