Technology Showcase: Bionano Genomics, Inc.

7:30 – 7:50 am – Dr. Sven Bocklandt, Director of Scientific Affairs, Bionano Genomics

Genome Imaging with Bionano Saphyr: Resolving Structural Variants Across the Genome to Power Your Next Discovery in Cancer & Human Genetics

7:50 – 8:30 am – Dr. James Broach, Director, Penn State Institute for Personalized Medicine
Penn State College of Medicine

Identification of structural variants in leukemia and HPV+ Head and Neck cancer

We have applied a combination of whole genome imaging and whole genome sequencing to comprehensively identify somatic structural variants in acute myeloid leukemia patients and to determine the viral state in HPV positive head and neck cancers. Most of the variants in leukemia cells were unrecognizable by standard genomic techniques and many of them affected genes not previously associated with cancer but whose expression and/or copy number was highly prognostic for survival of AML patients. For HPV positive head and neck cancers we found that in approximately half of the patients’ tumors, HPV remained extrachromosomal, whereas in other half of patient tumors portions of the virus integrated in the host genome with focal amplification of the host genome sequences. Moreover, integration of the virus completely correlated with whole genome instability and was associated with poorer patient outcomes. These studies demonstrate the effectiveness of this combined methodology for detailed analysis of human genome organization and comprehensive identification of somatic structural variants in cancer. Further application of this method will provide information enhancing the prognostic capabilities of clinicians and in many cases offer the opportunity of developing agents for novel therapeutic targets, with significantly improved health outcomes.