Cancer Genomics: Heme Malignancies and
Solid Tumor Research

The Bionano Genome Imaging workflow starts with mega-base size DNA isolation. A single enzymatic reaction labels the genome at a specific sequence motif occurring approximately 15 times per 100 kbp in the human genome. The long, labeled DNA molecules are linearized in nanochannel arrays on a Saphyr chip® and imaged in an extremely high throughput, automated manner by the Saphyr® Genome Imaging Instrument. Using pairwise alignments, the molecules are assembled into local maps or whole genome de novo assemblies. Changes in patterning or spacing of the labels are detected automatically, genome wide, to call all structural variants.

Mutations inactivating BAP1 gene are a hallmark of Uveal Melanoma. In a patient derived model, no mutation or epigenetic event was found explaining the loss of expression of that gene but Bionano identified a 740 bp deletion in the promoter of BAP1. This variant was missed by sequencing due to the high GC content of that region.

Cancer samples often display a high number of structural rearrangements or changes and the limitation caused by the short-read length of NGS is particularly detrimental for making sense of complex successions of event, such as in chromothripsis. In this patient-derived breast cancer cell line, a consensus map resulting from the alignment of dozens of molecules spanning the region allowed optical mapping to identify a succession of a translocation, deletions and an inversion missed by short-read and long read-sequencing.

The ability to stratify patient samples based on mutational profile usually requires extensive bioinformatic data curation downstream of sequencing. In a hepatocellular carcinoma study, our built-in pipeline automatically provides enough information to distinguish samples with or without a replication stress signature, resulting from a Hepatitis B Virus insertion 9 kb upstream of the Cyclin E1 gene. With the development of innovative therapies such as PARP inhibitors, patient stratification based on accumulation of DNA damage is critical.

In a large systematic comparative study between optical mapping and classical cytogenetics, Bionano identified novel, non-recurrent fusions never reported before. In both cases shown here, one of the two fusion partners is well known in leukemia from other gene fusions. These events were missed by classical cytogenetics either because of their low allelic frequencies or because of the targeted FISH approach classically used in a diagnostics context.

Oncogenes are commonly amplified on particles of extrachromosomal circular DNA (ecDNA) in cancer, but our understanding of the structure of ecDNA and its effect on gene expression is limited. Bionano was used to build a detailed map of ecDNA in a colorectal adenocarcinoma cell line, showing the circular structure, gene amplifications and fusion breakpoints.