Accurate analysis of structural variants begins with isolating ultra-high molecular weight DNA. Obtaining high-quality UHMW DNA can present a challenge since sample collection, preservation, the DNA isolation process and subsequent handling of isolated DNA can significantly affect its quality.
In this webinar, Dr. Ben Clifford, Sr. Application Scientist at Bionano Genomics, discusses tips and tricks for isolating high quality UHMW DNA – right from sample collection, preservation and gentle handling of isolated DNA to minimize shearing and fragmentation.
In addition, we heard from Dr. Sven Bocklandt, Director of Scientific affairs at Bionano Genomics to walk us through genome imaging technology and workflow to demonstrate how it has been used successfully in studying structural variations in cancer and genetic diseases.
“Bionano’s optical mapping technology allowed us to characterize complex structural rearrangements in cancer with unprecedented precision. The results are incredibly robust and easy to interpret with Bionano software, and the team was really helpful for data analysis!”
-Dr. Eric Letouzé
Cyclins A2 and E1 regulate the cell cycle by promoting S phase entry and progression. We recently identified a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms, including HBV and AAV2 viral insertions, gene fusions and enhancer hijacking. Those poor-prognosis HCCs display a unique signature of structural rearrangements, triggered by replicative stress. This signature is strongly enriched in early-replicated active chromatin regions and is characterized by hundreds of tandem duplications and more complex events called Templated Insertion Cycle (T.I.C.).
Structural variation calling from short-read Whole Genome Sequencing provides abnormal junctions by comparing chimeric reads with a reference genome. However, those independent breakpoints are too distant, thus this method is not enough to reconstruct highly complex rearrangements, which may involve up to dozens of regions of the genome linked together. Here we used Bionano data to characterize with certainty large DNA molecules resulting from complex T.I.C.. This analysis allowed us to know which regions of the genome are the acceptor of such complex structural rearrangements. This information is critical in the understanding of how those rearrangements affect genes involved in tumorigenesis by placing oncogenes in different genomic contexts.
Accumulation of structural variations (SVs) across the genome is a known trigger factor for oncogenesis. Identifying these structural genomic alterations – accurately and comprehensively – is crucial for improving research and ultimately therapies for cancer patients, yet one of primary challenges when solely relied on short read sequencing and standard cytogenetic methods (e.g. karyotyping, FISH and chromosomal microarrays).
Optical mapping with genome imaging, enabled by the Bionano Saphyr® System, can accurately assemble and assay relevant regions for complex genomic disorders like cancer, even those involving very large segmental duplications. Genome imaging has to date unraveled a number of genes, never implicated in cancer and shown how they are affected by structural variations, along with deciphering novel structural variants. Listen to this webinar to learn how combining genome imaging with whole genome sequencing offers a strong integrative approach to understand small and large genomic variations in cancers.
This webinar outlines how a team at Radboud University Medical Center is assessing ultra-long read optical mapping on the Bionano Saphyr System to replace classical cytogenetics approaches in routine testing and for the discovery of novel structural variants with potential scientific, prognostic, or therapeutic value that are missed by standard approaches.