A New Tool in the Genomics Kit with Ivan Liachko of Phase Genomics

Have you ever heard of proximity ligation? We knew of it in research form back in the day, but not that it had been commercialized until this summer. It’s not every day we come across a powerful new genomics tool on this program. Which begs the question, where have Ivan Liachko and his company, Phase Genomics, been hiding?

The company received a grant this summer from the Bill Gates Foundation as well as the NIH to pursue phage therapeutics. That’s using viruses to go after bacterial infections, particularly those which are developing antibiotic resistance.

The company is also using its cool new platform for cytogenetics. There are over 2 billion cancer samples stored in FFPE which cannot be traditionally cytogenetically profiled. However, Phase’s proximity ligation technology has no issue with the fact that the formallin breaks up DNA. How can this be?

Speaking of platform, this new tech is just a kit, not an instrument. There are low barriers to entry.

Ivan joins us to explain how this new genomics tool takes researchers and clinical applications into fresh new territory.

“We’ve figured out a way to capture a unique type of genetic information. Our technology tells you which parts of the genome are touching which other parts of the genome. Which sounds like a crazy piece of information. It’s extremely useful in solving a number of problems. You can solve things in creative and unique ways that in some cases are completely impossible with other methods."

The Studies Are In—Optical Mapping Can Replace Traditional Cytogenetics Tests

We’re all aware of the way that next gen sequencing has changed many tests in the clinical laboratory. But some testing has held stubbornly resistant to change. This has been the case in cytogenetics, or the analysis of chromosomes. That is now changing thanks to a technology that is making inroads where next gen sequencing could not.

Alex Hoischen, Associate Professor of Genetics at Radboud University Medical Center in the Netherlands, is the lead author of two landmark back-to-back studies out this week demonstrating the power of optical genome mapping (OGM). The studies show 100% concordance of OGM to traditional cytogenetic techniques (karyotyping, FISH, and CNV microarrays) across both constitutional and hematological malignancy applications.

In today’s show, Alex says that the traditional cytogenetic testing hasn’t changed or been replaced by any sequencing approach for roughly 50 years.

“So it’s about time to change that. And in these two studies, we gave the first glimpse that OGM is on track to do so.”

Alex goes into some of the challenges of traditional testing and the benefits that optical mapping brings. It’s a single test replacing various tests. It also can be easily analyzed by lab personnel without the need for intensive bioinformatics resources, as is the case for whole genome sequencing.

The studies point to a change in standard of care in the clinic, but Alex says that optical mapping holds new possibilities for the research lab as well.