A New “Middle Way” for Genomics, with Physical Chemist, Yuval Ebenstein

Yuval Ebenstein, Professor in the Department of Chemical Physics at Tel Aviv University

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Chapters:

0:00 How did you come to the genome?

8:26 A new “middle way”

14:47 NGS and too much data

16:51 Where are we at today with epigenetics?

18:27 What’s the CATCH?

“I love low tech,” says today’s guest.

It’s not your typical catch phrase for 2017. But then today’s guest is not your typical genome scientist.

A professor in the Department of Chemical Physics at Tel Aviv University in Israel where he runs the NanoBioPhotonix Lab, Yuval Ebenstein came to the genome from an unusual direction. As a physical chemist he started working with DNA as “just a material.”

The low tech is the method of visualizing genomes with microscopy, such as the old FISH or cytogenetic experiments. However, with the advances in imaging and single molecule analysis, he can now go far beyond these dated methodologies and "take dense chromosomes and stretch them out and read information along them in a very sensitive and informative way that is not accessible to other established genomics techniques."

“I love low tech and then giving it a little twist and turning it into high tech," he adds.

Yuval calls the twist a new “middle way” in genomics, between the large structural cytogenomics of the past and all the specific base calling going on now with next gen sequencing. Will his lab’s work turn into a new instrument able to be commercialized?

He says that PacBio, Oxford Nanopore, and BioNano are making headway in filling in this third or middle way, but that yes, there are new techniques that everyone should be able to use.

One specific paper Yuval’s group has recently preprinted is a method for isolating and cloning very long fragments of DNA using Cas9, or what his group calls CATCH (Cas Assisted Targeting of Chromosome Segments).

“This is a nice demonstration of taking low tech and reviving it,” he says.

It’s also an example of what Yuval says is the problem today with NGS, which is too much data.

To look at certain regions of the genome, such as BRCA, one does whole genome sequencing, or exome sequencing and ends up with a confusing amount of data. With CATCH, he suggests one can take advantage of CRISPR to isolate just the target DNA one is looking for. As our audience will know, most of the methods we use today, say in cancer diagnostics, are looking “under the lamppost,” using templates of known mutations rather than being able to discover what’s actually there.

“You could PCR out large pieces of the genome, but it’s hard and tedious, because you need a lot of primer sets. If it’s a very variable region like BRCA, you may have problems with your primer design, which won’t fit. This is another, hopefully more elegant way of taking out the intact region of interest of the genome and analyzing it very deeply,” he says.

Yuval’s lab is one to keep on our radar.



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