Charting the Dark Matter of Cancer Genomes with Jim Broach

Jim Broach, Chair of the Department of Biochemistry and Molecular Biology at Penn State Hershey, Director of the Penn State Institute for Personalized Medicine and Professor Emeritus of Princeton University

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0:00 Why de novo sequencing of cancer genomes?

4:52 Optical mapping giving the best view of cell lines to date

10:55 Will optical mapping replace karyotyping?

13:06 How might this impact treatment?

20:33 Necessary, but not sufficient . . .

We’ve heard a lot this year about the search for new structural variants and the hope that scientists will find new causal linkages for diseases such as cancer. But will the genome still yield dramatic genetic signatures such as KRAS, BRAF and EGFR that have been so helpful in cancer treatment?

Today’s guest says, yes, and he’s on the trail.

Jim Broach is the Director of Penn State’s Center for Personalized Medicine. He and his team have come up with the highest resolution genomic data to date on certain cancer cell lines using sequencing and mapping tools. In some cell lines his research has revealed 150-200 more structural variants than had previously been discovered.

“There are a whole set of structural variants which haven’t been taken into consideration to date,” he says in today’s interview. "For the next couple of years, this is the dark matter of the cancer genome. We’ve got to sort out which of these structural variants are going to be relevant in understanding how best to treat the patients. Once we generate that information, I think these structural variants will be just as relevant as the point mutations or as as large scale translocations."

Jim mentions paired end reads and Pac Bio’s new long read technology, but the main tool he talks about is Bionano’s optical mapping technology. Previously the field used karyotyping to look for variants of this size, but he says Bionano has got their technology to the quality and price point where it will now replace the older technology.

How will Jim’s research impact treatment in the clinic? He is doing de novo sequences of cancer cell lines. Does he envision the need for de novo sequencing of a patient’s cells as part of a commercial assay?

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