cancer genomics


Charting the Dark Matter of Cancer Genomes with Jim Broach

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 large scale translocations."

Jim mentions paired end reads and PacBio’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?

Green Light for DTC, Blood Mammograms, and Ancient DNA: April 2017 with Nathan and Laura

For genomics nerds, April 2017 will be remembered as the date when the FDA adopted a more open policy towards 23andMe and direct-to-consumer (DTC) genetic testing. What does this decision mean, and just where is the FDA drawing the line? A genetic counselor herself, Laura found the decision “head turning.”

“There’s lots of reasons why some genetic counselors are not going to be thrilled to deal with everyone’s 23andMe results,” she says.

For the “cool new studies” section of today’s show, Laura is excited about a research project announced by Grail, a spinoff from Illumina working on a pan cancer screening test. And Nathan points out that the trend for researchers to look back at ancient DNA sharpened this month with two new studies that not only open up the possibilities for historians and archeologists but also have relevance to human health longterm.

“We’re getting much better at doing it,” he says. “So look for more of this ancient meta genomics where we can find little fragments of DNA outside of cells but intact in sites like soil. They’re very diverse, but we're starting to figure out really what was going on at a place some time in the past."

We finish with a couple stories that are giving pause to researchers working on gene therapy and immunotherapy.

It’s commentators Nathan Pearson and Laura Hercher joining Theral to talk genomics for April.

Many Biologists Today Don’t Have Enough Computer Science to Use the Databases

Moray Campbell was for all intents and purposes an accomplished and successful cancer biologist at the renowned Roswell Park Cancer Center. Then one day he woke up and realized he was becoming irrelevant. He was a traditionally trained wet lab biologist who was getting left behind by computer science. Any scientist must keep up with their field, but this was different. A few conferences and journals--reading the news everyday was not going to be enough. Facing reality, Moray enrolled in a bioinformatics masters program at Johns Hopkins.

That was in 2013.

"Biology is genomics. And genomics is basically computer science,” says Moray at the outset of today’s program. “In 2013 I would have said I look at the epigenetics of prostate cancer. Now I say that I look at the epigenomics of prostate cancer. I’ve become genomically literate."

What was it like for Moray to go back to school mid-career with teachers and homework and finals? Did he doubt his decision when the going got tough? Is it harder for biologists to learn coding or coders to learn biology?

Moray is now finished with his degree and in the process learned that as a discipline, we're still struggling with how to teach genomics to biologists.

He gives the example of datasets such as TCGA that many biologists today don’t even know how to use.

“These data are there. And they’re being used very deeply,” he says. "But I suspect by quite a restricted community. If you don’t even know how to download a file, how are you going to be able to analyze it?"

It's been a dramatic transition for Moray. Looking back now he says, "biology is dead; long live biology."



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