Mendelspod Podcast

Sequencing goes to the world of infectious disease.

We can all recognize that PacBio has laid down the railroad tracks in the frontier of long read sequencing. What many are asking is just how close on their caboose is Oxford Nanopore? And just what exactly will be the differences between the two technologies? Chia-Lin Wei is the Director of Genome Technologies at the Jackson Laboratories. When we called her up for today’s interview to talk about how she is using nanopore sequencing, she said, “I’ve been using nanopore for years, why the interest this year by the media?”

Hanlee Ji is the Senior Associate Director of the Stanford Genome Technology Center as well as an oncologist at Stanford. He’s also a clinical geneticist. In other words, he doesn’t need to take off his glasses and spin around in a phone booth to be able to do about everything. “I was in fellowship for a long time,” he says in todays interview.

23andMe steals the headlines yet again. “If somebody is worried about breast cancer susceptibility in their family, they should certainly not be using this test.” That’s our monthly commentator and genetic counselor, Laura Hercher, talking about BRCA going DTC. But wait a minute. Then she says the test could be good in some instances.

“I think the field has just really come to life over the last five or seven years. We’ve got all this sequence data. We’ve got the population data. We’ve got gene editing. I’ve been at this thirty plus years, and we haven’t had a culmination of technology and data like this before. I think everyone has to be excited in some way or other.”

The Personalized Medicine Coalition advocates for a wide group of constituents, including scientists, health care providers, entrepreneurs, payers, and patients. Which is why we’ve often wondered how the organization can be absolutely clear in their priorities. Today, PMC President Edward Abrahams joins us to answer that question.

"We like to refer to it as consumer initiated, but physician supervised,” says Eric Schadt today when asked if his new test is direct-to-consumer. Eric is the Dean for Precision Medicine at the Icahn School of Medicine at Mount Sinai in New York and since 2016 has served as CEO of Sema4, a spinoff that he founded out of the Mount Sinai Health System. Sema4 launched a newborn screening panel, Sema4 Natalis, in February of this year covering over 190 disorders.

Booking 26 million viewers, the voice of Warren buffet, the endorsements of Olympians Joey Cheek and Tara Lipinski—this company was going for the gold with their ads during the Olympics this year. Of course, we’re talking of the direct-to-consumer genetic testing company, 23andMe. What was the take of our monthly commentators, Nathan Pearson of Root and Laura Hercher of Sarah Lawrence College? Also, for all the doomsday predictions, has Donald Trump been any worse after one year for our industry than the biohacker? Join us for this month’s look back over the headlines.

Sequencing geeks are fresh off the trail from AGBT, and it’s time for our annual look at the sequencing tools space. This year we sit down with the longtime Omics! Omics! blogger, Keith Robison, who not only can answer all your questions about the topic, he even knows which sequencer you’re using right now, and in which department. Keith jauntily runs through the Big 3--Illumina, Pac-Bio, and Oxford Nanopore--and has a few odds and ends to say about the "niche developers."

Nanopore sequencing has arrived. Passing test after test this past year--including one we discuss today--this technology which was being hyped decades ago is delivering on its promise. Winston Timp joins us today. He's an assistant professor at Johns Hopkins and one of the leaders on a recent large scale project to directly sequence RNA on an array of nanopores. Winston's is the first in a series of shows we've lined up with users of Oxford Nanopore's technology. Why RNA-seq? Hasn’t this been done for years?

Some stocks are up on news of big biotech mergers, but others are down on hearing of the latest difficulties of gene therapy. One thing’s for sure—blood diseases are where it’s at. Speaking of the latest difficulties, we start our January review by going back to that paper out of Stanford about a new obstacle to using CRISPR as a new drug platform. It’s called the human immune system. Major roadblock or small warning light?

Fifteen years ago, folks in the industry were buzzing about RNAi the way they talk about CRISPR today. Then things went quiet for the technology, at least in the news. Until last year. In September of 2017, Alnylam Pharmaceuticals, the leader in the RNAi space, announced such positive phase III study results that most experts in the business expect an FDA approval soon. It will be the first for an RNAi drug.

A major chapter in the history of medicine has been written by UC San Francisco. They are writing the next for precision medicine.

Reproductive testing is one of the hottest fields in which genetics is going mainstream, a field hurdling us rapidly into the future. It’s an area we’ll be following closely in 2018. Gary Harton serves as the Chief Operating Officer in the US for Igenomix, a company in the reproductive testing space with a vast global presence. The company has labs in the US, Japan, India, Turkey, Rome, Brazil, Mexico, Canada, and are headquartered in Valencia, Spain.

Our first show of the year is an outlook on genomics for 2018. To do this we’re joined by our regular commentators, Nathan Pearson and Laura Hercher, and also by a special guest to mix things up a bit, Misha Angrist, Associate Professor at Duke University and Editor in Chief of Genome Magazine.

Sharon Begley joins us for our last show of the year to look back over some of the year’s top stories. She’s the senior science writer at STAT News where she covers genetics, cancer, neuroscience and other fields of biomedical research. Prior to joining STAT, Sharon was the senior health and science correspondent at Reuters, the science columnist at the Wall Street Journal, and the science editor at Newsweek.

“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.”

Our topic today: biotech leadership. What makes a good biotech CEO? Are there unique issues to biotech and diagnostics that shape and demand a different kind of leadership?

It didn’t take long to come up with our lead story for November’s month in review show. Looking at the pictures of the boy in Germany playing soccer after successful treatment of his rare skin disease is just the kind of images we had in mind when we first heard of stem cell therapies.

Carla Grandori was for thirty years a cancer researcher most recently at the Fred Hutch in Seattle. She had her personal reasons for working on cancer, she tells us in today’s show. Now, she’s the CEO and founder of SEngine, a startup offering something completely new for oncologists around the country. Carla says she was motivated to step out of the research lab when two patients came to her personally and asked her, “can you study my cancer?”