Mendelspod Podcast

To begin the year, we head across the pond for an outlook on the thriving community of synthetic biology in the United Kingdom. Paul Freemont was a co-author of the UK's synthetic biology roadmap and co-directs SynbiCITE, the national center for the commercialization of synthetic biology. A few years ago the government put an initial investment of $300 million pounds into the field, and "everything was going swimmingly well," says Paul. "Then COVID happened."

Our goal with today’s show was twofold: bring you a practical holiday gift idea and to take you into the world of a synthetic biology entrepreneur. Our guest: Zack Abbott, CEO of ZBiotics. Zack is a scientist turned businessman who is on a mission to change the conversation around GMOs. His first product is a genetically engineered probiotic that alleviates the morning-after hangover by breaking down acetaldehyde. Zack says he chose this product because it’s something consumers can choose to take—unlike a medicine that’s necessary like insulin.

When excitement around early cancer detection first surfaced, we heard about the “pan-cancer” test that would look for any and all cancers, and early. Now that we’re some years into it, the approach is turning out to be more of a narrow one. Which cancer will we likely see targeted first with an FDA cleared test? Colorectal, according to today’s guest.

Winter is here. In America, we're just back from the Thanksgiving holiday when many of us travel and get together. And so far there is no great COVID surge this year. Or is there? Today's guest says there likely is, and we don't know it because of the most significant shift in our pandemic response: at-home testing.

It’s the age of multi omics. Or multi comics, if you don't catch spell check. A few weeks ago at the annual meeting of the American Society for Human Genetics, we were pleased to find not only genomics companies but some proteomics outfits finding a home. As we chatted with one of these, Olink Proteomics, we were blown away to hear that they were announcing the publication of 1,000 scientific papers. It wasn’t so long ago that genomics companies were boasting this kind of milestone. Has proteomics finally achieved scale?

Pharmacogenomic testing, or PGx, is considered low-hanging fruit, a no-brainer for the application of genetic testing in the clinic. And some may think it is small fruit. Not so, says today’s guest, Kristine Ashcraft. "Currently we lose a life every two minutes in the United States to non-optimized medications,” says Kristine in today’s show. She has spent over twenty years working to see pharmacogenomic testing adopted into standard-of-care medicine. Kristine serves today as the Medical Affairs Director for PGx at the genetic testing company Invitae.

Last week with a crowd of 1,200 customers in a Los Angeles nightclub, sequencing company Pacific Bioscience launched two new sequencers, both long and short read, Revio and Onso. It was a night of great technology, music, and anticipation. Their customers have waited a long time for this moment. Revio offers long read whole genomes at scale for under $1,000.

Last week, during the first International Conference on Newborn Sequencing, a landmark study to sequence the genomes of 100,000 newborns was announced. Called the GUARDIAN study, the project is the brainchild of Wendy Chung, Professor of Pediatrics at Columbia University. The study will take place in New York State and is somewhat similar to an ongoing project in the U.K. being done by Genomics England.

Today spatial biology company, Vizgen, makes their debut on on the program. When Vizgen CEO Terry Lo was first involved in developing what we now call spatial biology at Perkin Elmer, he admits that he never thought it would have a genomics side to it.

One thinks of Invitae as a leading genetic testing company that has worked to improve clinical quality while bringing prices down. And they are, and they have. But after listening to today's show, you will see that their vision is bigger than that. Farid Vij is the President and General Manager of Data at Invitae. A year ago Invitae bought a company he co-founded called Ciitizen which was focused on providing patients with access to their complete medical records.

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.

Satellite Bio is named descriptively for the way its platform works. Out of stealth in the past few months with what you might call a middle ground approach to generative medicine between stem cell therapy and organ transplant, the company takes its name from the tissue therapy constructs they surgically implant in patients.

A new generation of biologists is pushing the limits of third-generation sequencing, furthering the technology's development and defining new applications to answer biology’s most pressing questions. This is the express goal for the lab of Vijay Ramani, assistant professor at UCSF in the department of Biophysics and Biochemistry. Vijay also has an appointment in the Institute of Data Science and Biotechnology at the Gladstone Institute, and in 2019 he was named to the Forbes 30 under 30 rising stars in healthcare list.

In our age of specialization, today’s guest, Dr. Will Hwang of Massachusetts General, went against the trend and received three bachelor degrees in different fields. Or is this the new trend? Will says that despite the diversity of pursuits, there was a thread that ran throughout his life as a student. He always liked to look at things at the fundamental unit.

While we’re able to sit outside on a warm summer’s night under the ocean of stars, let us contemplate some of the bigger questions. We’re very excited to start out our twelfth season of the podcast with the chemist, Lee Cronin, from the University of Glasgow. Lee published an original and fundamental theory about the universe in the weeks after we taped which has profound implications for the question about the origin of life and could have some interesting applications in genomics.

Arutha Kulasinghe was pumped for the AGBT (Advances in Genome Biology and Technology) Conference this year. He is the Principal Investigator for the Clinical-oMx Lab at the University of Queensland. Dr. Kulasinghe has pioneered spatial transcriptomics using digital spatial profiling approaches in the Asia-Pacific region, contributing to world-first studies for lung, head, and neck cancer and COVID-19. Not gathering last year due to the pandemic, the AGBT conference has became a kind of revival for genome biologists.

Dr. Eric Green has been the Director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH) since 2009. Two years ago, he and his colleagues at the Institute came up with a strategic plan for the next ten years. Today we discuss the plan with the director and get his outlook on the future of human genomics. Dr. Green says human genomics can be roughly divided into four chapters.

There was a tweet thread at the end of the recent Advances in Genome Biology and Technology (AGBT) conference where researchers took a moment of silence for all the sequencing companies that have announced big plans at the conference and then died. It was clearly aimed at this year’s sequencing tools entrant and buzz-generating Ultima Genomics. The company emerged from stealth the week before AGBT announcing the $100 genome with a purse of $600 million backed by funders including Khosla Ventures, Andreessen, and Founders Fund.

Has the pandemic unleashed the molecule of RNA to be the new future of drug development? Tim Mercer is the Director of the BASE Lab at the University of Queensland which has recently become one of Australia’s leading national facilities for the manufacture and research of RNA technologies. Tim is the next guest in our series on enzymatic DNA synthesis which he says is "a quantum shift” in our ability to synthesize DNA. Tim then goes on to explore the future of mRNA vaccines and other RNA therapeutics.

Heidi Rehm’s talents for genomics are legendary. Our field has devoured them like a hungry beast. Discovering an appreciation for the natural logic of genetics in her early school years, Heidi would later learn she was good at the standardization of genomic databases for clinical use. This would make her a pioneering superstar of genomic medicine.