Mendelspod Podcast

Mara Aspinall, a leader in genomics and diagnostics, discusses trends in the industry, including valuations and new regulations. Topics include challenges in cancer detection, FDA support for monitoring minimal residual disease, liquid biopsy in personalized medicine, pandemic preparedness, and investing in diagnostic tools for future pandemics.

The genome has been the core focus of biomedical research for twenty years. Although the genome is prewritten and predetermined, much biology happens after it appears. One area is epigenomics, which is the modification of genomic outcomes.Bret Barnes has spent his career at Illumina developing the DNA methylation Infinium arrays that have become the workhorse of epigenomic studies around the world. Barnes says he was torn as a young person between biochemistry and computer science. He fortuitously ended up at UC Santa Cruz when they launched the first bioinformatics degree. Early on, he was interested in protein structure prediction.“There are 20 amino acids,” he said. “Way more exciting than DNA with only four bases.”But then he discovered the fifth base.“Methylated cystine is the fifth base. So five, not four — a little better,” he continues. At the time of the Solexa acquisition, Illumina recruited Bret to do bioinformatics work on DNA methylation.“If the king and queen of DNA methylation at Illumina were Kevin Gunderson and Marina Bibikova, then you could think of me as the prince or maybe the joker,” he says, tongue in cheek.Where are we at today in epigenomics? What applications does Barnes see for the actionable epigenome, and how is the field developing? This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.mendelspod.com/subscribe

This is a free preview of a paid episode. To hear more, visit www.mendelspod.comNot content to offer “me too” products, a new company in the prenatal arena, Billion to One (BTO), is reimagining prenatal testing. Last year, their new Unity Fetal Risk Screen was featured in the American Journal of Human Genomics as a top advancement in applying genomics to clinical care. Joining us today is Jennifer Hoskovec, Senior Director of Medical Affairs at BTO. She says the new Unity Screen offers two steps in testing: the first screen and, if necessary, a risk assessment for the baby. These can both be done with a single blood draw from the mother. Up until now, the father’s DNA was needed as well as the mother’s to determine risk assessment. Because a sample of the father’s DNA may not be easily attainable or can just cost more, Jennifer says that the new Unity Screen is further democratizing prenatal testing.

This week, we saw Dr. Anthony Fauci being grilled by an angry congress over, among other things, the origin of COVID-19, which is estimated killed at least 25 million people.  He was asked about how the National Institute of Allergy and Infectious Diseases, which he directed until 2022, funded risky virus research at the Wuhan lab in China.Ever since the pandemic broke out, scientists, as well as policymakers, have been debating new restrictions on pathogen research, and last month, the White House released a new policy for what it calls “dual use research of concern and pathogens with enhanced pandemic potential.Marc Lipsitch is Professor of Epidemiology and Director of the Center for Communicable Disease Dynamics at the Harvard Chan School of Public Health.  He joins us to talk about the pros and cons of the new policy and explain how it might work moving forward.Marc acknowledges there is legitimate disagreement among scientists, but these are value-laden questions, so it's for more than scientists to decide. It should include ethicists and the public. What are some of these value-laden questions? Will this impact privately funded research, and what are some of the alternative possibilities to high-risk research? This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.mendelspod.com/subscribe

A new precision medicine startup has launched that uses transcriptomic and epigenetic information to help with therapy for a wide range of chronic disorders. Hayward, California-based Aqtual emerged from stealth at the end of last year with data on its first assay, a blood-based test for rheumatoid arthritis.Today, we’re joined by Diana Abdueva, Aqtual’s Founder and CEO, and Maggie Louie, VP of Translational Research and Strategic Partnerships."We are complex organisms that work beautifully for many years,” says Diana in today’s interview.  "But when something goes wrong, it is very hard to detect where the pathology originates.  There are many applications other than oncology, such as dermatology or immunology.”We explore Aqtual’s technology and history and consider the exciting possibilities for liquid biopsy beyond oncology. This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.mendelspod.com/subscribe

This is a free preview of a paid episode. To hear more, visit www.mendelspod.comToday, we pursue an exciting area of medicine for the first time:  cell therapy for solid tumors.Most, if not all, of our audience will be familiar with the success of CAR-T therapies for blood cancers.  But only 10% of cancer is in the blood.  The other 90% develop solid tumors. Jason Bock is the CEO and founder of CTMC, a new company aiming to speed the advancement of the entire field of cell therapies. First, we cover this new treatment for solid tumors and discuss the near-science-fiction action of tumor-infiltrating lymphocytes (til). 

The Clinical Knowledge Base (CKB) powered by The Jackson Laboratory (JAX) is a dynamic digital resource for interpreting complex cancer genomic profiles in the context of gene variant knowledge and protein impact, therapies, and clinical trials. Illumina has teamed up with JAX in the newly released Connected Insights software, which integrates CKB as a knowledge source.We’re joined by Cara Statz from JAX and Erica Schnettler from Illumina to discuss how their combined technologies are helping researchers and oncologists deal with the increasing complexity of cancer genomic data. They discuss oncologists' experience with an overwhelming amount of new scientific data, and both guests give their advice for new labs setting up cancer testing. This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.mendelspod.com/subscribe

A paper out this week in Nature Methods demonstrates a new technology which shows novel patterns of protein spatial polarization and co-localization in immune cells. The technology launched by Swedish startup Pixelgen has been dubbed “molecular pixelation” because it uses DNA pixels to tag and reveal relative locations. Unlike most other spatial technologies, molecular pixelation does not involve microscopy.Lead author of the paper, Filip Karlsson, joins us today to explain the technology and how it might enable new proteomics research.  He says that immunology is a great application area.How does this technology fit in the spatial landscape, and how might it enable new medicine that could impact patients? This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.mendelspod.com/subscribe

Damon Hostin has had an active and exciting journey in genomic medicine.  He’s now at Illumina, where his title is illuminative:  Lead, Health System Market Access.A regular on the precision medicine stage, Damon has some insights into what he calls the “blindingly fast progression” of genomic medicine that should convince the most jaded of its critics.  Compared to other areas of medicine, we are witnessing a rapid uptake of new science.  Damon’s biography includes work at Celera in the age of the Drosophila and Human Genome papers and at a large community health system, Catholic Health Initiatives, where he was in charge of precision medicine.   At Illumina, he’s part of the large vision of seeing that genomic medicine has every chance at adoption.Today, we ask Damon what has changed about access to genomic testing in the past five years and where we are seeing success. Damon brings a refreshingly optimistic viewpoint to the show. We talk about everything from PGx testing to whole genome sequencing, which he calls an “amazing win” for reimbursement. This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit www.mendelspod.com/subscribe

This is a free preview of a paid episode. To hear more, visit www.mendelspod.comSarah LeBaron von Baeyer studied anthropology at Yale. Today she serves as the Director of Ethics Engagement at the new drug development company, Variant Bio, not a job she ever imagined at university.