Mendelspod Podcast

As we look back at January’s headlines with our two regular commentators, Nathan and Laura, the question becomes: How much should we ignore the fire raging across America to focus on the science? Speaking of Trump's new immigration order and the very real threat of a "brain drain," Nathan tells of his own personal time doing research in Iran, commending scientists there and the many Iranian scientists here. But he says Iran has already announced they're going to retaliate.

Why are there no viable psychiatric genetic tests, we ask today’s guest. Rob Philibert is a geneticist and psychiatrist working at the University of Iowa. He admits at the outset of today’s interview that the field of psychiatric genetics is in a “quandary.” “The results are not matching the hype,” he says.

Podcast brought to you by: Slone Partners - Providing the leaders that shape the clinical trials space. About six years ago there was a wave of genome interpretation startups getting their first rounds of funding. One of them was Personalis, a company founded by a well known group of Stanford geneticists and bioinformaticians.

Mark Akeson has been working on nanopore sequencing at UC Santa Cruz’s biophysics lab for twenty years. Up until the past few years with the launch of Oxford Nanopore’s sequencers, that work was mostly the methodical toil of the quiet inventor. Today it is quite ordinary to see a sequencer the size of your wallet being taken out into the field for DNA work. But for years, the naysayers dominated. “Back in the day, the skeptics outnumbered the proponents 99 to 1,” Mark says in today’s show.

Each year at this time, sequencing tools leader, Illumina, generates another round of sequencing buzz in the industry, this year by announcing the $100 genome is around the corner with their latest boxes. But more and more, people are asking just what they will get with that $100. Indeed, what do they get today with a $1,500 genome? Illumina sells short read sequencing technology which is unable to characterize much of the human genome, particularly complex regions which are responsible for many of the known and unknown diseases.

From new CRISPR trials in humans to mitochondrial transfer therapy, from the spinout by Illumina of two new genomics health companies to the complete and utter failure of Theranos, from the approval by the FDA of GM mosquitos to the FDA giving up on LDT regulation as a result of the election, the genomics headlines of 2016 didn’t fail to dazzle, deliver, and disappoint. Hear which stories our regular commentators, Laura Hercher and Nathan Pearson, chose as their top and also most underreported of the year in today’s look back on 2016.

Each year at this time we bring on a guest who is somewhat out of the way of our normal lineup, for example, a science fiction writer or a philosopher. Today Theral interviews a law professor who loves to philosophize and write about the impact of biotechnology on our lives now and in the near future. His newest book out this year, “The End of Sex and the Future of Human Reproduction,” is another comprehensive and provocative example of what has made Stanford’s Hank Greely such an in-demand speaker both to scientist and non-scientist audiences alike.

Back in 2009 at the annual AGBT meeting for sequencing, Marco Marra presented one of the first cases of cancer treatment using whole genome sequencing. We caught up with Marco at his office at the University of British Columbia where he heads the Department of Medical Genetics. Marco also directs the Genome Sciences Center which is part of a very special organization called the BC Cancer Agency.

While everyone is asking what will become of Obamacare, we ask our regular commentators, Nathan Pearson and Laura Hercher, specifically about genomics and medicine. Nathan begins by saying that data scientists everywhere should be humbled. Does the failure to predict the election send out warnings about big data predictions in genomics?

Today Ethan Perlstein joins us on the program for a third time. His path as a ‘rogue scientist’ has become a bit of a case study here at Mendelspod as we look into alternate paths for scientists and for drug development.

When we talk precision medicine on Mendelspod, we’re usually talking about oncology. But today we shift our focus to diabetes. Raghu Mirmira is an MD PhD at Indiana University who is working on a panel of biomarkers that would predict Type 1 diabetes. That’s right. Predict. Having already found a DNA biomarker candidate which detects dying beta cells using the new technology of digital PCR, Raghu is now working to improve the panel with other metabolites.

Let’s take a break from the US and head over to the UK, home of the world’s largest single disease medical research charity. Cancer Research UK (CRUK) raises five hundred million pounds a year for research and drug discovery into any and all of the two hundred plus types of cancer. The charity is extremely well integrated into U.K. culture, and uniquely English in that the donations are mostly small and come from all corners of society. A third of CRUK’s funding comes from donations averaging £10 or less.

Are you lactose tolerant? If you’re of Northern European ancestry this is because of a stretch of DNA in a gene enhancer that developed some 9,000 years ago. That's the same time Northern Europeans began domesticating cattle for milk. If you’re of African ancestry, you may have one of three mutations which appeared independently of the European mutation--and of each other--about 6,000 years ago, again when dairying began.

Today’s show was recorded on Halloween, which now feels so yesterday. Forgive us for some spookiness. What doesn’t feel so yesterday is the launch this past month of Helix, a company spun out of Illumina that aims to add exomes to the lineup of direct-to-consumer testing. Nathan points out their model for delivering data incrementally through various apps. Laura questions how Helix will vet the apps.

There’s a basic assumption in our field today that has been around for some time. We think of medicine as on a direct and even continuum with science. That discoveries in genomics, for example, will lead directly to breakthroughs in medicine. But the breakthroughs on the medical side have been much more rare to date than those coming from the study of biology and genomics.

As we get closer to the election and the end of 2016, the debate over LDT regulation has gone quiet. At this time last year, there was one hearing after another, first in the Senate, then in the House. The FDA’s Jeffrey Shuren was called before congress and drilled over the nuances of the guidance as well as asked when it would be released. He said, in the first half of 2016.

A couple months back, we reported on a study showing that genetic tests for an inherited heart disorder were more likely to come back with false positive results for black Americans than for whites. The study provoked many in our industry to urge scientists to incorporate more ethnic diversity in their studies. So far, biology has been too Eurocentric—the databases are implicitly racist, they argue.

There were many headlines this past week heralding the first three parent baby to be born. But in fact, as our commentators point out in today’s look back on last month’s genomics news, three parent babies have been around for some time. So why are couples going to Mexico for mitochondrial transfer today? Why is it not legal in the U.S.?

There is tons of life science journalism. Our coffee tables and inboxes fill up each week with that quarterly or that daily. We sift through headlines and product advertisements to assess what’s going on in our industry. It’s our job to know. In this age of several-times-per-day newsletters and 24 hrs a day Twitter, we catch what we can. And occasionally, we come across a carefully written piece or a well done interview, and we take a moment to realize with some awe the history that is being made in our industry.

Most of the time, when we talk about personalized medicine, it’s not that personalized. What we’re really talking about is population-based medicine. However, there is a growing number of clinical/research groups around the world, including the folks at the Finnish Institute for Molecular Medicine (FIMM) who are combining an older method of functional profiling with new molecular profiling to come up with what the Fins call 'Individualized Systems Medicine.'