Mendelspod Podcast

We hear from some that soon each baby's genome will be sequenced at birth. This vast amount of genomic information will be stored in a person's medical record for life and be referenced for personalized healthcare, be it for a diagnostic, a prognostic, or a prediction. But others say that it is still way too early to be generating so much information on each person when we know so little about the genome. This camp argues that we should deal with patients on a case by case basis using a more targeted approach.

A renewed effort has been underway by leading biologists this year to persuade their colleagues to preprint. This is the posting of a paper to an open access server before peer review and publication. The proponents argue that preprinting will be good for science because discoveries will be made available sooner. The peer review process can take several months, and by preprinting, a biologist doesn’t have to wait to get their work out there and begin interacting with the community.

The promise of rational drug design has driven pharma companies for years. The history of the industry has been one of trial and error, or “guess and check”, as scientists often say. Companies have screened thousands and thousands of compounds looking for one that might work—the proverbial needle in the haystack.

Which company offers the gold standard of sequencing? Nathan starts us out with a metaphor to compare linked reads with real long reads. Then it’s on to this month’s “knockout paper” that moves us yet further from a deterministic view of genetics. Or is this genomic Jenga part of the “proper design of the Creator”? Laura links a new Indiana law banning abortion due to chromosomal abnormalities such as Down Syndrome to a larger effort by the anti-abortion lobby to go after all genetic testing. Theranos plays the Donald Trump of our industry.

Are drug prices really too high? If so, how do we bring them down? Is precision medicine and the use of molecular profiles really making a difference in healthcare today? These are questions that regularly haunt our industry and the journalists who cover it. But there will be no answers until we face the grand question of all, what today's guest calls the most nagging question in medicine: What is health? Today we begin a new series focused on just this question.

When 10X Genomics launched their GemCode sequencing instrument at last year’s AGBT conference, what they offered seemed too good to be true. 10X was promising researchers a machine that could generate long reads using Illumina’s short read technology at a price lower than what PacBio could offer with their “real” long read instruments. A year earlier, Illumina had announced they were buying Moleculo, a company that promised to offer long read data out of the short reads. But good data with the Moleculo platform failed to materialize.

Jonas Korlach is a natural storyteller—a rare trait in a scientist who is more comfortable presenting data than talking of himself. Jonas is the co-inventor of PacBio’s SMRT (single molecule, real time) sequencing, and we wanted to hear from him directly how it all got started, and also when the team realized that they had something big with long reads and close to 100X coverage. How many of us can boast of hitting it out of the park on our first try?

It’s the beginning of the age of liquid biopsies, when less invasive, regular blood draws will provide more information than the occasional solid tissue biopsy. Companies that offer tests based on circulating tumor cells or cell free DNA in the blood are popping up like genome interpretation companies were a few years ago. As our understanding of biology at the molecular level advances--particularly in the field of cancer research--the more this practical and focused approach for teasing out the information in the cell, in the body gains steady adoption.

It’s time again to look back on another month with Nathan and Laura.

If you attended or followed the recent AGBT conference about all things sequencing, you probably saw a few BioNano Genomics t-shirts with the slogan, “Back to the Map.” They’re referring of course, to a genome map. Just like Google Maps, a genome map consists of landmarks that tell scientists where on the genome they are. But unlike Google Maps and more like the maps North America that were made by European explorers in the 17th century, the map of the human genome is quite incomplete, the map of a frontier.

With constant news topping the headlines about the Zika virus, a synthetic biology company out of Oxford England, Oxitec, has been getting some good press. For over ten years now, Oxitec has been developing their genetically engineered mosquitos as a way to lower virus spreading mosquito populations.

We’re all familiar with the announcement in the year 2000 by US President, Bill Clinton, and the UK’s Prime Minister, Tony Blair, that scientists had completed the first draft of the human genome. It was a big deal. But the actual publications didn’t happen until the next year, February of 2001. Which means that this February is the fifteenth anniversary of the publication of the first human genome. For our commemorative show we’re joined by Mike Hunkapiller, the CEO of Pacific Biosciences.

“It being the month of Hypeuary, go hither through break in yonder wall called LanderGate, and thou wilt be on route to reach the Grail. Drink from this to find your Cure, and Death shall haunt you even more.” -Pithy Monton

OK, so we get it. Long read sequencing technology is cool. But how cool? Is it another great player on the field, or does it change the game altogether? 

Pharma companies face escalated flack over high drug prices. Meanwhile the diagnostics industry toils away at comparative pennies to the dollar.

It’s now been over ten years since John Ioannidis published his now famous paper, Why Most Published Research Findings Are False.   What response has John seen from the scientific community? How has the paper changed his career and role in the scientific community? Join us for a look at science itself.

As we begin the countdown to the new year, we take a look back at 2015 in cancer research, treatment and prevention. Mendelspod is increasingly becoming known for the coverage of genomics and precision medicine, and cancer as a disease area offers a specific window whereby we can look at practical outcomes.

At the end of the year our goal is to bring the audience some unusual programming, some new outside perspectives on the topics we cover. As with last year, we talk today with science fiction writer, Kim Stanley Robinson, author of the Mars Trilogy, 2312, and Shaman. 

We set up an interview with David Spetzler, the CSO of Caris Life Sciences, to hear about some promising new liquid biopsy tests they are developing. And we do that in today’s show. But first, the interview takes a turn toward the regulation of molecular tests. Spetzler says that Caris is already doing as many quality certifications as possible short of FDA oversight.

Angel Pizarro has watched as genomics and cloud computing have grown up together. Formerly a bioinformatics director at University of Pennsylvania, Angel is now the Technical Business Development Manager at Amazon Web Services. At U Penn, Angel was part of the shift from setting up one’s own facility with expensive computer equipment for handling the rapid growth of omics data to using a third party service, such as AWS. He says that genomics and the cloud are both going through a "second puberty.” In today's show, Angel explains growing pains involved.