Matt Loose on "Read Until" or Adaptive Sequencing

Back before the world turned upside down, you know, all those years ago--early this February--a paper popped up on bioRxiv called, “Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels." It’s an interesting paper.

In the paper, the authors, led by Matt Loose from the DeepSeq lab at the University of Nottingham, describe a method unique to nanopore sequencing where one can do "selective sequencing of single molecules in real time by individually reversing the voltage across specific nanopores.”

In other words, one can decide in the middle of sequencing a molecule that, nah . . . , this molecule bores me. I'll choose another.

Matt says Oxford Nanopore mentions the ability to do this back in 2014 in an aside. But he doesn’t fault us for just getting around to doing a podcast on it.

We do fault ourselves for just getting around to having Matt on the program. Hailing from the land of Robin Hood, it’s Matt Loose, Director of DeepSeq, previous record holder for sequencing the longest read, talking developmental biology, nanopore sequencing, and COG-UK, the UK’s collaborative effort to sequence the coronavirus.

The Current State of Coronavirus Vaccines with Jeff Stein, Cidara Therapeutics

What is the key to getting a coronavirus vaccine? “Manufacturing,” says today’s guest, Jeff Stein of Cidara Therapeutics.

Jeff joined us just last fall to talk about his company’s exciting new technology, an immunotherapy, that is a universal flu preventative and therapy. Yes, you read that right. A universal flu preventative.

So we were eager to have Jeff on the podcast again and ask the burning $64 million question: Will Cidara’s technology work on the coronavirus? Indeed, it will. Jeff says the company has a clinical development candidate, CD377, which will work on all members of the coronavirus family.

While Jeff is here, he gives an update on the various vaccine programs going on around the world, including the mRNA product we all heard about this week from Moderna Therapeutics.

Is Jeff as optimistic as President Trump about having a vaccine by end of year?

“It’s possible, but not probable.”

Lab Director Speaks to the Challenges of COVID-19 Testing: Elaine Lyon, HudsonAlpha

Why have diagnostic tests for the Coronavirus been slow on the scene? What have been the challenges for lab directors? Were they scientific? Were they regulatory? Were they scaling challenges? Are they still scaling challenges? Supply chain problems?

Elaine Lyon worked for many years at the molecular genetics lab at ARUP at the University of Utah and is now the Clinical Services Lab Director at Hudson Alpha. In both of these jobs she has designed and overseen the design of many diagnostic tests.

She takes us behind the scenes and talks about the many challenges so many lab directors have been facing over the past month in developing good diagnostic tests for the Coronavirus. Perhaps she will answer some of your questions.

“It got to us before we had many papers to be looking at. We’ve been doing it so quickly. Usually in the scientific field, you do appropriate experiments, you analyze, you draw your conclusions, write up your findings, submit for publications, which is then peer reviewed and published and disseminated to the scientific community. Obviously that wasn’t able to happen here. So we’ve been communicating in other ways. Still going to what is published online. And yet we need to make sure this information is correct."

FDA in the Time of Coronavirus: Understanding the New VALID Act with Turna Ray, GenomeWeb

After the virus reached American shores, was the FDA quick enough to allow companies and labs to develop their own tests without restrictive oversight? The question sparked a sweeping new bill in congress, the VALID Act that could overhaul FDA oversight of diagnostics altogether—something that has been clamored for for a generation.

Turna Ray has been covering the FDA and diagnostics for GenomeWeb since 2006. She has recently written a piece on the new VALID Act that includes responses from various members of the community.

As Turna says in her piece, now could be an odd time for Congress to be putting through such important legislation regarding FDA’s oversight of diagnostics and LDTs with everyone in crisis mode. It could be an appropriate time as well. As one community member told Turna:

“Historically it often takes a big public health catastrophe to change the regulatory system for medical products."

What is the general state of testing today? Why was the CDC so slow? Will at-home tests happen? Turna covers all of this in her interview.

March 2020 Review with Nathan & Laura: Corona Gets Personal, Where Are the Tests?, the VALID Act, Some non-Corona Science

Laura comes to us from her flat in New York, Nathan is stuck in San Diego, but they are here and ready to discuss what a month ago was a warning and now is a full blown world crisis. What have they faced personally? What are their thoughts on testing? And what are some of their early big picture reactions as to how this will all go down?

We make some time for some Corona-free science as well.

February 2020 Review with Nathan and Laura: Coronavirus, Medicare for All, and Live from AGBT

What do we actually know about the novel coronavirus, we ask our two monthly commentators at the outset of February’s review show. Then, speaking of pandemics, as Bernie fever sweeps America, we explore the charge that Medicare for All means an end to innovation.

Laura gives an update on the status of the genetic counseling bill, and Nathan comes to us live from AGBT with highlights from Marco Island.