sequencing


PacBio and Labcorp Team Up on a Global Pan-Pathogen Surveillance Network

Will there be a fourth surge of COVID here in the U.S.? Already that we’re asking the question and it’s not an inevitability is a good sign. It’s become a race between vaccination clinics and viral variants.

The U.S. was a bit slow to this race, but we are catching up. Viral surveillance has become a key part of any nation’s pandemic strategy. This past month, PacBio and Labcorp announced a partnership that brings the tool of long read sequencing to this effort.

Jonas Korlach, CSO at PacBio, and Brian Caveney, President and CMO at Labcorp, join us to discuss their joint surveillance work. Their partnerhsip is not only national but is putting in place what they call a “global pan-pathogen surveillance network."

Jonas compares the network to the kind of close surveillance that global weather systems have been doing for many years. Brian says that Labcorp has an international footprint. He's optimistic that those countries that have been viral hotspots around the world will be working together in close scientific collaboration aided by new laboratory tools to prevent the next pandemic.

Since this podcast was recorded, the Biden administration has announced huge investments in innovation and research as part of their new $2 trillion Jobs Plan. We can hope that there is money marked specifically for the pandemic preparedness infrastructure Jonas and Brian are calling for today and that some version of this plan passes.

The Future of Big Biology: Bionano at AGBT

Mendelspod was live this week at AGBT 2021 where Theral interviewed CEO Erik Holmlin and CMO Alka Chaubey of Bionano Genomics on Tuesday. The topic was the future of big biology.

Bionano is having an incredible year. They've just come off a fundraise of $400 million, and their stock, though suffering a recent setback, is significantly up. Structural variation is the theme of the day. Whether it's long read sequencing, spatial biology or large genome mapping, biologists are interested in the "rest of the story." They want context. Short read sequencing has its limitations. Sequencing by synthesis destroys genomes.

Erik was on Mendelspod back in 2016 talking about structural variation, so why does it still feel so new, Theral asks.

Alka was last on the show as the lab director for the Greenwood Genetic Center. When asked why she came to Bionano, Alka says genome mapping is the dream instrument for a cytogenomicist.

Where do the two think big biology and the company are headed in the next few years? Enjoy a full hour with two leaders from one of our field's hottest instrument companies in 2021.

PacBio’s Never Been Stronger: New CEO, Christian Henry, Shares His Vision

At the beginning of the year, we were all holding our breath for the future of PacBio. And by all, I mean all. It seems everyone has been rooting for this sequencing technology company.

And why? It’s simple. Pretty much everyone is in agreement that they have the highest quality reads on the market.

So why was their future in question? This could have been asked of many famous companies at one time or another. Apple computer faced their dark days. Disney overcame initial failure. A company’s success in the market does not always align perfectly with the quality of their product. There are other variables.

PacBio at the end of this year is a different company. They have raised two rounds of financing. They have released their Sequel IIe, and they have a new CEO, Christian Henry. From August to November, their stock tripled in price. So what happened? And what is Christian’s new vision for the company?

The main takeaway today is that Christian believes in PacBio’s existing core story: long reads will take science, medicine, and the world to new heights. He thinks this story has been undersold and plans to change that.

Keith Robison on the State of Sequencing: 2020 Edition

We speak directly with the Oracle today. It's Keith Robison, blogger at Omics Omics. Your All Knowingness, we ask, what has happened in the world of sequencing technology this year?

“The companies may need a mulligan,” he quips and laughs.

But then, maybe, not. It turns out the great Pandemic has driven sequencing technology in its own way. There’s been an explosion of sequencing based diagnostics. That trend was already happening, but the pace was mightily booted along. And all of the technologies have been involved—some new entrants as well--used for their own strengths, to track the powerful virus and all its speeding variations.

We take the flagships one by one, from 10X to the small Genapsys, asking the Oracle in the end whether there is any more room for a shakeup in this mature space. We finish with an impressive story of clinical sequencing for rare disease diagnosis at a world record speed. Oh, Oracle, tell us the future.

January 2020 Review: Genetic Counselors vs ACMG, 23andMe Layoffs, Privacy

23andMe lays off over 100 employees. Illumina comes to the JP Morgan empty-handed. Has Precision Medicine seen it’s heyday already? Or are we gearing up for another wave of innovation? Nathan and Laura are again ready for the tough questions of genomics.

We begin with the current spat between genetic counselors and the ACMG. Like, . . . huh?

The Era of the Social Genome with Rodrigo Martinez, Veritas Genetics

Two years ago Veritas Genetics began offering whole genome sequencing for a thousand dollars. It was a significant milestone—and still is!—not only for what it means about the company providing the genomes but also what it means about the demand for such a product.

Today we talk to Rodrigo Martinez, the Chief Marketing and Design Officer at Veritas and co-author of a recent blog, Next in The Genomics Revolution: The Era of the Social Genome. The blog puts the current offer of whole genome sequencing into the larger context of the history of genomics, compares the availability of the whole genome to that of the personal computer, and anticipates how interacting with our genomic data may begin to shape our lives.

We have two core questions for Rodrigo: What does a whole genome mean to Veritas? And why should one order a whole genome test?

Rodrigo argues that the time of having single one-off genetic tests or even panels of tests has been superseded. Why not get a whole genome test at the same low price, open an online account with all of our genomic information, and have it all there ready for any future interaction?

Veritas offers their product to physicians and to consumers, giving us another perfect chance to continue our ongoing discussion here on the program about the blurring of DTC borders.

It’s our first interview with someone from Veritas. And it’s a lively and long one.  Rodrigo is a deep diver and never short of breath or ideas.  Enjoy.

Meet Christian, Janos, and the New World of 3D Oncology

Today we engage in a rare discussion between a startup founder who is going beyond sequencing and working directly with cancer patient cells in 3D cultures and with one of his customers, the husband of a cancer patient.

Meet Christian Regenbrecht, the CEO of CPO or Cellular Phenomics and Oncology based in Berlin, Germany and Janos Flosser, a fund manager who invests in technology from Copenhagen, Denmark.

Today’s show is not only special for the fact that we have a researcher/entrepreneur sitting down directly with a patient for the interview, but also for a bold new approach to cancer genomics. Christian is not shy with his attitude about how we must shift our thinking toward oncology.

“Sequencing alone has proved remarkably unhelpful. And the belief that sequencing your DNA is going to extend your life is a cruel illusion,” says Christian at the outset of the interview.

So just what is Christian up to at CPO? How did Janos, a fund manager in another country, find Christian? And is this the new face of cancer treatment?

Illumina Concedes on Long Reads, Buys PacBio

At 1:02 pm today, there was a tremor in the world of genomics as it was announced that the two leaders in the field of sequencing have become one company. Goliath has opted to pick David up and put him on his shoulders. Upon first reaction, I'd say three things. 1. High quality long reads are the future of sequencing. Disrupting a standard carried for years in the drive toward the $1,000 genome of quantity over quality, PacBio stepped in and raised the bar for the technology of DNA sequencing.

Liquid Biopsy for Infectious Disease with Mickey Kertesz, Karius

Sequencing goes to the world of infectious disease.

Building on the work with cell free DNA in prenatal diagnostics and cancer genomics, the team out of Steve Quake’s lab that brought us Moleculo has now launched a new company in infectious disease called Karius. In today’s interview, Karius CEO and co-founder, Mickey Kertesz, recalls the day four years ago when a clinician urgently contacted he and his team with an infected patient that could not be diagnosed by any traditional method. The team took on the case, and though the patient died within a couple days--Mickey recalls the Saturday when the team heard—they went on working on the diagnosis.

“We were very focused and went on fixing the software as if not wanting to believe what we heard.”

After a week the team did arrive at a diagnosis which was confirmed by the autopsy. That patient became patient zero, and the event turned Mickey again into an entrepreneur.

"This was not just cool research, this needs to go quickly into patient and clinician hands,” he thought.

Today Karius is an active company, selling their tests to hospitals around the country, working first on the most difficult cases.

Will these diagnostic tests by sequencing replace the traditional blood tests some day?

“Oh yeah. In a few years, this will be the first line of defense," Mickey says.



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