Have We Been Missing the Big Picture in NGS? Erik Holmlin, CEO, BioNano Genomics

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Erik Holmlin, PhD, CEO, BioNano Genomics Bio and Contact Info

Listen (4:46) There is a lot of information lost with short read technology

Listen (5:06) What is an example of the practical impact of structural perspective?

Listen (8:49) Is it possible to have one platform that is good at short read and structural view?

Listen (11:28) From the clinic back to the tools space to persue the bottleneck

Listen (1:40) Thoughts on Moleculo

With all the advancement in next gen sequencing, have we actually been missing something important? Erik Holmlin thinks so. He's the CEO of BioNano Genomics, and he's left a career delivering diagnostics to the clinic to go back into the tools space and develop a new sequencing technology that would give a better structural view of the human genome. "I believe, broadly speaking, that the bottleneck in genomic medicine is unique and clinically significant genomic content. And the reason we don't have that is we don't have all the tools that scientists need. So I'm trying to develop those tools." That is a bold statement. In today's interview, I ask Holmlin if there is a new NGS Gospel to be spread?

SEQUENCING: Hunkapiller Chips Away at PacBio's 'Perception Issue'

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. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing


Mike Hunkapiller, PhD, CEO, Pacific Biosciences Bio and Contact Info

Chapters: (Advance the marker)

0:53 How does PacBio fit into the overall sequencing picture at the beginning of 2013?

5:45 Limitations of 2nd generation technology

14:18 What has been your goal as CEO?

20:11 Are there plans for a less expensive technology?

26:25 How would you characterize yourself?

30:31 Has PacBio already spent their reputation?

35:30 Thoughts on Ion Torrent, Oxford Nanopore, and Illumina

Is PacBio a solid company that has been victim of an over-hyped industry?

Sequencing has become a high stakes, treacherous business. No other technology in the life science industry has seen the same hype. For many years, including those when the human genome was first sequenced, Sanger type or first generation automated sequencing remained relatively unchanged. Applied BioSystems was the leader, providing their 3700 Automated Sequencer to both groups which worked on the first human genome. Then Illumina bought Solexa in 2006 and everything changed. This was next generation sequencing, and since then the pace of development has gone on a steep improvement curve that everyone is familiar with. Slides showing this curve sit in most industry leaders' slide decks.

Where is the technology in 2013? Last year began with the announcement from the two major players, Life Tech and Illumina, that they'd be sequencing a human genome in a day. But according to Shawn Baker, CSO at BlueSEQ and regular guest at Mendelspod, neither delivered. Baker maintains a neutral database on the various sequencing technologies over at

"They haven't quite reached the 'genome in a day' goal. Illumina is closer with a 36 hour run from the HiSeq 2500 generating enough material. Life will have to wait until the PII chip, slated to launch sometime in the first half of 2013, is able to generate at least 50Gb per run," he said in an email. (Stay tuned for an upcoming overview with Shawn.)

At the beginning of 2012 Roche made a move on Illumina, showing how important the technology has become to drug development. In our 2012 series on sequencing, we featured some of the promising newcomers touting 3rd generation technology. PacBio had just launched their RS system. And we heard from some of the nanotechnology companies promising disruption soon, Genia and Nabsys.

Yet this year so far, we have heard none of the hype we have come to expect. Is the news this year that there is no news? Has the technology reached a more stable zone? To explore this question and find out what's happening in this exciting sub-industry, we'll be featuring another series on sequencing. And we launch it today with PacBio, and their new CEO, Mike Hunkapiller.

Mike has had an incredible view of the sequencing business. He was president of Applied Bio during their heyday with the 3700. He recruited Craig Venter and helped found Celera, the private enterprise which co-announced the sequencing of the human genome. He's been a partner at Alloy Ventures, the VC firm which funded Applied Bio and PacBio. He has seen and heard the hype that surrounded PacBio as they secured funding of $370 million, went public with a market valuation of $800 million and promised a 15 minute genome for $1,000 by 2013. And he saw them launch their system, burn through $500 million, and see their stock devalue quarter after quarter. So it's 2013 and where is the technology?

Mike's experience and steady, methodical approach shines through in this interview. He has a way of cutting through the hype as he talks about the limits of 2nd generation, or what he calls 'short read' technology and establishes an important place for PacBio and their success with long reads. I've heard several times this last year that PacBio had serious problems, among them accuracy. And this for a machine that cost more than any of the other technologies. Industry experts have wondered aloud if PacBio would suffer the fate of a meteor burning out.

I came away from the interview with much less skepticism. Hunkapiller says that PacBio has suffered from some "perception issues," and this year they've proved that their "accuracy is actually extremely good." His approach has been to focus on their existing customers and make sure they had success with the technology. The company has upgraded their software and their chemistry. Last month their stock shot up 46% on news that UC Davis would use the RS for the 100K Genome Project. What about Oxford Nanopore and their new technology? What about Illumina's recent investment in longer read technology? Hunkapiller answers these questions with great aplomb and is quite convincing that PacBio is certainly not out of the picture.

Note: The following correction has been made to this article. Originally it was stated that Illumina and Life Tech had both delivered on their claim to be able to sequence a human genome in one day, if not at the price they predicted. In fact, neither has delivered on the promise.

BlueSEQ's Michael Heltzen

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Michael Heltzen, CEO, BlueSEQ Bio and Contact Info

Listen (2:26) Why BlueSEQ?

Listen (5:20) How does the service work?

Listen (3:53) Platform agnostic

Listen (1:47) Who are the providers?

Listen (2:35) Thoughts on Roche action

Listen (2:22) Will you add bioinformatics?

Listen (1:54) Being an entrepreneur

Listen (5:03) Bio in Denmark

To wrap up our series on Sequencing and Genomic Medicine, we’d like to welcome Michael Heltzen. He’s the founder and CEO of BlueSEQ, a new start-up based in Arhus Denmark, serving as an online sequencing exchange, matching providers and researchers. Michael has served as Director of Partner Sales at CLC Bio, a bioinformatics company also based in Denmark and as VP at BGI Europe. Michael is a board member of both Startup City Denmark and the Copenhagenomics Foundation.

Sequencing: An Overview with Shawn Baker, BlueSEQ

Podcast Sponsor: DNAnexus- Unlocking the potential of DNA-based medicine and biotechnology with a collaborative and scalable DNA data management and analysis technology platform.


Shawn Baker, Curator, BlueSEQ Bio and Contact Info

Listen (1:00) Curator at BlueSEQ

Listen (6:40) Roche's move on Illumina

Listen (4:44) Big news at JP Morgan 2012

Listen (1:47) Is speed really the issue?

Listen (2:35) Breakdown of market share

Listen (8:52) Advantages, disadvantages among major sequencers

Listen (9:58) Emerging Companies

Listen (1:17) AGBT

As we close out our series Sequencing and Genomic Medicine, we invited Shawn Baker, an advisor for sequencing technology at mendelspod, to join us and give an overview of the industry. He is the Curator for BlueSEQ's next generation sequencing Knowledge Bank. Having received his Ph.D. at the University of California, Davis, Shawn started his career as a Research Scientist at Illumina when it was a 15 person startup. Shawn is the founder of and a blogger at

Our Take on Personalized Medicine World Conference 2012: The Road to Commercialization

This week we attended the <a href="" targe=_blank">Personalized Medicine World Conference 2012 in Mountain View, CA. Though sequencing continues to dominate the show, this year there was much more focus on the commercialization of existing technologies for better, more tailored health outcomes. Some news that came just after the conference gave a nice punctuation to the feeling that personalized medicine is here to stay.

Sequencing (of course)

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