Big Data and Precision Medicine Trending at CHI Tri-Con in SF

Moscone North Hall, Feb. 17, 2015. After walking the halls in the exhibit area at the recent annual CHI Tri-Con event in San Francisco, I discovered that a theme came together after I passed by various booths.

For one thing, the words “precision medicine” seemed to be resonating among those firms that were exhibiting and I asked some of them, “Is that the same thing as “personalized medicine” or “individualized medicine?”” I noted to that person that President Obama had recently made some kind of a speech that was promoting the idea of precision medicine so maybe the time has come for precision medicine to take the spotlight.

In any event I also found that there are other themes there such as big data. It is being used in a number of different biomedical research areas. I stopped by the Illumina booth spoke with the lady there whose name was Kathleen. She said that she had just joined the company about two months ago from Roche where she was involved in the clinical area. She said that her firm is moving into the data management side of their business with a focus on clinical diagnostics and take advantage of the fact that a lot of NexGen sequencing is now being used for clinical types of applications and will be generating lots and lots of data.  So big date is the theme here as well. They’re hoping to sell their systems into the clinic and hospital type settings so that they develop some very useful software systems to make sense of all that data. Data analytics is going to be a big deal.

I walked around and came across another booth that was also telling the story of powerful computer power and big data and that was the guy at Cray Computer that is famous for supercomputers in the past, but today they are using many many computers together as a cluster, a Hadoop and have another one they called SPARK. I’ll have to check out what “Spark” means. It seems to me that quite a lot is happening in the software.

CHI had other usual events that they have at the Exhibit Hall such as a raffle in which an attendee might win some kind of electronic gadget. This part of the event also featured a discussion tables. There were 40 tables that could handle as many as 8 to 10 people.  I noticed that just about every table was filled up in the hall and some of the tables had probably 10 to 15 people there, so they must have had some very popular topics to discuss. Traditionally, this part of the exhibit area has been very popular in past meetings that I’ve attended.

ThermoFisher Aims to Get FDA OK for its Ion Torrent PGM

By Paula Myers

At this year’s CHI Molecular Medicine Tri-Conference at the Moscone Convention Center, San Francisco, February 11th, there were over 3000 attendees and more than 200 exhibitors. I visited some of the many booths on the exhibit floor. One of those was the ThermoFisher booth. I spoke with Zhen Mahoney,Sr. Clinical Sales Specialist/Pharma Business. Mahoney talked about the acquisition of Life Technology and how it affects ThermoFisher.  Thermo will have to absorb Life’s 9,000 employees. Thermo currently has 40,000 employees. Mahoney pointed out that Life has a broad product portfolio. Ion Torrent, which Life acquired in 2010, is located at Oyster Point near South San Francisco. The rest of company is located at Carlsbad, California, near San Diego, including the Invitrogen and Gibco brands. These groups are staying intact, according to Mahoney.

She also pointed out that the company submitted an application for 510K marketing clearance to the FDA for its Ion PGM system for use as a diagnostics medical device. They are hoping for a 3 to 4 month approval timeframe. By comparison, the Illumina MiSeq took about 9 months to get FDA 510K approval because it was the first of its kind. The Illumina MiSeq received a relatively fast approval because the company worked closely with FDA reviewers so that they can understand its technology. The MiSeq platform serves as a template to the FDA for follow-on platforms from Illumina and other desktop sequencer vendors. Mahoney said that the next revision for their Ion Torrent electronic P-2 Chip is coming later in 2014. It will have 660 million wells.

Some of the other firms that I visited included: Guardant Health, Diagenode, and Epitomics. I focused on companies involved in epigenetics. Guardant Health is a two-year-old service company for individuals. In February, they released GUARDANT360, the first pan-cancer blood test that provides doctors with real-time genetic information to help them prescribe the right treatments for their cancer patients.

  Diagenode is a company originally from Belgium and sells Japanese made disruptor shearing machines such as the Bioruptor Pico for DNA, chromatin, and RNA shearing. Epitomics, located in Burlingame, California, offers custom antibody services for use in epigenetics research. Li Fang, Project Manager of Custom Antibody Services at Epitomics, said that Abcam is buying the company. Abcam is a supplier of antibodies,proteins, kits and reagents.

Spotlight on New Medtech Firms at the 12th BIO Investor Forum Meeting in SF

Palace Hotel, 12th Annual BIO Investor Forum meeting in San Francisco Oct 8-9, 2013.  According to David Thorcirus, the host of the opening meeting, this year’s BIO Investor Forum had about 700 attendees, 900 one-on-one partnering meetings and had a 30% increase in attendees compared to last year. The meeting focus is about small companies seeking funding or commercial partners. Of the 120 presenting companies, about 2/3 were private and about 1/3 were public stock firms.

Small Company Presentations Of Note.

  I found four new interesting medtech firms that were worth a first look.

1. Nano3D Biosciences (n3D) is new company run by Glonco Souza, the President and CSO.  The company is a spin-off of Rice University and the MD Anderson Cancer Center in Texas.  n3D’s mission is to develop the “Bio-Assembler” technology. They said it is a big paradigm shift in the developing of complex 3D tissue models.  They do this by levitating cells in dish. The Bio-Assembler (TM) is a nnao shuttle refill.  The product is covered by patent IP.

They get in-vivo -like results.  They claim to have the fastest 3D cell-based assay. It can produce results overnight vs. in 10 days. n3D uses Apple iPod Touch 4G mobile devices as computer controllers.

The “Magnetic Levitation Grows Realistic Lung Tissue…” in a headline in Science Magazine. The company uses ten Apple iPod Touch mobile devices for its compute platform.  Souza said that the limitation of existing 3D tools and assays for a small company. So far, n3D has raised $2.3 million.  Souza said that the investor exit strategy is to sell itself to a large company.  The firm is looking for customers, partners and investors.  Souza said that they currently need $600,000 in new funding.

2.Another new company, Nanofiber Solutions creates poly-nanofiber structures.  Ross Kayula, CEO, said that they place cells in fiber and look normal (cancer cells).  Their plates replace 2D plates. Their idea is similar to those of Nano 3D Biosciences.

The CEO said that their scaffold for implants prevents rejection and scarring in a trachea.  Their idea is a platform technology for organ regeneration — as implantable products.  Product status: Trachea in clinical trials; Other products are in pre-clinicals.

Ross said that IP is their largest cost and said that they need to raise a VC-backed seed-funding round of about $2 million.

3. iNanoBio is a new firm based in Tempe, Az. The company develops nanoscale sensors for combining nanoscale and diagnostics.  iNnaoBio seeks $7.5 million in a VC funding series.  The company is developing ultrafast next generation sequencing technology over the past nine months. The initial phase of their development is to make kinase activity high throughput screening. The CEO said that their technology is ultra fast an will sequence DNA in just fifteen minutes for about $200. They expect to target clinical applications using nanopore diagnostic technology. iNanoBio will make nanowire sensors attached to a nanopore to detect DNA in one pass at high speed. The firm is involved in an NIH program to develop their platform technology. The technology provides real-time detection of kinase proteins when compared to competing technologies from Thermo, Life Technologies, DiscoverX or others. The CEO said that their next step is to integrate microfluidics.  The manufacturing process is the same as in making semiconductor chips on a six-inch wafer. They can make a 1×3-inch slide with 10,000 wells to make an alpha-p53 assay. Their future n-MEDD product lines include: 1. Kinase chip assays, 2. Inhibitor discovery assay, 3. Target-ID assays for phenotypic screens. A key value is the real time kinetic results.  They are talking with Big Phama companies about their technology. iNanoBio plans to seek series A and B funding from VC firms.  The n-MEDD system development beta product is being shipped to customers.  They are developing a prototype genome sequencing device.

4. Metactive Medical is a medical device company run by CEO, Nicholas Franano MD.  He is the former founder of Proteon Therapeutics. The firm is developing two vascular repair products. Nicholas said that their first product involves a device for treating cereberal aneurisms that have a narrow neck. He said that cereberal aneurisms impact about 4% of the population. A rupture of an aneurism produces a hemorragic stroke which is often fatal. Patients usually have very bad headache symptom prior to an aneurism occurring. If they can detect the aneurism in time, the Dr. uses a catheter to put a coil of wire into the ball of the aneurism. The wire coiling procedure is the standard of care for treating cerebral aneurisms. This is a $500 million market segment. Dr. Franano said that wire coiling procedure is delicate, difficult and takes about two hours to complete.  He said that doctors need about two years training to perform this procedure. Unfortunately, about 3-5% of the aneurisms are punctured by dosctors. Each coil costs about $1,000 and some aneurisms require up to twenty wire coils.

Metactive Medical is developing a better device, the Ball Stent which is attached to a microcatheter. The Ball Stent is guided up to and into the ball of the aneurism. When activated, the end of the stent expands and fills the ball of the aneurism. A wire seals off the bloodflow from the artery at the neck of the aneurism. The procedure takes about twenty minutes. The company tested the idea in a pilot study in dogs by testing an 8mm Ball Stent. The successful procedure delivers a permanent treatment. The FDA classify would the Ball Stent as Class-2 Device and would require a 510K filing application. The second product is vacular device to repair peripheral artery occlusion.  This is a $50 to $75 million market. The Firm’s device deploys a ballon that repairs the artery wall. Dr. Franano estinmated that the market for the Ball Stent is $1 billion and the peripheral artery occlusion device market is $100 million.  He said that the company would sell itself for $200-250 million to a buyer or develop its products further. I asked when might the Ball Stent likely reach the market and Dr. Franano said that, if developed, it could reach Europe by 2020.

Biotech Experts Highlight Clinical Sequencing at Rx/Dx Summits

I recently attended the IBC Rx/Dx Summits held in San Francisco in the first week of August 2012.  The meeting was held at the Westin San Francisco Market Street Hotel.  I was attracted to this event because it gave me the opportunity to learn about some of the new emerging market dynamics in next generation sequencing (NGS) and other areas that I track for my firm.

I listened to a talk comparing desktop sequencing systems by Jason Lih, Ph.D., Principal Scientist, SAIC-Frederick.  His talk was called Assay Development for Detecting Somatic Mutations in Cancer by Targeted Amplicon Sequencing: A Technical Comparison between PGM  and MiSeq.

Dr. Lih’s talk compared two desktop NGS machines, the Life Technologies, Ion Torrent, PGM with the Illumina MiSeq. At the beginning of his discussion, he said that he would not say which NGS platform is better.

In his NGS application, he used targeted amplicon sequencing to develop assays to detect somatic mutations in cancer.  Jason said that the PGM used AmpliSeq  v. Illumina’s TruSeq Custom Amplicon  (TSCA) technology.  He said that Life’s PGM requires just 20 ng of DNA sample, whereas the Illumina MiSeq requires 250 ng of DNA sample.  The Life PGM uses a 4-plex #‘316’ chip which outputs 1×200 base pairs of bi-directional sequence in one day plus 4 hours. (or 28 hrs).  The MiSeq takes 27 hrs (or 1 hr. less).

Using a comparison concept that he called the “Cosmic” MOI (Molecule Of Interest), he created a comparison chart comparing 1160 Cosmic MOIs.  He compared both vendor’s reagents.  His results showed that the PGM produced slightly more MOIs.

Vendor Model Reagents MOIs DNA Sample Run Time QScore
PGM AmpliSeq 1148 20ng 28 hrs 30
MiSeq TSCA 1108 250ng 27 hrs 30

The PGM variant caller was the Ampliseq Reporter.  He used a 3rd party software from CLC Bio.  The CLC Bio Integrated Genome Viewer showed a Qscore of 30 for each NGS machine.

What is interesting to me is that at end of his talk during the Q&A, an attendee asked Jason for his opinion about which was the best of the two NGS machines that he compared.  He said that his comparison was not intended to find the “best” NGS machine. My take away from his answer was that as far as Jason’s application was concerned, one could use either NGS machine and get comparable/ usable research data.  Also of note is that Roche Applied Systems demonstrated their 454 GS Junior desktop sequencer at the exhibit hall.  I wonder how the 454 GS Junior would compare against the PGM and MiSeq machines.

During the lunch- networking break in the exhibit hall, I met Robert Klein, Ph.D., Chief Business Development Officer, Complete Genomics, Inc. who said that he was giving a talk later in the day.  I attended his talk called: Large-scale, Accurate Whole Genome Sequencing to Enable Genomic Medicine. 

Robert gave a update on the business direction or activities at Complete Genomics (CG).  He said that CG v.1 was about research sequencing and that CG v.2 is more about clinical sequencing.  Dr. Klein said that in 2006 CG developed its proprietary sequencing technology and service model.  By 2011 they had delivered 3,000 genomes to customers.  Robert said that CG now produces 1,000 genomes per month.  He explained that they have a DNA factory in Mountain View and sends the data to its data center in the nearby city of Santa Clara.  CG does this because Santa Clara offers a lower cost for electricity.  CG provides “research ready” data to the customer and the customer analyzes the data.

Robert highlighted CG’s goals as including: Setup a CLIA facility 2H’12, Scale-up quality, Scale down cost, Scale-up throughput and Offering ‘clinical use’ sequencing.  CG will be focusing on new apps. including Idiopathic kids, Refractory cancers, Replacing cytogenetic arrays and Replacing targeted panels.  Dr. Klein also added that CG is interested in Wellness/ concierge medicine and Reproductive genetics.  He mentioned that CG is exploring other market spaces such as Prenatal screening, Newborn screening, and Reproduction Issues.  Dr. Klein predicted that the first areas that whole genome (clinical) sequencing would show clinical utility would be in studies of copy number, neuroblastomas and translocations. Robert said that NGS will likely democratize genomic medicine.

Several speakers echoed TGEN’s David Craig, Ph.D., Deputy Director for Bioinformatics and Professor of Neurogenomics,  comment that “the cost of NGS went up in 2011 because the analysis bottleneck is the culprit.”  My take on that is that in clinical NGS, the all-in $1,000 genome might be postponed to beyond 2014 by perhaps a few more years.

Ion Torrent Launches $1,000 Genome Sequencer in SF

On January 10, 2012, San Francisco, The Ruby Skye nightclub — just a block from the 30th Annual J.P.Morgan Healthcare Conference.

Life TechnologiesIon Torrent division hosted a reception and gave a product launch presentation for their new genome sequencer, The Ion Proton.  The invited guests enjoyed a cocktail reception for about 45 minutes before taking their seats at the theater-like presentation space.

Greg Lucier, Life’s CEO appeared, made some opening remarks and introduced Dr. Jonathan Rothberg, Ion Torrant’s founder.  Jonathan spoke for about thirty minutes and recapped the history of Sanger sequencing, 454 sequencing, comparisons to advancements in the computer industry and how his son got him to think about semiconductor-based sequencing.  He explained the rationale for using semiconductor technology for the Ion Torrent sequencer. Rothberg said that using the Ion Personal Genome Machine (PGM) to quickly sequence the genome of the virulent e.coli strain found in a contaminated food outbreak that killed 50 in Germany last year demonstrated the value of the PGM for public health. He said that as a result of the e.coli outbreak experience, Ion Torrent developed assays that turned out to be ideal for healthcare research applications.

At this point, Jonathan stepped back to a black draped structure at the back of the stage and unveiled a rack containing four new benchtop Ion Proton genome sequencers.  Rothberg spent about ten minutes explaining the key details about the new Ion Proton machine.  Life Technnologies is taking orders for the the Ion Proton, which sells for $149,000. He said that these machines are ideal for customers that need to sequence exomes and genomes.  The machines are designed to sequence exomes for $500 and genomes for $1,000 in 24 hours. The costs mentioned are material costs. The Ion Proton uses two new chips.  The Proton I chip has 10X the density of the current 318 chip (1.65 million wells) used in the PGM, is for exome sequencing and will be available later in the Spring. The Proton II chip has even higher density, with about 660 million wells, is for genome sequencing and will be available later in 2012.  Jonathan said that he was impressed that at a starting point of just using the PGM chemistry kit, the Ion Proton produced 200 base pairs of sequence.

Greg Lucier and Jonathan Rothberg on stage with Four Ion Protons

After the presentation, I had an opportunity to see and touch the new Ion Proton machine located at the back of the reception area and spoke with the Director of Product Marketing who was there to demo some of the new machine’s key features.  He said that Life Technologies was taking its sequencers on the road in their new Ion Torrent Bus which was parked out front.  After our discussion, I went outside and climbed aboard their mobile sequencing lab in a bus.  The two spokeswomen there said that bus the has two PGM machines and will soon be outfitted with two Ion Proton sequencers for a total of four machines that can sequence DNA as they drive.  I asked if they would be visiting the upcomimg genome conference at Marco Island.  They said yes and would also be visiting universities and commercial centers.

Pros and Cons of Sharing Personal Genomes on Social Media

I recently particpated in an online conference session held by NGS Leaders when CHI held its Beyond Sequencing conference in San Francisco recently on June 21, 2011. The session was moderated by NGSLeaders’ Eric Glazer and a panel of NGS experts.  The panelists included Kevin Davies, PhD.(Bio-IT World) Pillar Ossorio , PhD. (Univ. of Wisconsin), Johnathan Eisen, PhD, (UC Davis), and Kamamiesh (Kam) Patel, PhD. (Sandia National Labs).  This panel session was about “When People Share Their Genomes on Facebook.”  Both Kevin and Kam participated by telephone and the others were with a live audience in the meeting room.  The session used WebEx to link remote participants.

Kevin summarized the recent history of personal genomics services since the field was started by and deCode Genomics.  He pointed out that these services were marketed as services that enabled consumers to learn much about their genetic make up.  The services just provide information that might help people learn more about their risk for common disease or for geneology.  The customers’ genetic information is not to be used as a diagnostic. While the technology is initially based on microarrays and SNPs, some companies hoped to use NGS when the cost gets low enough.  However, Kevin said that the future of personal genomics is still in the hands of the FDA to decide on guidance to the industry.  Johnathan predicted that we will see a lot of push inside of genomes and personal microbiomes.  Microbiomes are the total kinds of microscopic things that live in or on our bodies.

As the discussion turned to social media, Kam said that the social media giants have big potential uses for health information.  A person could meet with their doctor, then the doctor could later access the person’s Facebook page and follow the progress of a treatment regimen.  But there are pros and cons to watch out for such as exploiters and cost issues.

Johnathan spoke about ‘crowd sourcing’ would be useful for health information.  He said that Facebook is only partly open.  He noticed a new push for open science such as to post lab notebooks on a social media site.  As for citizen science, he predicted that personal genomics, open science projects and citizen science will merge together.  When that happensm then anybody can make or use the information for their own open science projects.

A big question is who owns the personal genetic information held on social media sites.  Pillar, a lawyer, said that  we can think about this in terms of copyrights and patents.  She said that for example, when I get genetic information, I might just get a license for personal use, — it might be limited or unlimited.  The media site rules migth determine who can use the information, etc. At least we have the GINA law to protect our rights regarding employment and insurance discrimation.  However, she thinks that much of this is unknowns.  Pilliar said that the courts would likely say that if you put your genetic information on a public social media site, you are effectively giving away information to the public domain.  She said that people need to be educated about the subject so people would know who should participate.  She said that George Church has a screening process to weed out ignorant people.  He makes applicants take a genomics class and his program has a high cost.

Eric asked the panel when might clinical use will happen or become routine.  Johnathan said that technology will happen soon, but he did not know when clinical practice will happen.  Kevin said that the clinical use of personal genomics is happening now and cited the case of the boy from Wisconsin who was helped by NGS based diagnostics.  He said that there is a huge amount of genetic medical education that is needed.  Pillar said that she believes that the clinical context will take some time to work out.  My take on personal genomics and social media is that we are still in the early early days.

Low-Cost sequencers to Drive Growth in NGS Installed Base

First quarter announcements by two early makers of low-cost NGS machines suggests that brisk sales of the platforms will likely boost the overall installed base of NGS machines deployed into labs worldwide.  In mid-April, a spokes person from Roche 454 Life Scicences said that “We are pleased with the rapid adoption of the GS Junior System in the market.”  The person also said that 454 had “placed hundreds of GS Junior instruments in laboratories worldwide.”

To me, “hundreds of instruments” could be interpreted as at least 300-400 instruments. That’s quite a lot of 454 GS Junior instruments shipped since its launch last May. Most of what I have read about the GS Junior suggested that the instument have limited utility and may  have disappointed some users.  Brisk sales of the GS Junior is a surprise to me.

Life Technologies made an announcement about its low-cost Ion Torrent sequencer as part of its first quarter financial release. They said that their Q1 orders were greater than what they had expected.  They said the the strong order rate suggests that they might sell more Ion Torrent PGMs over the next 12-months that will exceed the installed base of the leading NGS instrument.  I assumed that he was referring to the installed base of the Illumina GA series of NGS machines. The Univ. of Birminkgham website shows that the self-reported installed base for Illumina GAs to be over 660.  I suspect that this website lags the real installed base by a few hundred. I read that LIfe Technologies had initial orders for 60 or so PGMs.  So I would expect that exceeding their original expections could be interpreted as 100 to 130 shipments for the PGMs for Q1. If LIfe’ shipment estimates do materialize, then sometime next April the installed base of Ion Torrent PGMs will reach about 670.

I estimate that the accumulated installed base of 454 GS Junior machines that might be deployed by next April would be about 650. So together, The installed base for the two low-cost NGS platforms might reach an installed base of 1,320 instruments.

If I assume that Illumina’s MiSeq instrument rolls out sometime in August and they have a run rate that is similar to the Ion Torrent, they might ship about 400 by next April.  Add that number to the mix and a conservative guestimate of the installed base for low-cost NGS machines might reach 1,720 machines by then. I can see that democratization of DNA sequencing will begin to take effect in mid-2012.

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