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.

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iPhone 5 More Powerful than the Curiosity Mars Rover

SAN FRANCISCO (Takeda Pacific HighTech Reports), Moscone West, January 30, 2013 — MacWorld/iWorld 2013.  NASA experts spoke about NASA’s Curiosity Mars Rover and its connection to Apple products at a meeting here.  The session was titled “Software, Hardware, and Flying to Mars. How We Built, Programmed and Operate NASA’s Curiosity Mars Rover.”  David Oh, Lead Flight Director and Software Engineer at JPL/Caltech Mars Science Lab, asked the question, “Why are we at MacWorld?”  The answer was shown in a slide of the NASA control room at the JPL in Pasadena, California.  On the desk was a mixture of Apple products such as MacBook Pros, iPhones and iPads during the Rover’s Mars landing.  The Macs were running Mac OS X.

Ben Cichy, Chief Flight Software Engineer, compared the processing power of the iPhone 5 to Curiosity’s processing power.  The iPhone 5 has 1.3 GHz and the Curiosity has only 132 MHz.  In addition, the iPhone 5 has 1GB of memory and 64GB of storage and the Rover has 128MB of memory and 4GB of storage.  The cost of an iPhone 5 is $399 while the cost of the Curiosity was $1.8 billion.

During the session, the audience was shown a video of the landing of the Curiosity on Mars.  It only took 7 minutes, but a very tense 7 minutes.  It was very exciting watching the landing of the Mars Rover all over again.  “The Rover’s goal is to explore and see if Mars ever sustained life or is now,” Ben said.

David showed a slide that described the different parts that make up the Rover.  He added that the heart of the mission is the SAM (Sample Analysis at Mars).  The SAM analyzes the chemical and isotopic composition of the planet’s atmosphere and surface.  He said that the “Curiosity has two brains (computers) in its belly.  One is the primary computer and the other is the backup.”  This time social media plays a big part in providing people access to seeing what is happening with the Curiosity as it explores the surface of Mars.  The Curiosity has its own Facebook page and iPhone app.

OvaScience, Seattle Genetics, and Qiagen Present at 31st J.P. Morgan Heathcare Event

This year’s 2013 J.P. Morgan Healthcare Conference at the Westin St. Francis in San Francisco (January 7  to 10) had around 8400 attendees and around 400 company presentations.  Navigating through the hallways to the numerous presentations was a challenge.  These are three of the many company presentations I attended.

OvaScience’s CEO Michelle Dipp gave a very interesting presentation about new infertility treatment options. The U.S. fertility market is over $4 billion and it is seeing rapid worldwide growth, said Dipp.  Some other interesting statistics included that every year there are 7.3 million childbearing women that are infertile and 1.2 million women seeking treatment.  There are over 400 IVF clinics in the U.S.  Most of them are in the East and West Coast.  Unfortunately, most IVF treatments fail because many women are delaying childbirth. Apparently, energy in eggs decreases with age.

OvaScience has discovered that adding mitochondria to human eggs increases IVF success. The company’s new approach to infertility is called the Egg Precursor Cell (EggPC).  The discovery of these EggPCs (germline stem cells) that mature into eggs offers new fertility treatment options, said Dipp.

The company has two product candidates that include Augment and OvaTure.  There is a study underway for the firm’s first product, Augment.  Augment uses EggPC mitochondria to rejuvenate eggs.  The company’s second product OvaTure involves fresh, young, healthy eggs matured in the lab from EggPCs.  The OvaTure program is currently being designed.  According to Dipp, the goal is to improve the IVF success rate for older women while reducing the number of embryos that need to be transferred to the uterus thus decreasing the number of multiple births.  That would be great news for the many infertile women who could benefit from this treatment and not have to worry about the potential of multiple births.

Seattle Genetics’ President and CEO Clay Siegall began his presentation with the company’s key value drivers.  They include building the Adcetris franchise, advancing the antibody-drug conjugate (ADC) pipeline and technology along with its strong financial position and collaborations to fund a very robust research.  Adcetris targets the CD30 cell membrane protein, which is expressed on the surface of certain types of lymphoma cells.  Adcetris is FDA approved for relapsed Hodgkin lymphoma and systemic anaplastic large cell lymphoma.

The firm also received EU approval for Adcetris in October 2012.  Seattle Genetics has 20 internal and collaborator ongoing clinical programs for Hodgkin lymphoma and other cancers.  The company has collaborations with Millennium/Takeda, Genentech, Celldex, Bayer, and Abbott just to name a few.  According to Siegall, “ADC collaborations have generated over $200 million to date with the potential for around $3.8 billion in future milestones plus royalties.”  Net product sales of Adcetris since launch in August 2011 are over $145 million.  Siegall said they are “making strong progress towards a fully global brand.”

Peer Schatz, President and CEO at QIAGEN N.V., began by saying that “2012 was a very important and successful year.”  He said that QIAsymphony is the company’s fastest growing product in molecular diagnostic placements with Europe being the biggest at 40 percent and the U.S. coming in at 35 percent.  Another of its products is the Therascreen KRAS test, a companion diagnostic for metastatic colon cancer to help guide doctors in the use of Erbitux.  “The U.S. KRAS market conversion is progressing well.  Doctors are demanding the Therascreen test,” said Schatz.

Over the next 2 years, the firm will be developing several new molecular diagnostic assays.  Qiagen is also developing new biomarkers with the potential as companion diagnostics.  One of the company’s goals is to “expand NGS from research to routine clinical use.”  Qiagen is preparing the launch of its first NGS workflows in 2013, which includes a broad range of its products such as the QIAsymphony NGS version.  In closing, Schatz said the company will be “executing on its 2013 initiatives to drive growth and innovation at a faster pace.”

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.

Circulating Tumor Cells Emerging as a Hot Topic In Cancer Research

While visiting CHI’s Molecular Medicine Tri-Conference back on February 20th at the Moscone Convention Center, in  San Francisco, I had a chance to walk around the exhibit hall and talk with some of the people working at their trade show booths.

I spoke with Sally Hall, who was working at the Transgenomic, Inc. booth, and asked her, “What are some of the hot topics at the show?.” She said that it seems that this year, a hot topic at the CHI MMTC is about circulating tumor cells (CTCs).  Sally said that “this year there are about twenty companies working in this field.”

I mentioned that I noticed that the number of conference talks about CTCs at the CHI MMTC had grown over the last three years.  She agreed that she had seen increased research activity in the CTC field.

As I understand it, when cancer tumors reach a certain size or age, some of the cells break off and migrate through pores in the walls of  blood vessels and circulate in the blood stream as CTCs. The CTCs may remain dormant for months or years in the circulatory system before migrating through pores in the blood vessels to spread to other organs or tissues.

Scientists are using CTCs as a new type of biomarker.  Several research tools and technology companies have developed technology platforms to identify, isolate or characterize CTCs.

Some companies are working to develop a platform that utilizes CTCs as basis for a future personalized diagnostic.  Researchers might someday develop blood  tests that can accurately identify specific kinds of cancer tumors long before they spread to other organs.  Blood test based companion diagnostics might be developed using CTCs in concert with targeted medicines to kill tumor cells before a cancer tumor has a chance to spread.

On the other side of the exhibit hall, I spent a few moments to see a talk from the founder of Rarecells, Inc.who discussed their progress in developing a CTC-based diagnostic method that they called ISET.  I was impressed by their concept. The table below lists a few of the commercial companies working in CTCs.  Whereas the CTC field is an emerging niche market today, it may be too soon to tell what the size and shape that this market might take.

Selected companies working in CTCs

Application Company Comment
Clinical Use of CTCs Fluxion Biosciences, Inc. IsoFlux system for  analyzing CTCs
Clinical Use of CTCs On-Q-ity, Inc. Microfluidic system for selecting CTCs
Clinical Use of CTCs BioCept, Inc. OncoCEE™ Platform for capture and detecting CTCs for molecular analysis
Clinical Use of CTCs Rarecells, Inc. ISET, a diagnostic method for isolation and immuno-molecular characterization of CTCs
CTCs in Clinical Trials Johnson and Johnson, Oncology Biomarkers Liquid biopsy – the use of CTCs in clinical trials as prognostic and predictive markers.
Novel Technologies ScreenCell, Inc. A mini device to isolate rare circulating tumor cells (CTCs).
Novel Technologies Advanced Cell Diagnostics, Inc. The CTCscope platform for detection and character-ization of CTCs

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.

Using Nanofibers to Build Better Brain Tissue

I recently watched a video about nanofibers that was amazing.  Engineers and medical researchers at Nanofiber Solutions and the Ohio State University Comprehensive Cancer Center (OSUCCC) are using polymer nanofibers to simulate the three-dimensional structure of human tissue in plastic petri dishes.  These translucent spider-web like nanofibers are 100 times thinner than a human hair.

Normally, researchers would study live cancer cells under the microscope in petri dishes but it does not tell them how they interact in humans.  Since nanofibers are the exact size and spacing as human brain tissue, cancer cells behave more naturally on this than they would on plastic.  This gives scientists a more realistic environment to develop drugs that work.

This new approach could change how tumors are treated.  Doctors could someday take a biopsy of a tumor, put it in this tissue and try out different drugs on it all in the lab.  According to researcher Mariano Viapiano, PhD at OSUCCC, “the treatments that we are doing are specific for that biopsy for that patient.  So that will allow us to eventually to say this is the potentially best treatment for that particularly patient.”

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