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.

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.

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.”

BIOInvestor Forum: Biotechs Fight Cancer Stem Cells

The CSC workshop was a hot topic at the BIOInvestor Forum at the Palace Hotel in San Francisco on October 9, 2012,.  At the “Cancer Stem Cell Therapy—Real or Just Hype?” workshop moderated by Nathan Sadeghi-Nejad, Contributor at Forbes & TheStreet, panelists talked about the difficulty of developing therapies for cancer stem cells (CSCs).

CSCs Can Evolve to Resist Chemo

John Lewicki, Executive Vice President and CSO, at OncoMed Pharma. Inc. said, “CSCs can resist attacks easily. They are fundamentally resistant to chemotherapy.  At OncoMed, we are trying to reduce that resistance with our antibodies by having multiple approaches.”  “Early on, we have seen data that is impressive with unique results.  We managed to control extremely aggressive ovarian cancer,” said Lewicki.

Tom Cirrito, VP of Research and Development, at Stemline Therapeutics, talked about the company’s SL-401 lead compound, for treating advanced acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Cirrito said, “We’ve treated 76 patients with a large body of preclinical evidence.”

Leslie Crews, Project Scientist, at Sanford Consortium for Regenerative Medicine/UC San Diego Cancer Center said, “We need to distinguish between tumor bulk and CSCs.  We also need a combination of strategies. These are evolving targets.  Cells evolve and evade therapies.  We should introduce CSC therapies later.”

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

Vitamin D Controversy Leaves Many Confused

On May 24, 2012, I watched an online presentation given by Neil Binkley, M.D.  (University of Wisconsin School of Medicine and Public Health) at the 3rd Annual Clinical Diagnostics BioConference Live virtual event sponsored by LabRoots.com.  His topic was “Vitamin D, Common Sense and the Goldilocks Principle.”  Binkley presented some very interesting statistics about vitamin D and how it may or may not effect our health.

He is not surprised that clinicians and the lay public are confused.  It is also not a surprise to anyone that people around the world are not getting enough vitamin D.  Some of the reasons for this include not enough in our diet, low sun exposure, and greater skin pigmentation.  I know that I worry about being in the sun too much because of skin cancer worries so I take calcium with vitamin D supplements.  However, the latest news about the dangers of too much calcium weigh on my mind.

Binkley talked about the one size fits all idea.  We need to recognize that we are not all the same.  I agree that you cannot give the same daily recommendations for everyone.  Expert guidelines differ widely.  For example, the Ministry of Health for Australia and New Zealand recommend 200-600 IU daily.  The Endocrine Society recommends 1500-2000 IU daily.  This is a very broad gap.  “We need to recognize that public health guidelines differ from patient care,” said Binkley.

He also said that despite issues and uncertainties, 25(OH)D measurement is currently accepted as the best measure of an individual’s Vitamin D status and he agrees with Mark Bolland and others that we don’t need to meta-analyses inadequate data.  He urges the Vitamin D field to stop the “boxing matches” over this issue.  He believes clinicians should take a common sense approach with their patients.  According to the American Association of Clinical Endocrinologists, 1000-2000 IU of Vitamin D daily is required to maintain a 25(OH)D level at 30 ng/ml or above.

Binkley concluded by saying that “vitamin D inadequacy is common,  but fixing this is cheap and virtually side effect free.”  There is not a downside to aiming for 25(OH)D in the 30-50 ng/ml range.  This may require around 800-1000 IU/day (or more).  He also said that vitamin D is not the “fountain of youth”, but has a number of health benefits beyond bone.  It may also reduce all-cancer risk in postmenopausal women.  It is always best to talk to your doctor and have them decide what is best for you while the controversy rages on.  Like “Goldilocks” when looking for what is just the right amount, Binkley believes that the 30-40 ng/ml range is just right.

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