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.

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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.

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.

Next Gen. Sequencing for Dx – Exome v. Whole Genome?

While I was at CHI’s Molecular Medicine Tri-Con in San Francisco last week (Feb 23rd), I had a chance to sit in at a discussion table at the end of the day.  The topic at Table 6 was about diagnostic applications that used next generation sequencing (NGS).  About 16 people discussed the pros and cons of targeted resequencing versus whole genome sequencing. Karl Voelkerding M.D.,(Assoc. Professor, Pathology, Univ. of Utah; Medical Director, Advanced Technology and Bioinformatics, ARUP Laboratories), moderated the discussion. Karl said that NGS is being applied to multi-gene panels, exomes and whole genomes in clinical research and diagnostics. Each approach has different costs and complexity of data analysis and interpretation.

NGS for Multi-gene Panels v. Whole Genome
Karl started off by talking about multi-gene panels and NGS. Karl briefly talked about using multi-gene panels and Marfan Syndrome.  He said that the challenge involves sample preparation and noted that Fluidigm has a workable solution for this.

He asked the group “What’s being seen in Europe?” A person from Europe said that he has seen targeted NGS vs. whole genome NGS used by a fee-for-service company in Europe.  A person from Genomic Health said that, “if cost is not an issue, it’s OK to use whole genome.  But otherwise it’s better to use targeted resequencing.”  Karl said that at his lab, it takes over a year to do a CE- based multi-gene sequence [ vs. NGS].

Others at the table asked about costs.  The person from RainDance said that they have an in-solution capture method that could reduce costs.  Karl said that even there, there are non-trivial labor costs.  He said that “Some commercial companies do use robatic liquid handlers to reduce cost.”

Scenarios, Approaches, Costs
He said that this area is a moving target.  Amplified appproaches in multi-gene panels increase specificity for up to ten genes.  Otherwise if over ten genes, it takes many months of CE sequencing work. Researchers need to develop a special workflow for this type of CE- sequencing.  Karl said “An elusive goal is to make sequencing work like PCR.”  They are not there yet.

One person asked about simplifying the data content in a database by choosing some data as benign.  Karl said that academics are randomly updating their data by using a grad student or even an undergrad student.  But this approach gives inconsistant data quality.  He said that some commercial-based databases use more regularly scheduled updating.

He said that you need to ask the question “Are the genes associated with pathology?  Some genes are benign, some others are linked to disease.  We need to know, over time, what data items get classified as a changed data set.”
Some companies do targeted resequencing as a business and make IP from the database content. The database tells what is benign or what is something else.

A consultant asked “It would be interesting to see what in the database is predictive.”  Karl said “Extract the DNA, do PCR, do CE-seq, and analyze.”
The consultant also asked “What if you do NGS, then find genes, then pass data on to CE-seq to verify for Dx accuracy?” Karl said “Some research corelabs do exome sequencing for genome sequencing.  NHGRI is good with that approach.  He does 30x coverage at his lab.

Another person asked “What is the control level for false positives?
Karl said that, downstream, it depends on technologies used such as mass spec, v. NGS v. CE sequencing v. PCR.  Karl mentioned that the American College of Cardiology considered testing for hypertrophic cardiomyopathy (HCM)  and asked “Should we do multi-gene testing”  They test by using using echocardiograms.  Karl give the statitics for WW incidence.

So with the exome v. whole genome question. Karl asked, “When can you use gDNA for Illumina. The workflow is to do DNA sonograph, do Agilent Bioanalyzer 2100 to get total DNA, do qPCR to get fragment library which can go to the SOLiD or to the Illumina cluster [for HiSeq2000].

The sequencing workflow is:

  • Day 1 do gDNA
  • Day 2 do qPCR,  then transfer to Cbot
  • Day 3 run the HiSeq2000 at 2×100 for 8 days
  • Then run SeqTest, run QSeqTest, then output in Qfile format

Karl said it takes 105 days from start to end.

He said that, if you do exome sequencing, you need to do a purification step at the beginning, which adds 3-4 days to the workflow, but the exome sequencing is at a lower cost. Karl said the his lab is hooked up to the Univ. of Utah’s cluster computer and can do a data alignment in 1-day.  The cluster computer at the Univ. of Utah is also HIPPA compliant for privacy.

So cost drives exome sequencing. Karl said that “When doing exome sequencing you are doing a lot less sequencing, but you do more sample preparation.  You sequence on 2 lanes v. on 8 lanes [on Illumina].

Some List Prices
Karl gave some cost numbers.

  • For whole genome sequencing it costs $10K  with all reagents, including for library preparation.
  • For exome sequencing, it costs $1,200-$1,300 at 200X to 900X coverage.

So an answer for supporting multi-gene sequencing is to use exome sequencing of all genes in a panel.  e.g. Broad can sequence 2000 exomes per week. They streamlined a special workflow for this. Anyway, at the end of the day, you need to do down stream validation.

Consent Approaches that Should be Considered
A woman asked, “But in the clinical environment, what if you find other genetic information?, Some other genetic information?, Do you not tell the clinician?”
Karl said that “the key is informed consent.”  He said “ARUP is developing a tiered consent process — its mostly used for pediatrics now. So if they set out looking for one genetic area, but what if they find something else?  They age-level at age-14 for consent.”

Karl gave an example about the rare disease area at the NIH..  The NIH does exome sequencing.  Their success rate is 20% to identify a suspicious gene.  “So why just 20% with de novo mutations?”  He said that they are using exome sequencing and they just use a small population.  He mentioned a paper in Nature Genetics involving a group in the Netherlands  that saw a lot of power in NGS of a child that is an alternative to use laborious CE sequencing.

Karl said that the items not covered in the consented area are marked off.  He said that this is usually done in laboratory medicine.  When it comes to a recessive gene, the answer is often guided by family history.  Therefore “consent with tiering” is the way to be able to manage what diagnostic information is delivered to clinicians.  Karl wrapped up the discussion by saying that “NGS is pushing the envelope!”

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