Cliff Reid to Resign as CEO of Complete after BGI Shakeup

Theral Timpson


Genome Web reported today that BGI has put Complete Genomics' recent launch of the Revolocity super sequencer "on hold." According to Complete CEO, Cliff Reid, BGI has been undergoing "a strategic reevaluation" since the surprise departure of their founder and chief executive, Jun Wang, back in July.

This must come as a complete shock to Cliff and his team over in Mountain View. In an interview here at Mendelspod just last month, Cliff was bullish about the new super sequencer and had just presented some data on the Revolocity at ASHG in October.  Cliff told GenomeWeb that he plans to resign.

Cliff has been an eloquent spokesperson for genomic medicine since co-founding Complete Genomics back in 2006, then the world's first large-scale human genome sequencing company. Rather than sell instruments, Cliff and Complete set themselves apart as a service company. When Complete had to sell out to BGI in 2013, it was already apparent that the product model had won out over the service model, as most major research centers chose to have their own tools to sequence human genomes.

In our recent interview with Cliff, he said that it's not really about product vs. service anymore, but rather about centralized and decentralized. "There is still a nationalistic view of DNA," he said, pointing out that every country is concerned about shipping their genomic data overseas. And that means that "you gotta take the instruments and the data to the customers where the patients live."

I hope Cliff sticks around in the genomics space. He's got some strong ideas about how genomic medicine will play out and has always been excited about the possibilities of the direct-to-consumer model.  In a post I wrote back in 2013, 5 Myths of Genomic Medicine, Cliff said:

"If there’s any revolution that will change medicine, it’s not the science of biology as much as the phenomenon of social media.  It is changing the way humans interact.  It is changing our culture and turning existing hierarchies on their head.  Patients are talking with each other.  They are talking directly to researchers, and as seen in the previous myth, they are developing a different relationship with their physicians." 

Prior to starting Complete, Cliff founded a search engine company (before Google) and a video sharing site (before YouTube), neither of which panned out.   He told me once that the joke around his house is "fourth time is the charm."  

An Industry Policy Update: The LDT Hearing, a Dx Reimbursement Win, and a Bold Look at Drug Pricing

Theral Timpson


Congress Questions FDA and CMS on LDT Regulation

Over the past several years we have been closely following the move by the FDA to regulate laboratory developed tests, or LDTs.  Most recently we had Scott McGoohan from BIO on the program summarizing the  group of alternate plans which have recently been presented to Congress.  The sponsors of these plans--the main four being AMA,  AMP, CAP and the Diagnostic Test Working Group--hope to persuade Congress to intervene and change the FDA’s current course.  The plans have been presented both to the House Committee on Energy and Commerce (E & C) and to the Senate HELP Committee.

This week, E & C held a hearing on the topic of LDT regulation and invited as witnesses, Jeffrey Shuren, director of FDA’s Center for Devices and Radiological Health, and Patrick Conway, chief medical officer at CMS. 

There were two important developments at the hearing.  First of all, in preparation for the hearing, the FDA released a report making their case as to why they should regulate LDTs.  This report is something that members of Congress had asked for last year, and this week we got to see a list of  20 examples of non-regulated LDTs that the FDA feels are bad for patients.   Some of the cases involve false-positive tests where patients have been told they have conditions they do not really have. The report argues this "has caused unnecessary distress and resulted in unneeded treatment." In other cases, the LDTs were offered false-negative results and  patients’ life-threatening diseases went undetected. Here, patients have failed to receive effective treatments. 

The examples were all anecdotal and Dr. Shuren got drilled on this by the committee.  Are these stories sufficient evidence of harm? Shuren assured the committee that the FDA does use case studies such as these when validating tests.  He also pointed out that evidence of unregulated tests causing patients harm is actually hard to come by for the very reason that there is no system in place for post market review.  Upcoming LDT guidance will fix just that.  

The second development that struck me is that CMS totally had the FDA's back on this.  Dr. Conway of CMS always agreed with Dr. Shuren and frankly told the committee that CMS doesn’t have the personnel, the resources, or the expertise to provide oversight.  Dr. Conway offered numbers, saying that CMS has only 25 “survey staff,” and they are trained in lab and equipment protocols.  They “do not have scientific staff capable of reviewing complex medical and scientific literature to determine clinical validity,” he said.  “This expertise resides within the FDA.”

All summer we’ve been hearing about these alternate proposals for oversight which mostly call for a "beefed up" CLIA.  It turns out that CMS, the folks who run CLIA, don't want to do it.  Dr. Conway says that they can't and furthermore, it would lead to "inefficient and duplicative" oversight.  It's reassuring to see the FDA and CMS in such full agreement.  We got this one, the two agencies already in place are telling Congress.

So where does this leave us?  Dr. Shuren of FDA was specifically asked when final guidance would be finished and published.  He reluctantly volunteered “early 2016."  Whichever way it goes, there will be more politics involved.  On the one side, when the FDA puts out final guidance, it must still be cleared by the Office of Management and Budget, which was widely believed to have held up the draft guidance by a year.  On the other side, if one or a combination of the proposals before Congress is drafted into a bill, it must, of course, pass the House, the Senate, and the President’s desk (unless Congress musters the votes to override a veto.)

There is a third option.  LDT reform could be done through MDUFA, or the Medical Device User Fee Amendments.  This is a legislated user fee system where medical device companies pay fees to the FDA to fund review activities.  The user fee programs must be periodically renewed by Congress and are next up for renewal in October of 2017.  This would provide Congress with an opportunity to take legislative control of LDTs without a new standalone bill on the topic.  

A new bill  could perhaps take years and the MDUFA option wouldn't work until late 2017.  With the FDA’s final guidance on LDTs out much sooner, will resistance have settled down by then?

CMS Reverses Course on Diagnostics “Disimbursement”

Earlier today I heard from a very happy guest we had on the program a month ago, Peter Maag of CareDx.  When I interviewed Peter he was in a fight for the life of his company as CMS had proposed a decrease in the reimbursement rate of CareDx’s Allomap test for heart transplant recipients.   In an email titled, "Patients Win", Peter wrote today that CMS had reversed course and that reimbursement rates will stay the same.  After a coalition of diagnostics companies and policy experts mobilized to fight against the decrease in rates, CMS chose to go with the “gapfill” method of pricing vs. the “crosswalk” method.  

"How the original decision to crosswalk AlloMap and several other molecular diagnostics to single codes remains unclear," wrote Peter.  "However, it is apparent that the [CMS] Advisory Group was able to listen and amend the recommendation prior to any significant impact to patient care."

This is great news for CareDx and many other diagnostics companies who would have been affected, including Genomic Health, Vericyte, and Myriad Genetics.  Shares of CareDx surged today as much as 40%  after  the news.

As discussed in a recent interview with diagnostics reimbursement consultant, Bruce Quinn, CMS' outdated reimbursement methods will fortunately be changing next year as the result of the new PAMA (Protecting Access to Medicare) legislation.  Pricing in the future will be set in the way it’s done on the drug side of the industry, with a market-based payment system.

Drug Pricing Controversy

As diagnostics move to a market centric approach, unfortunately that approach is being abused by more drug companies than would like to admit it.  The topic is becoming an issue for the presidential election.  In the Democratic debate this past Saturday evening, we heard more attacks on drug companies.  As would be expected, the self-proclaimed revolutionary Bernie Sanders said drug companies are "ripping people off every day."    We expect to hear this kind of lambasting and outrage at debates.   So it was great to hear Hillary Clinton put forth a substantive idea asking,  “why isn’t Medicare able to negotiate drug pricing?”  Many leading physicians and healthcare journalists are arguing for just such reform.

For further insight into the drug pricing issue,  Luke Timmerman of the Timmerman Report had a refreshingly bold and introspective chat  this week with Alnylam CEO, John Maraganore with a call for the industry to  face itself: 

"LT: Who ARE you, really, as an industry?

JM: Yes, who ARE we as an industry? Martin [Shkreli] has got us all asking ourselves, ‘What is it all about?’ Oddly enough, I think it’s been good for the industry. I really do. What we are about as an industry is innovation, and patients. We’re about 21st century cures, not 1950s drugs. Most Americans, I think, appreciate that if you work really hard, and do something that is gigantic, you ought to get rewarded. Most Americans don’t like people that try to get rich quick, those who try to cheat the system. That’s why the distaste in people’s mouths with Turing, and maybe others like Valeant, is so appropriate. It doesn’t fit our work ethic. That’s the stuff we want to teach our children."

I Prefer My Bacon Crispy: Why I Don’t Think CRISPR is Really That Big of a Deal

Sultan Meghji

With all the recent news around CRISPR my reaction is “meh” (coincidentally, the same reaction I’m having to the current US presidential election noise). We are a wee bit early for both.

Is Jurassic Park – and now Jurassic World real? No.

“Cutting and pasting” of genetic material is a well-used mechanism. It replaced the (ahem) ever so accurate and useful “shoot a bb gun into a petri dish” model a while back. Restriction enzymes have been out there for well over 20 years. The focus on T cells in the blood streams and the usage of electroporation is interesting. Of course, not blowing up the cells would be useful, and there is a non-zero chance of that happening currently.

The net result would be the ability to perform genetic dialysis of the bloodstream to counter disease or inherited traits (and gene therapy).

Let’s push the hype meter down a few notches.

This isn’t a massive leap that will be available in market next week. Like most technologies in this space, you are looking at 10+ years of research validation prior to market entrance. Let’s also remember that the first market entrance will be focused on people deep in sickness, where their wallets will pay anything to ward off death.

My hypothesis is that the first commercial (or end person usable nature) would be in places where modification of existing blood stream traits would be useful – cancer, certainly. Other possibilities are other blood related indications such as diabetes, heart disease, and more. Surely some company will raise $10m and more designing a genetic dialysis, zero-effort weight loss, or hair loss reversal pill. Cialis or Viagra 2.0 is an equal possibility.

The recently announced $120m fund raised by Editas Medicine was a private sector step forward outside of the public view. It will be five or more years before anything actionable comes out of it. Then, of course, the company will face what could be massive and uncharted regulatory issues.

There’s a larger trend here that is worth noting: just because we’ve added a tool to the toolbox doesn’t mean that it is available or useful. Just because we have a better hammer doesn’t mean we can build a flying car.

And this is me: the futurist, idealist, and massive proponent of all things genetic talking!

Where is Oxford Nanopore by the way?

Sultan Meghji is the founder and Managing Partner of Virtova.  This post was orignially published at

The Genomics Grinch

Theral Timpson

One of the handy tools a journalist can use is a sharp pin.  It’s quite helpful when encountering over inflated balloons, such as the politican’s ego,  a financial bubble, or the hype around going to war.   When the pin is used at the right time, and on the right target, there is no question that the resulting “pop” is heard by everyone.  

However, when there is no over inflated balloon to pop, and a journalist still pulls out his pin, he just comes across as a nasty grinch.  This was the case with a piece in BuzzFeed last week by the science journalist, David Dobbs.

“We live in an age of hype,” writes Dobbs, questioning the value of genomics research and the money we are spending on it.   "It is as if they [geneticists] cracked a safe they knew was packed with cash and found almost nothing." 

That there is hype around genomics, I’ll concede.  But Dobbs is way too soon to say the strides we're making in precision medicine are almost nothing.  It’s akin to Senator Jim Inhofe bringing the snowball into the senate floor as proof against global warming.  Or citing the one scientist out of a hundred who questions whether the planet is heating up as a result of increased amounts of CO2 in the atmosphere.

Shouldn’t we err on the side of caution with the future of our planet?  And shouldn’t we be willing to put up with some natural hype ( a scientist overselling their discovery, a journalist adding some lustre, a businessman jumping in on a hot IPO) about what are some remarkable accomplishments in biotechnology and keep our gaze on the long view?

I know what hype is.  I go to the same conferences as Dobbs where we hear of new studies that promise to show this or that.  We hear about new technologies that will “impact patient outcomes.”   I’ll never forget the first time I interviewed someone in Silicon Valley who told me that we could achieve eternal life by reversing aging.   I had an extra beer that night for sure.

Unfortunately, Dobbs confuses capitalism, genuine hope on the part of patients, and the power of the human will to survive and learn with hype.  

“It would be responsible, however, for researchers to temper their hype — though this seems unlikely, because hype pays.”

And . . .?  That particular version of hype is called capitalism.  It funds science.

Dobbs says that the hype around genomics warps the expectations of patients and the incentives of scientists.  

I’ve interviewed a lot of scientists, and doctors, business leaders, policy experts, and patients.  Yes, my job is to cut through the hype and get to the real story.    I’ll share one such interview that I did with Jay Lake, a sci-fi writer with lung cancer who ended the show thanking and pleading with our audience of researchers:  “Please keep up the great work.   Please continue.”

Jay came on the program back in 2013 to tell about his experience getting his genome sequenced.  Jay’s oncologist was at the end of his rope with known treatments.  But that wasn’t enough for Jay.  Jay wanted to try every possible option, so he and his father, a former US ambassador, spent a great deal of time and energy getting Jay’s genome sequenced and interpreted.   And with this new tool, a new prognosis.  Jay would blog up to four times a day about his journey with cancer, and on our show he was honest about how “painful and difficult” it was getting help from genomic experts.  (It’s much cheaper and more available now.)  Still he persevered to find answers in his genome until the end.   In June of 2014, he died.

Now Dobbs would say I'm providing another example of warped expectations.

No, Dobbs.    You have it the wrong way around.  More than scientists warping the expectations of patients, I’d argue that patients like Jay Lake have been pushing the scientists.

Jay fought long and hard, and in the process compelled his doctors to push the envelope, scientists to make new hypotheses, and translational  researchers to go the next step.  Most of all, Jay showed great heart against the odds.  

This wasn’t hype, David, but the will to live.

What is overlooked in Dobbs' piece is a long view on the incredible achievement that has been made in the study of biology.  The response on Twitter to this article didn’t reveal too many warped expectations on the part of the scientists either.

“We were promised flying cars, all we got was fundamental insight into the nature of human variation,” tweeted a snarky computational human geneticist, Joe Pickerell.

So, no, I don’t question that there are cases at the ready to use in pooh-poohing genomics.  (Dobbs begins with the recent bad news that the one gene therapy drug that has been in use is now showing some limits.)  I poked fun a couple weeks ago at the poor case our industry has made for persons to have their genome sequenced in our comic weekly wrap.  But let’s remember the proverb we heard as kids.  For every two steps forward, we see a step back.   How about the story of Dr. Sidney Farber that was told in the  recent Ken Burns documentary on cancer?  Farber pioneered the first use of chemo therapy.  Kids with leukemia who had death sentences were gaining back health.  There was a lot of hope generated.  Journalists emptied their pens.  Then?  After six months, the revived children succumbed again to their cancer.  Should Farber have given up?  

I mean, just who is David Dobbs to call quits on the genomics revolution anyway?

Beyond the long list of practical genomics based assays being used in the clinic or drug development, from new options in cancer therapy to non-invasive prenatal testing, genomics is one of the greatest scientific stories of the past fifty years.  That humans developed the technology to see our own genetic code -- all 3 billion bases -- ranks with the discoveries of Darwin and Mendel.  It’s perhaps our greatest achievement since the landing on the moon.    Let’s tell that story for many, many more generations!

But no, Dobbs will have none of it, insisting on a sinister reading of history.

“After 110 years of genetics, and 15 years after the $3.8 billion Human Genome Project promised fast cures, after more billions spent and endless hype about results just around the corner, we have few cures,” David provokes. “And we basically know diddly-squat.”

Should we really tell nameless breast cancer patients who’ve had 10 or 20 years added to their lives-- to name just one example -- that it’s just “diddlly-squat?”

Dobbs has made a name for himself by combining a comfortable knowledge of biology with a blunt discourse.   In a New York Times editorial he called Nick Wade’s book about race and genes, “dangerous.”  (I think he was right about that.)  He’s also demonstrated an ambition to mess about with the science of biology itself, as he did with his article at Aeon, Die Selfish Gene, Die.   Here Dobbs was attempting to call it quits on an established scientific meme.  The piece was lambasted by several evolutionary biologists, including Jerry Coyne, who wrote two long pieces about how “Dobbs mucks up evolution.”  Coyne muses about whether it was "ambition or boredom" on Dobbs' part.  Whatever it was, such was the outcry among scientists that Dobbs significanlty revised and republished the article with a toned down version.  

Though Dobbs attempts here to see the age of genomics as an over-inflated balloon and he, the enlightened journalist, standing there with his trusty pin, we never hear the “pop.”  Rather we hear an “ouch” as he retreats to a very narrow view of biomedical history filled with diminishing language.

On the Mendelspod program, we continually hear from our leading geneticists,  “we’re just at the beginning of all this.”  Geneticists like David Schwartz from the University of Wisconsin Madison, who compared today’s biology methods with the first days of tinkering around with televisions.  Perhaps there’s a reason scientists maintain an optimistic view of the future.    It inspires them, and fills us all with wonder. 

This is no balloon.  Just below some surface hype is a hard-wired human drive to know.  What you're really writing about, Dobbs, is the human heart.  And it doesn’t pop.


Mendelspod Back on iTunes

Theral Timpson

Good news!

Mendelspod is back up and running on iTunes. You can access it at our new link:

If you wish to subscribe, click 'View in iTunes' under the Mendelspod logo. This will open iTunes on your desktop. Now click 'Subscribe' below the Mendelspod logo, and the podcast will automatically populate in your iTunes.

To access via your smartphone, first download Apple's 'Podcast' app. Then use the app to search 'Mendelspod' and subscribe. We apologize for the delay. It took several weeks of emails back and forth with Apple.

Enjoy the shows.


Garbage In, Garbage Out: A New Look at Biospecimen Quality

Theral Timpson


If you had told me a year ago that there are no regulated standards as to the quality of the biospecimen samples that are used to conduct biomedical research, I wouldn’t have believed it. Yet that’s been the case.

This was brought to our attention by the indomitable Carolyn Compton, a former pathologist and now the Chief Medical Officer for the National Biomarker Development Alliance (NBDA). Carolyn served at the National Cancer Institute with the express purpose of bringing more awareness to the issue of sample quality. It was there that she came to connect the dots between poor sample collection, handling, and storage and the upward trend of non-reproducible research. Bad sampling is leading to bad science.

We were so struck by her hypothesis that we asked Carolyn to help us put together an entire series on the topic with links to each show posted below.

Jim Vaught started us off with an overview of the topic, giving a stunning example of how bad sampling is not just affecting research, but medicine as well. We then delved into just what can go wrong with sample collection and handling with Scott Jewell of the Van Andel Institute.

Diane Farhi is the Chief Medical Officer at Quintiles, the world’s largest CRO. Diane and her team have to deal with problems in collecting samples for clinical trials on a global scale. Next, we explored the new Biospecimen Science, a new sub-discipline which has emerged to offer training and basic education on the topic--albeit not near where it should be according to David Rimm of Yale. We talked with the director of the biorepository that handles samples for 4 NIH Institutes, Andy Brooks. He says that there are so many variables that are beyond our control that perhaps the best thing would be a score to test the quality of the sample in storage.

Carolyn returned to the program with some good news. Through NBDA she had been able to assemble much of the sampling community, including the head and former head of the College of American Pathologists (CAP), and they agreed on an initial framework for sampling standards. It was an historic event.

The Open Secret about the HER2 Assay with Jim Vaught

Biosampling Basics: Scott Jewel, Van Andel Institute

The Daunting Task of Managing Biospecimens at the World's Largest CRO: Diane Farhi, Quintiles

The Sad State of Biospecimen Science with David Rimm, Yale

"It's Pretty Bad": Andy Brooks on Sample Quality

Historic Consensus Reached on Biospecimen Standards: Carolyn Compton, NBDA

Note:  Thanks to Quintiles and Fluidigm for sponsoring this series.


Why We Are Underwriting 'The Faces of Leadership in Diagnostics’ at Mendelspod

Zachary Helminiak

It’s no secret that the diagnostic industry is changing. Outside pressures like reimbursement and regulation, and internal forces like innovation, have produced tectonic shifts and allowed new landforms to rise from the ocean that is the diagnostic industry.

DNA testing in the consumer market is just one example of a volcanic event shaping the industry. Anne Wojcicki made headlines with 23andme on a regular basis the past year, giving a keynote speech to an eager audience of 20-something techies at South by Southwest. Thanks to Elizabeth Holmes and Theranos, soon you will be able to get lab tests at Walgreens with just one drop of blood. And egg freezing, offered by Ovascience, is now a company benefit at Apple and Google.

The faces of the leaders who are innovating in this space and challenging the healthcare status quo are changing as well. They are younger, and more often than before, they are women.

What does this mean for companies trying to compete in this space? What new demands are placed on your company culture if you want to attract an innovative leader?

Slone Partners embraces this change and is proud to partner with Mendelspod by underwriting a new series engaging some of the new faces of leadership.  

In these interviews, beginning next week, Mendelspod host, Theral Timpson, will talk with three women who are expanding the paradigm of leadership in the diagnostic industry.

We hope you enjoy the series.

ASHG 2014 in Review: Exhibitors Open the Kimono

Stephane Budel

The 64th annual meeting of the American Society of Human Genetics (ASHG) this week in San Diego, CA offered a glimpse into current progress in genetic testing. Not surprisingly, next generation sequencing (NGS) was omnipresent. In this blog entry, I highlight some interesting factoids ascertained while visiting select exhibitor booths.


“PrimeFlow enables researchers to look at up to 3 RNA transcripts and protein expression at the single cell level. There seems to be a lot of interest for infectious diseases applications –especially for HIV and HCV– and for stem cell research. One of the key advantages of branched DNA is that we amplify the signal, not the DNA.“


“Our AriaMx qPCR instrument is generating a lot of interest this year. It has a modular design that enables users to easily switch filter sets, and multiplex up to 6 channels.”


“We have conducted 55K WGS, 75 WES and 60K whole transcriptomes. We have access to 200 sequencers, including many in 2 labs in the U.S. We can match Wuxi’s price [of $1,600 per WGS], although we don’t have access to the X-ten in-house. […] For an extra $30 per sample, we’ll extract the DNA from blood samples, so we really offer end to end solutions.”


“After a year on the market, we’ve installed 25-30 systems to date. Our customers include a mix of basic research and government agencies, as well as a couple of clinical customers. The primary use is for genome scaffolding. The system lists for $295K, and then it’s $1,100 per sample [$900 for the chip and $200 for labelling].”


“We’re very proud of the QX200. It now runs not only TaqMan chemistry, but also EvaGreen. The combined system with the automated droplet generator lists at $135K. That’d be $90K with just the manual droplet generator. […] The QX100 and QX200 have been used in 150 publications combined.”


“We deliver a full WES clinical report in 30 days from date of reception for $3,900. We probably process 50-100 NGS samples per week, including 40 exomes. We continue to see a strong transition to WES.”

EMD Millipore:

“We’re introducing two technologies for functional genomics focused on the emergence of RNA as the next frontier of biomarkers. The first, SmartFlare Live Cell RNA Probes, enables direct detection of native RNA in living cells which can be used for downstream functional experiments and isolation of cell subtypes from heterogeneous populations – particularly useful for single cell genomics applications. SmartRNAPlex is a revolutionary multiplex miRNA profiling technology based on encoded hydrogel particles that can turn any standard benchtop flow cytometer (including the $15k Muse Cell Analyzer) into a genomics workhorse.”


“We released the C1 with programmability back in June. A couple of weeks ago, we released a protocol for single cell WES that complements are single-cell targeted resequencing workflow.   And you know that WGS is going to come next. It’s interesting to see the variety of applications that users want to program their C1 for: RNA-sequencing, bacterial sequencing, epigenetic applications, etc.  We also pre-announced our new Juno System for automated genotyping that combines pre amplification and genotyping into one platform.  It offers a robust workflow to support highly variable quality and quantities of genomic DNA input.  It’s the ideal solution those laboratories looking for more efficient solutions for candidate gene or replication studies or sample QC for their biobank samples.”


In the center of the exhibit hall, Illumina displayed a number of their instruments, including the awaited Neoprep platform (release date: H1 2015). Their dominant position was confirmed in yesterday’s earnings call (updated 2014 revenue growth guidance: 30%!).

“I think one of the most exciting recent development for us is the new 250 bp paired-end chemistry that will launched by the end of the year on the X-ten. Besides that, we’re excited to see continued growth in BaseSpace, which now has more than 50 apps available.”


“We sequence 220 genes at 450x coverage and only report what our customers want to know. It’s $1,500 whether you want 2 genes or 30 genes with appropriate clinical indication. Our test menu will expand in the coming year.”


“We released v3.1 of knoSYS this week. We continue to believe that many clinical customers do not want their data on the cloud, so having an appliance that can store data behind their firewall is important. We hear a lot of customers being interested in in silico panels.”

Life Technologies:

“We’re proud to announce the launch of the PGM Dx at ASHG. […] We’ve also received great reception of the Ion Chef. We’ve placed more than 10 [Chefs] in the San Diego area alone in the last 6 months. At $50K, it’s a relatively affordable instrument, but many researchers are waiting for the next round of funding to purchase it. […] The P II chip should be released in early 2015, and deliver about ~50 Gb of data.”


“We’ve put a strong focus on translational research, and done a good job at bringing the research conducted on our platforms into the clinic.”


“I expect us to launch the GeneReader in late 2015. There is really no point in us releasing the instrument before it is fully integrated with our end to end solutions, and the CLC and Ingenuity integration take time. Our NGS products have proven their medals in research settings, and we expect to do well as we move to diagnostics.”


“We don’t offer WGS, although unlike many other [smaller] CROs, we would have the infrastructure to support it. There are plenty of companies that you could get WGS from at an affordable price. About 70%+ of our genomics customers are biopharma customers; others are institutional.”


“My customers are going to miss the GS Junior. Many of them are asking me: ‘what are you going to get rid off next?’ But I think we have a very smart team of people working on the next generation of NGS instruments.”

Oxford Nanopore:

“Well, you’ll have to talk to [blank] about this. We want to let our MinION Access Programme (MAP) customers tell the story of what the technology can do.”

Pathway genomics:

“We’re proud of our weightloss test. It sells for $399 and genotypes thousands of SNPs”


“We’ve installed the Thunderstorm at more than 50 customer sites. Myriad has been using it for all of its myRisk tests very successfully. You just don’t get better amplification uniformity than with our systems.”


“We offer our services mostly to pharmaceutical customers. We charge about $1,600 per genome for high volume customers.”

Note:  This article was orginially posted at

Are We Insane? How Can We Expect Great Biomarkers and Therapies when There Is Poor Sampling?

Theral Timpson

When the former deputy director of the NCI, Anna Barker, suggested we start this year’s Biomarker Development Series with a show on biospecimen quality, I admit: I wondered how I was going to make it interesting.  

Biosampling?  What is there to talk about?

Then I met Carolyn Compton, a former pathologist and now the Chief Medical and Science Officer for the Naitonal Biomarker Development Alliance. Carolyn has a provocative message:  sampling issues are becoming one of the core problems in biomedical research. 

Today, I’m happy to announce the upcoming series, Back to Basics: Improving Biospecimens.  This series of five interviews will give us a chance to explore how big of a problem we have with sampling issues and what can be done about it. Quintiles is one of the largest CROs in the world who deals with sampling issues on a massive scale.  They’ve agreed to underwrite the series to bring more awareness to a topic that is too often overlooked. 

And just why should we talk about sampling?

Let’s start with the issue of non-reproducible research.  According to a study by Amgen in 2012 (Nature 483, 531-533, 2012), only 11% of 53 seminal publications on drug targets or toxicity could be reproduced by their team.  Let's add to that a fact that ASU’s George Poste points out in a Nature article of 2011 (Poste G. Nature-469, 156-157, Jan 2011) that out of over 150,000 biomarkers that have been written about in scientific and medical literature, only about 100 have been commercialized.  Why the stunning lack of success?  

“Garbage in, garbage out,” Carolyn says, borrowing a phrase from the big data folks.

The samples are not procured correctly, they’re mishandled, and they degrade.  It's critical that the industry works to improve standards.

I pulled the studies mentioned above from a talk Carolyn gave on these issues at a recent skin cancer conference in Scotland.  It’s a terrific introduction to the topic and is embedded at the end of this post.  

We’re going to unroll the series in the following format:

Our first show will be an overview.  We talk with Jim Vaught, President-elect of the International Society for Biological and Environmental Repositories (ISBER).  In his interview, Jim gives a shocking example of where poor sampling is causing an issue.  He says there is such variability between various labs and their assays for doing the Her2 testing for breast cancer.  Jim says that about 20% of the Her2 testing generates a false positive and about 20% generates a false negative.  This means that too many women with breast cancer are treated with the companion therapy, Herceptin, that is not making any difference.  And too many are not treated with Herceptin when they could be.  Jim ties this back to lack of standards in handling the biospecimens.

In our second show we’ll be looking at just what is involved in procuring, handling, and storing a sample.

With the third show, we talk to the Medical Director of Quintiles, Diane Fahri, about the issues she sees in sampling for clinical trials.  Diane has made it a priority to ensure that there is “harmonization” in procuring and shipping samples.  

One country may have a holiday and their shipping lines close.  This can affect the samples, Diane says.   There’s a myriad of issues when it comes to working with samples from such diverse labs around the world.

Fortunately, a new science of sampling has been emerging.  There are new programs, particularly in Europe which are offering training, even a Ph D in handling biospecimens  Our fourth show will be devoted to understanding better this new science.

To finish up, we’ll again have Carolyn Compton to the program to talk about the work she’s doing to improve standards.  So far SOPs have varied largely from institution to institution.  Carolyn is hosting a special conference in early December with many of the key opinion leaders to come up with some basic standards which can then be adopted by the professional organizations, such as the College of American Pathologists or CAP.

Nonreproducible science has become one of the worst plagues of our industry.  Better standards in sample collection, handling, and storage will go a long ways toward improving research and clinical efforts to bring great diagnostics and therapies to patients.

Whoa! Did You See the '60 Minutes' Piece on Drug Pricing?

Theral Timpson

60 Minutes has just produced a piece that is a must watch for anyone in the industry.  And where is big pharma?  

The details of the story are familiar.  60 Minutes caught up with two doctors who in 2012 told drug makers, “enough.”  

In October of 2012, these doctors wrote an op-ed in the New York Times explaining why their hospital, Memorial Sloan Kettering, would not cover one of the new cancer drugs, Zaltrap.  Their reasoning was straightforward:

“The drug, Zaltrap, has proved to be no better than a similar medicine we already have for advanced colorectal cancer, while its price - at $11,063 on average for a month of treatment - is more that twice as high,” they wrote

Drug pricing has been a hot topic this year with much of the pressure being put on Gilead for their breakthrough HCV drug, Sovaldi. 

But yesterday's 60 Minutes piece put the focus back on Sanofi, the company that makes Zaltrap.   They tell the story that after Dr.'s Salz and Bach wrote their op-ed in the New York Times, Sanofi actually dropped the price of Zaltrap by half.  But not to the patients, the doctors explain to the reporter, Leslie Stahl.  Rather than drop the price across the board, Sanofi made a special deal for doctors who would get  the difference in kickbacks for prescribing the drug.  This works because Medicare and the other insurance companies are still billed at the original price of $11K.

OK, so that's the story of two doctors.  How about the other side that we expect from a program like 60 Minutes?  

Unfortunately, no one from Sanofi would talk to the news program about why Zaltrap was twice as expensive as Avastin for the same indication, or why Sanofi made the deal with doctors rather than pass the savings to patients.    Novartis, too, will not comment about Gleevec and why its price has tripled since 2001 from $24K to $93K.  The only one to defend pharma to 60 Minutes is John Castellani, the CEO of the industry group, PhRMA.  And he gets a bit trapped up.

“I can’t comment on specific drugs,” he dead pans.

After a popular journalism piece like this, the image of pharma in the eyes of the American people is likely to get only worse, if it could.  Which is sad.  These are life extending drugs, and they are created by some of the greatest heroes of our time.  

The piece also brings to light something that perhaps most Americans don't know:  Medicare cannot negotiate pricing, by law.  Payers have to pay whatever price the drug companies come up with.  This is in stark contrast to other countries who, able to negotiate, are paying 50 - 80% less than Americans.  

So why can't Medicare negoiate? It does seem strange that the country which champions capitalism like we do has our hands tied when it comes to negotiating drug prices.  

Where was the representative from Medicare explaining this?  

Our American insurance system is complicated for sure.  In truth, it is unsustainable, including Medicare.  Obamacare didn’t come close to fixing it.  The Brits and the Germans negotiate, and determine whether a drug is worth it at a goverment level.  But in America this negotiation is seen as unethical.  If there’s a drug that will help, then surely it should be covered, no matter the cost.  

We in the industry are all too familiar with the high cost of drug development.  But as Matt Herper over at Forbes writes, industry leaders now carry the onus of explaining why a company like Sanofi can drop the price of a drug by half when the original price was supposedly set based on the development costs.

The Zaltrap vs Avastin case is one of the more simple.  But with widespread media coverage, this simple case could set a precedent and embolden other hospitals, insurance carriers, and perhaps even lawmakers to end the system of pay whatever the drug makers ask.

Interestingly, the drug companies mentioned in the piece, Sanofi, Novartis, and Roche are all European companies benefiting from our American system of pay whatever the drug companies ask.

Will our system change?  Should there be an American government agency whose job is to negotiate pricing like Germany and the U.K. have?  Or is it part of the success of our system, that because we don’t have a government agency bargaining, it’s left to the patients and doctors to ask on their own, is this drug worth it? 

60 Minutes has delivered a powerful punch here.  We'll get some folks to the program to reply.  

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