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Siddharta Mukherjee's Writing Career Just Got Dealt a Sucker Punch

Author: 
Theral Timpson

Siddharha Mukherjee won the 2011 Pulitzer Prize in non-fiction for his book, The Emporer of All Maladies.  The book has received widespread acclaim among lay audience, physicians, and scientists alike.  Last year the book was turned into a special PBS series.  But, according to a slew of scientists, we should all be skeptical of his next book scheduled to hit book shelves this month, The Gene, An Intimate History.

Publishing an article on epigenetics in the New Yorker this week--perhaps a selection from his new book--Mukherjee has waltzed into one of the most active scientific debates in all of biology: that of gene regulation, or epigenetics.

Jerry Coyne, the evolutionary biologist known for keeping journalists honest, has published a two part critique of Mukherjee’s New Yorker piece.  The first part--wildly tweeted yesterday--is a list of quotes from Coyne’s colleagues and those who have written in to the New Yorker, including two Nobel prize winners, Wally Gilbert and Sidney Altman, offering some very unfriendly sentences.

Wally Gilbert: “The New Yorker article is so wildly wrong that it defies rational analysis.”

Sidney Altman:  "I am not aware that there is such a thing as an epigenetic code.  It is unfortunate to inflict this article, without proper scientific review, on the audience of the New Yorker.”

The second part is a thorough scientific rebuttal of the Mukherjee piece.  It all serves as a great drama about one of the most contested ideas in biology and also as a cautionary tale to journalists, even experienced writers such as Mukherjee, about the dangers of wading into scientific arguments.  Readers may remember that a few years ago, science writer, David Dobbs, similarly skated into the same topic with his piece, Die, Selfish Gene, Die, and which raised a similar shitstorm, much of it from Coyne.

Mukherjee's mistake is in giving credence to only one side of a very fierce debate--that the environment causes changes in the genome which can be passed on; another kind of evolution--as though it were settled science.   Either Mukherjee, a physicisan coming off from a successful book and PBS miniseries on cancer, is setting himself up as a scientist, or he has been a truly naive science reporter.   If he got this chapter so wrong, what does it mean about an entire book on the gene?

Coyne quotes one of his colleagues who raised some questions about the New Yorker's science reporting, one particular question we’ve been asking here at Mendelspod.  How do we know what we know?  Does science now have an edge on any other discipline for being able to create knowledge?

Coyne’s colleague is troubled by science coverage in the New Yorker, and goes so far as to write that the New Yorker has been waging a “war on behalf of cultural critics and literary intellectuals against scientists and technologists.”     

From my experience, it’s not quite that tidy.  First of all, the New Yorker is the best writing I read each week.  Period.  Second, I haven’t found their science writing to have the slant claimed in the quote above.  For example, most other mainstream outlets--including the New York Times with the Amy Harmon pieces--have given the anti-GMO crowd an equal say in the mistaken search for a “balance” on whether GMOs are harmful.  (Remember John Stewart’s criticism of Fox News?  That they give a false equivalent between two sides even when there is no equivalent on the other side?)

But the New Yorker has not fallen into this trap on GMOs and most of their pieces on the topic--mainly by Michael Specter--have been decidedly pro science and therefore decided pro GMO.

So what led Mukherjee to play scientist as well as journalist?  There's no question about whether I enjoy his prose.  His writing beautifully whisks me away so that I don’t feel that I'm really working to understand.  There is a poetic complexity that constantly brings different threads effortlessly together, weaving them into the same light.  At one point he uses the metaphor of a web for the genome, with the epigenome being the stuff that sticks to the web.  He borrows the metaphor from the Hindu notion of "being", or jaal.

“Genes form the threads of the web; the detritus that adheres to it transforms every web into a singular being.”  

There have been a few writers on Twitter defending Mukherjee’s piece.  Tech Review’s Antonio Regalado called Coyne and his colleagues “tedious literalists” who have an “issue with epigenetic poetry.”  

At his best, Mukherjee can take us down the sweet alleys of his metaphors and family stories with a new curiosity for the scientific truth.  He can hold a mirror up to scientists, or put the spotlight on their work.   At their worst, Coyne and his scientific colleagues can reek of a fear of language and therefore metaphor.  The always outspoken scientist and author, Richard Dawkins, who made his name by personifying the gene, was quick to personify epigentics in a tweet:   “It’s high time the 15 minutes of underserved fame for “epigenetics” came to an overdue end.”  Dawkins is that rare scientist who has consistently been as comfortable with rhetoric and language as he is with data.

Hats off to Coyne who reminds us that a metaphor--however lovely--does not some science make. If Mukherjee wants to play scientist, let him create and gather data. If it’s the role of science journalist he wants, let him collect all the science he can before he begins to pour it into his poetry.

Gene and Tonic: A 2016 Timeline

Author: 
Theral Timpson

 

Journalists listen to others telling them what actually happened all year long.  But for this one week at the first of the year, we like to make up our own stuff.

January - The general mood at the annual J.P. Morgan Healthcare conference in San Francisco is one of relief.  

“Last month the FBI caught the lead mastermind behind the pharma industry’s high drug prices, and he’ll be brought to justice,” says the CEO of a pharma giant to a room full of investors and journalists at the historic St. Francis Hotel.  “Problem solved.”

Also at the J.P. Morgan, Illumina releases a new sequencing instrument called, JuniorSeq.    Hailed as a major milestone in the forward progress of health and disease prevention and wellness and all that is good and proper for mankind, the new machine represents a partnership between Illumina  and Facebook.  Within months, we're told, we’ll be seeing the new JuniorSeq and accompanying software in elementaries and high schools and universities around the world.

To a room full of sober faced but giddy investors, Illumina CEO, Jay Flatley, announces, “This is a new era when our children will have the ability--and therefore the right--to search their own genomes and share them with their friends on Facebook.”  

In attendance is Facebook's Mark Zuckerberg, who adds:  “I only wish I was in college again!”

February - Not to be outdone by Illumina, Pacific Biosciences releases their own new sequencing machine at the AGBT conference in Marcos Island, Florida.  They are calling it Prequel.

CEO Mike Hunkapiller:  “First of all, I’d like to remind everyone that this beach resort is the designated place to launch new sequencing products.   We’re very proud to launch our new Prequel.  If we could go back in time, this is the instrument we would have began the company with.    But anyway, here it is now.  All of the big sequencing projects should be redone with long read technology.  Maybe we can't rewrite history, but we can and must redo all those genomes . . including Craig’s.”

March - The covers of Forbes and Fortune feature healthcare’s latest wunderkind billionaire, the nineteen year old male-to-female transgender founder of Unicorn Health.  The cover articles reveal that the media’s newest darling started her company when she was just twelve in a Seattle elementary school and has been operating in stealth for seven years.  

A former teacher of the founder, who is on the Unicorn Health board of directors says: “I’m very proud of her.  She was a him when she was in my biology class.  And this is back when there were no JuniorSeqs around.”

According to Forbes, Unicorn Health will be changing healthcare and wellness for all in the very near future by enabling everyone on the planet to spit onto their mobile phones and get an immediate readout of something. 

Also on Unicorn’s board of directors are major dignitaries, including Gehngis Kahn and one of the original members of the 80’s popular music band, Milli Vanilli.

The company has not yet published any data.

The Forbes journalist was particularly exuberant in his article about the new startup and it’s innovative and disruptive founder.  “She not only disrupted gender, she’s disrupting health, business, and spit,” he writes.  “Furthermore, having a transgender is a new thing for the Forbes billionaire list and is really exciting.”  

May - The FDA releases their final guidance on Laboratory Developed Tests, or LDTs.  The new guidance groups LDTs in two categories:  WGTO or We Got This One and WHNC or We Have No Clue.  

June - The Festival of Genomics will be held again just outside Boston on an open field next to a dairy farm.  Bailing out of a helicopter in pouring rain two weeks prior to the event, the conference lead organizer runs to the barn and addresses a few reporters in a crisp West End London accent.

“This is the site where history will be made.  There will be five stages, all of which will hold great rock bands including U2, KISS and EditMyJeans.  There will be no scientific presentations, which comes closer to fulfilling our real vision of bringing scientists closer together with patients. . . . We’ll be handing out CRISPR kits, so if anyone wants to do a little CRISPRing on the side, then that’s fine.”

July - The FDA’s final guidance on LDTs is held up in the Congressional Budget Office, indefinitely.

A spokesman for the Diagnostic Test Working Group says:  "This is a victory for innovation and capitalism.  Now investors can go back to being uncertain about whether there is money in diagnostics rather than that unworkable certainty that there is not."

August - A New York Times journalist reveals that Unicorn Health has no new proprietary technology and has in fact been using some old equipment from a lab at MIT.  When queried by the Forbes journalist who wrote the cover article back in March about just how she found this out, the NYT journalist tweets back:  #made #some #calls.

September - Another #summit #meeting #convention #whatever-you-will called @GeneEditingEthics arrives at another consensus:  #opencarry.

The meeting is hailed as an important event by all the important news outlets.

Also, the word CRISPR and various forms of it, i.e., adjective: CRISPRed and present participle verb:  CRISPRing, are added to the Oxford English Dictionary.  

Novemember - Illumina launches the KinderSeq at ASHG.

December - Roche announces their list of 150 acquisitions for the year. 

“We thought one press release just simplified things,” says a Roche spokesperson.  

Cliff Reid to Resign as CEO of Complete after BGI Shakeup

Author: 
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

Author: 
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

Author: 
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 www.sultanmeghji.org.

The Genomics Grinch

Author: 
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

Author: 
Theral Timpson

Good news!

Mendelspod is back up and running on iTunes. You can access it at our new link: https://itunes.apple.com/gb/podcast/mendelspod-podcast/id988565102?mt=2

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

Author: 
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.

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

Author: 
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

Author: 
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.

Affymetrix:

“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.“

Agilent:

“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.”

BGI:

“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.”

Bionanogenomics:

“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].”

Bio-Rad:

“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.”

Centogene:

“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.”

Fluidigm:

“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.”

Illumina:

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.”

Invitae:

“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.”

Knome:

“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.”

Nanostring:

“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.”

Qiagen:

“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.”

Quintiles:

“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.”

Roche:

“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”

Raindance:

“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.”

Wuxi:

“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 www.decibio.com/blog



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