The Daily Scan

CAP Today: Regulators scanning the digital scanners

Of the FDA’s decision to regulate whole-slide imaging systems as Class III devices, Aperio president Dirk Soenksen says, “They’ve made up their mind.... You’re talking five years at the earliest when someone’s going to get approval.” How broad will Aperio's submission be? “As broad as FDA allows,” he says.

Hi y'all.  You're probably familiar with CAP Today already - it's a great publication for anyone interested in Pathology, and it's available free online - but today's new issue has great article about the FDA panel discussion held at Pathology Visions in October: Regulators scanning the digital scanners:

A recent panel on whole-slide imaging launched a clear message from the Food and Drug Administration: The agency views WSI systems as Class III medical devices and plans to regulate them as such.

Depending on one’s view, the news will slow efforts to bring WSI for primary diagnosis into U.S. laboratories, with some vendors looking to Europe for regulatory relief; have virtually no impact on large vendors, who, while not necessarily enamored of the FDA’s decision, concede it’s one they can live with; kill the market completely; choke innovation among vendors, especially component makers; possibly put laboratories in jeopardy if they try to validate these systems as laboratory-developed tests under CLIA; or encourage laboratories to use WSI for other, already approved purposes, readying themselves for the inevitable day when whole-slide imaging transforms surgical pathology.

It's an interesting article, please check it out.  Among other things it makes the point that while regulators and industry leaders debate the future of digital pathology for primary diagnosis, the technology is in active use today for many other clinical applications, such as QA, secondary consultations, and image analysis.

What the Healthcare Industry Can Learn From Technology Start-Ups

This is an interesting post on The Health Care Blog, by David Shaywitz: What the Healthcare Industry can learn from Technology Start-ups:

I’ve been struck by some of the profound differences between a tech start-up (even one ostensibly in the healthcare space) and a biopharma start-up. In the standard biopharma model, you spend years developing a product, without having any real idea of (a) whether it will work, (b) whether it will be safe and well-tolerated, and (c) whether by the time you’ve demonstrated (a) and (b), anyone will care, or pay you for your efforts.

In contrast, [tech startup] MassiveHealth has managed to get a product in customer hands after a few months of work. True, they’ve probably not made any money thus far, and (not insignificantly) it’s entirely unclear whether they have, or will ever impact anyone’s health, massively or otherwise. Nevertheless, they have an extraordinarily powerful opportunity, at this very early stage, and after spending (I suspect) very little money, to learn, gather feedback, iterate, and explore.

The ability to launch early with a minimum viable product and immediately get feedback and iterate is so valuable.  This is one of the things that has allowed online services to flourish, they can change must faster than desktop software.  A key trend and most interesting to watch.

The $1,000 genome

The Wall Street Journal reports Soon, $1,000 will map your genes:

The quest to harness the power of DNA to develop personalized medicine is on the threshold of a major milestone: the $1,000 genome sequencing.

Life Technologies Corp., a Carlsbad, Calif., genomics company, plans to introduce Tuesday a machine it says will be able to map an individual's entire genetic makeup for $1,000 by the end of this year. Moreover, the machine and accompanying microchip technology, both developed by the company's Ion Torrent unit, will deliver the information in a day, the company says.

That's pretty amazing.  The cost of mapping an entire genome is rapidly approaching the cost of individual genetic tests; you can imagine that soon it will be just as inexpensive to sequence an entire genome as to look for a particular gene locus.  (Of course, for cancer treatment it will still be necessary to sequence the genome of a tumor, as well as the normal genes, to determine the defects that caused the cancer and guide treatment.)

The role of pathologists in interpreting these tests and working with oncologists and other clinicians to determine treatment will likely expand, and perhaps genetic subspecialties will form.

Five years of iPhone

As the iPhone and iPad become an ever bigger and more important tool for physicians - including pathologists - it is interesting to ponder five years of iPhone:

Five years ago today, Steve Jobs unveiled the new iPhone at Macworld Expo. The company has since delivered five generations of new hardware and iOS software as its mobile competitors have scrambled to defend their positions and take share back.

Jobs started his keynote with the words, "We're going to make some history together today...  This is a day I've been looking forward to for two and a half years.".

"Every once in a while a revolutionary product comes along that changes everything. One is very fortunate if you get to work on just one of these in your career. Apple has been very fortunate that it's been able to introduce a few of these into the world. In 1984 we introduced the Macintosh. It didn't just change Apple, it changed the whole industry. In 2001 we introduced the first iPod, and it didn't just change the way we all listened to music, it changed the entire music industry," Jobs said.

"Well today, we're introducing three revolutionary new products! The first one is a widescreen iPod with touch controls," Jobs said to applause. "The second is a revolutionary new mobile phone," he added to even more fervent applause. "And the third is a breakthrough internet communications device," to which the audience continued to applaud with less certainty.

"So, three things," Jobs said, repeating each of the three. He then repeated all three again, as his backdrop animated between an iPod icon, a Phone icon and the Safari icon. "Are you getting it?" Jobs asked. "These are not three separate devices! This is one device. And we are calling it iPhone. Today Apple is going to reinvent the phone. Here it is."

At this point, five years later, to say the iPhone has changed everything is nearly an under-statement; not only are iPhones and iPads everywhere, but the technology has influenced a huge industry of competitors including Google's Android, Microsoft's Windows Phone, RIM's Blackberry, Nokia, and Palm (now HP) just to name a few.  Tablets have become by far the fastest growing segment of the computer industry.  Where will be in five years?  Hard to say, but we can be sure iPhones and iPads are here to stay, and will become ever more promiment in Healthcare applications.

Pathology Labs Replace Microscopes with Digital Imaging

LabMedica reports on mainstream adoption of digital pathology in Sweden: Pathology Labs Replace Microscopes with Digital Imaging:

Microscopes are being replaced with digital imaging in pathology laboratories in the southern part of Sweden.

Traditional microscope glass slides are turned into digital images, which are then analyzed by pathologists directly from the computer screen, instead of using regular microscopes.

The revolution, which has already occurred in radiology, is now taking place in pathology. The contracted delivery not only digitizes the slides but also will completely renew IT support for all workflows of the pathology laboratories in the Skåne region.

It is interesting to ponder why Sweden has become a world leader in the adoption of digital pathology for clinical applications.  There are many demographic factors which have created demand.  But perhaps a key reason is the close integration between Digital Pathology vendors like Aperio with LIS vendors like Software Point.  Perhaps this can be a model to foster adoption in other countries.

Happy New Year! 2011 was quite a year, and 2012 here we come...

Happy New Year everyone!  Well 2011 was quite a year, and 2012 here we come...  so what do we think will happen this year?  More adoption of digital pathology, more applications, more success stories, and more learning about the best uses of this incredible technology.  And more mainstream acceptance.  What do you think?  Please post your comments to let us know!

Happy Holidays from the Daily Scan

Greatings readers just wanted to wish everyone a Happy Holiday, whatever you may celebrate this time of year.

It's been quite an interesting year, and quite a year for the growth of digital pathology.  Many labs and pathologists have become more comfortable with this technology and are exploring the many ways it can deliver value for them, and adoption seems to be moving from "if" to "when".

And next year should be even more interesting...  I'm tempted to make predictions, but every time I do they are both too optimistic (regarding time) and yet not wild enough (regarding all the possible applications people will uncover).

Happy New Year and stay tuned!

Medscape: most-read Pathology articles of 2011

If you're a Medscape subscriber, you'll find this interesting: the most-read Pathology articles of 2011.  (Subscribing to Medscape is free.)

#3 on the list is FDA approves test to determine Her2 status in breast cancer, about a new ISH genetic test using digital pathology.

#2 on the list is Pathology Consultation: Reporting of Critical Values.  This is typical of the articles indexed by Medscape, a scholarly review article.

#1 on the list is NSCLC: Histology first, then mutation testing, a report from the National Comprehensive Cancer Network annual conference.

Check out the entire list, and Medscape itself if you haven't before, it's a great resource.  I wonder what will be the articles of most interest in 2012?

Skylight turns your smartphone into a microscope camera

This is pretty cool: PC World reports Skylight turns your smartphone into a microscope camera, about a Kickstarter project* to build a hardware mount that lets a smartphone be used to take pictures through a microscope eyepiece.

One of the highlights of science classes in school had to when we got to toy around with microscopes. Of course, while most microscopes in school were fairly basic models, the kits used in professional fields such as microbiology can cost thousands of dollars--money that not everyone has, meaning less access to the technology.

Andy Mill was trying to make a low-cost solution to this issue when he created Skylight, an adapter that can connect most smartphones to a variety of different microscopes. Skylight works by aligning your smartphone's camera with a microscope's eyepiece, allowing you to record a video or snap a photo through the lens.

I love this idea and have contributed to the project.  I look forward to getting one with great interest, and can't wait to play with it!

Stay tuned!

* BTW Kickstarter is a great website where people who have ideas can raise money from other people who like their ideas.  SkyLight has raised over $18,000 exceeding their $15,000 goal, enough for them to take their idea from making prototypes into production manufacturing.

Indolent or aggressive?

I touched on this the other day, with a post about Liron Pantanowitz' views, but The Economist has an article about the Stanford University Science Translational Medicine article: Indolent or Aggressive?  (A computerised pathologist that can outperform its human counterparts could transform the field of cancer diagnosis):

LOOKING for needles in haystacks is boring. But computers do not get bored. Contracting out to machines the tedious business of assessing the dangerousness of cancer cells in histological microscope slides ought thus to be an obvious thing to do. Cervical-cancer smear tests aside, however, such electronic intrusions into the pathology laboratory are limited. Grading cancer cells into “indolent” and “aggressive”, and hazarding an opinion about whether they spell a treatable condition or an untreatable one, has remained the realm of the human expert.

Of course for those of us who have been working in the field of digital pathology, this idea is nothing new, and in fact simply represents an evoluation of tools; pathologists have been using computer quantification of IHC and other biomarkers for quite a long time. 

Perhaps the thing that is new is this idea is attracting public attention.  Perhaps that will help create the right economic conditions for technologies which provide better outcomes to be adopted.

RSNA: Personal cloud servers offer a low-cost, secure option

HealthImaging reports from RNSA: Personal cloud servers offer a low-cost, secure option:

Commercial cloud computing data sharing such as Evernote and Dropbox are used every day by the general public and offer all the advantages of mobile data retrieval, but they are not appropriate for radiologists to share medical information with one another. One alternative could be the creation of a personal cloud that is maintained by the department that uses it, according to a poster presentation at the 97th Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA).

The most likely future is a combination, where commercial cloud services are used as a substrate upon which personal clouds are built.  There is little doubt that cloud-based storage is increasingly attractive as an alternative to locally maintained data, especially for large objects such as medical images.

Top pathologist looks at future of technology for breast cancer research

Northwestern University's Medill Reports has a nice article featuring Liron Pantanowitz of UPMC: Top pathologist looks at future of technology for breast cancer research.  He comments on a Stanford study which discussed computer analysis of breast tumors:

Q. Where do you see medicine and technology going from here?

A. While tools like this are definitely helping us move towards practicing better personalized medicine, I do not believe that they will replace the pathologist. Rather, in this new era of digital pathology, pathologists will be able to use more and hopefully better tools. In radiology, for example, even though their images have been converted to digital format for many years now, radiologists are still required to interpret these images, called upon to apply appropriate computerized tools, and are in the best position to interpret the results from these analyses. I think the future of digital pathology is bright and with studies like this I am pleased to see that we are headed in the right direction.

A measured response, I would agree.  As Digital Pathology becomes more accepted for various applications, it is becoming clear that it is a valuable tool for aiding pathologists, but it won't replace them.

Going Viral - the promise of viruses as biotech tools

In TheScientist viologist William McEwan ponders the promise of viruses as biotech tools: Going Viral:

Molecular biology has not achieved its potential. Why do people still die from cancer? Why are there so few effective antivirals? Where is the HIV/malaria/common cold vaccine? Why aren’t genetic diseases routinely treatable with gene therapy? Certainly we can point to plenty of successes—the papilloma virus vaccine made from recombinant pseudovirions and rapid diagnostics for many diseases are two examples—but even the optimists among us must concede that molecular biology is not where we might have hoped 25 years ago. What went wrong?

Simply put, life on the molecular scale is much more complicated than we imagined. Molecular biology roared onto the scene in the mid-20th century when James Watson and Francis Crick illuminated the “too beautiful not to be true” structure of DNA and the deciphering of the genetic code. But the simplicity and elegance ends right there. Biology at the protein level is far removed from the linear, digital code of nucleic acids. Biological organization at the cellular or organismal levels is even less linear. Understanding life on these scales is not impossible, but we have to work it out one interaction, mechanism, and pathway at a time. Making sense of the complexity will surely take the rest of this century (though I’d love to be wrong about that!). As each small piece of biology is understood, we gain something extra to work with, something tractable and, ultimately, engineerable.

...

As a virologist, I may be biased, but I believe the greatest advances in molecular therapies in the near future will involve viruses. Compact biological entities with little more than a handful of genes and a protein coat, viruses lend themselves to engineering. That’s not to say they aren’t also complex: HIV envelope protein for instance is known to associate with 176 human proteins at the last count. But viruses know their hosts well—they can break into cells undetected, switch off alarm systems, and undermine the cell’s authority in deciding which genes get expressed. It is this acuity, acquired by trial and error over millions of years of coevolution with their hosts, that researchers are tapping to design novel therapies.

Cool.  The trojan horse mechanism of cellular level therapy.

Why indoor navigation is so hard

This sounds like it wouldn't have anything to do with digital pathology, until you remember finding your way through any unfamiliar hospital: Why indoor navigation so hard.

Remember the days before you could pull your smartphone out of your pocket and get instant directions from your current location to anywhere in the world? It's kind of foggy for me, too.

In fact, I'm so used to relying on my smartphone that I feel increasingly flustered when wandering the aisles of Costco, locating the elephant house at the zoo, or searching for decent food at the airport. Shouldn't my magical pocket computer help me with this, too?

The answer is "yes," of course. But there are challenges to implementing indoor navigation today.

Personally I can't wait until technology catches up with this problem.  In the meantime, I allow 30 minutes after I reach any hospital for finding the person / department of interest...

Researchers transform iPhone into microscope

Wow, well you knew this was coming: GigaOm reports (a bit breathlessly) The iPhone: cheap medical super microscope.

Apple’s iPhone is getting an improved camera with the iPhone 4S, but a medical research team has gone a step further, turning the iPhone into a powerful, professional-caliber imaging and chemical detection device, according to The Optical Society. In other words, the $40 hack engineered by the team makes the iPhone a lab-worthy medical microscope.

Using a ball lens, which only offers five times magnification, the team was able to bump it up to 1.5 microns, which is small enough to spot different kinds of blood cells, thanks to smartphone camera augmentation. Digital image processing software corrects distortion resulting from the ball lens, and stitches together photos of the small focus area produced using the method to create a big enough picture for doctors or medical technicians to properly analyze.

There's some serious hype here - who knows if the iPhone-microscope is truly "lab-worthy" - but there's also some serious technology; with its built in camera, radios, processing power, and networkability the iPhone is a great platform for remote microscopy.  I regard this is somewhat of a preview, we'll no doubt have many more announcements of this kind to come.  Stay tuned :)

Cool technology: Frog Skin protects mobile devices in medical environments

How to you use iPads, iPhones, and other mobile devices in the messy world of the operating room?  Or the messy world of the grossing station?  John Halamka previews a new product called Frog Skin, which is a film-like covering that is clear and wraps around the device, making it waterproof.  This enables the device to be protected and even sterilized:

Last night we ran the big experiment, and placed a Frog Skin encased iPhone 3G in an ethylene oxide sterilizer (for surgical instruments that can't go in an autoclave).  We sterilized the iPhone. The cycle was  6 hours of gas time, and 12 for outgas.  I  turned the phone off, so no activity would occur causing heat or a spark, since ethylene oxide is flammable. I placed a gas detection strip inside the Frog Skin and one inside the sterile pack. The pack was placed in the sterilizer with all the other surgical instruments.

The photo above shows the iPhone inside the sterilization package (as it would be delivered to the Operating Room).  Note that both tags have turned blue. This means that gas got inside the Frog Skin.   The entire iPhone is sterile as the Frog Skin does not stop the gas. The phone booted without problems, and operates fine inside the skin.   In summary,  eth-ox doesn't affect the iPhone in any way.  The Frog Skin (polypropylene) does not stop the eth-ox form getting to the phone but will prevent Operating Room liquids from getting into the phone. And yes, you can operate the phone with gloves and the Frog Skin on.

Wow, excellent.  You can imagine the possiblities...

Rapid Ramp in Full Genome Sequencing: 30,000 in 2011

FuturePundit notes Rapid Ramp in Full Genome Sequencing: 30,000 in 2011.

The rate of full genome sequencing has risen by about 1000 in a couple of years. That's because costs have dropped by orders of magnitude. The rapid cost drop looks set to continue.

This year, the world's DNA-sequencing machines are expected to churn out 30,000 entire human genomes, according to estimates in Nature magazine. That is up from 2,700 last year and a few dozen in 2009. Recall that merely a decade ago, before the completion of the Human Genome Project, the number was zero.

The vast majority of us will be able to afford to get our full genomes sequenced in a few years. Costs are now below $10,000 per genome and in larger quantities below $5,000.

Wow, that's incredible.  Just the other day I noted New Semiconductor Technology Accelerates Whole Genome Sequencing, and here we see the results.

Related, ScienceRoll reports 23andMe Now Offers Sequencing for $999.  Wow.  How much would you pay to have your genome sequenced?

FDA mobile apps workshop: When is a car a medical device accessory?

From HealthImaging, a report on the recent FDA workshop on regulating mobile Apps: FDA mobile apps workshop: When is a car a medical device accessory?

How and when should the FDA regulate mobile medical apps that act as accessories to medical devices? When should it not regulate them at all? Those questions were taken up in a midday panel discussion on day one of FDA’s Sept. 12 and 13 workshop on its draft guidance for mobile medical device applications.

The workshop followed FDA’s July announcement that it is seeking input on its approach to oversight of “certain mobile applications specific to medicine or healthcare called mobile medical applications (apps) that are designed for use on smartphones and other mobile computing devices.”

An interesting challenge for the FDA; the growth of mobile applications is exploding, particularly driven by the adoption of iPads and other tablets for imaging applications, and regulating these Apps and devices will become increasingly important as they become used for medically critical applications.  As the article linked above notes, the issue is complicated by the fact that there are so many interconnected parts; a medical App might be created and maintained according to FDA QSRs, but what about the mobile device on which it runs?

Review of the current state of whole slide imaging in pathology

The Journal of Pathology Informatics has published an interesting article: Review of the current state of whole slide imaging in pathology (PDF).

Whole slide imaging (WSI), or "virtual" microscopy, involves the scanning (digitization) of glass slides to produce "digital slides".  WSI has been advocated for diagnostic, educational, and research purposes.  When used for remote frozen section diagnosis, WSI requires a thorough implementation protocol coupled with trained support personnel.  Adoption of WSI for rendering pathologic diagnoses on a routine basis has been shown to be successful in only a few "niche" applications.  Wider adoption will most likely require full integration with the laboratory information system, continuous automated scanning, high-bandwidth connectivity, massive storage capacity, and more intuitive user interfaces.  Nevertheless, WSI has been reported to enhance specific pathology practices, such as scanning slides received in consultation or of legal cases, of slides to be used for patient care conferences, for quality assurance purposes, to retain records of slides to be sent out or destroyed by ancillary testing, and for performing digital image analysis.  In addition to technical issues, regulatory and validation requirements related to WSI have yet to be adequately addressed.  Although limited validation studies have been published using WSI there are currently no standard guidelines for validating WSI for diagnostic use in the clinical laboratory,.  This review addresses the current status of WI in pathology related to regulation and validation, the provision of remote and routine pathologic diagnoses, educational uses, implementation issues, and the cost-benefit analysis of adopting WSI in routine clinical practice.

An interesting and comprehensive review.  The reviewers are appropriately cautious but you can sense their excitement at the possibilties of the technology to transform the field of Pathology.  It is interesting that the things noted for driving wider adoption are exactly the things Aperio is working to address.

New Semiconductor Technology Accelerates Whole Genome Sequencing

The Dark Report has an interesting article: New Semiconductor Technology Accelerates Whole Genome Sequencing at Reduced Cost:

Swift advances in whole human genome sequencing may bring clinical applications to pathology on a much faster timeline than expected.

One impressive example of the fast pace of technology improvements is the Ion Torrent, which is a semiconductor-based DNA sequencer now capable of sequencing 100 million base pairs. That is ten times the sequencer’s capacity when it was launched just last December!

Most clinical laboratory managers and pathologists recognize that, at a price point of $49,500, Ion Torrent’s Personal Genome Machine becomes affordable for any number of academic pathology departments and larger medical laboratories. It is the type of tool that can allow these laboratories to develop home brew diagnostic assays that require a great deal of gene sequencing “horsepower.”

The advances in the technology of whole genome sequencing are truly impressive.  And the combination of genetic data from these instruments with morphometric and molecular data from digital pathology will be especially powerful.