Lab Soft News

Using Big Data to Discover Comorbitities Associated with Psoriasis

I have made reference to "big data" in previous blog notes (see: Mount Sinai's Icahn School of Medicine Pioneers the Use of Big Data to Study Diabetes; More Discussion about Big Data; Relevance for Healthcare). A commonly accepted definition for big data is the use of extremely large data sets that may be analyzed computationally to reveal patterns, trends, and associations. I am particularly interested in the use of big data for predictive analytics in healthcare (see: Big data analytics in healthcare: promise and potential). Now comes an article about the use of big data to discover the co-morbidities associated with psoriasis (see: Researchers receive $6.5 million NIH grant to use big data to tackle psoriasis). Below is an excerpt from it:

An experienced interdisciplinary team of psoriasis and computational researchers from Case Western Reserve University School of Medicine (CWRU SOM) and University Hospitals Cleveland Medical Center (UHCMC) has received a $6.5M, 5-year grant from the National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS). The grant supports a Center of Research Translation in Psoriasis (CORT) at CWRU and UHCMC....The goal is to better identify and treat those psoriasis patients that are more susceptible to developing comorbidities ...associated with psoriasis, such as cardiovascular disease, diabetes, depression, and psoriatic arthritis. Currently it is difficult for physicians to determine which patients will develop these comorbidities. The researchers will cull data collected from blood and skin samples of UHCMC psoriasis patients and preclinical models, looking for new patterns and relationships developed using a systems biology approach.....This approach will use tailored computational processes to zero in on drug candidates or repurposed drugs matching the patient profiles from a large database of tens of thousands of drugs--and test the drugs in genetically engineered psoriasis mouse models. 

Psoriasis has as very large number of comorbities (see: COMORBIDITIES ASSOCIATED WITH PSORIATIC DISEASE). It's important not only to identify the range and frequency of them but also the criteria to use to predict which patients will suffer from them in the future. Moreover and as noted above, big data can be used to discover which drug candidates or repurposed drugs would be effective in initially treating both the psoriasis and future associated diseases. We can thus look forward to a future when a set of lab tests will be ordered for a patient with psoriasis and from the data it can be predicted which comorbidities can be expected in the future for him or her and which drugs can be used to forestall or best treat these additional problems.

Sunquest Signs Contract to Provide LIS Support for 124 Hospitals in Australia

Sunquest Information Systems is embarking on a project that has the potential to change the face of lab computing. It has signed a contract to provide lab computing support for all of the hospitals in the state of Queensland, Australia, which has a population of about 4.5 million people (see: Queensland Health partners with Sunquest for Laboratory Information System). Below is an excerpt from the press release:

The contemporary enterprise laboratory information system (LIS) and services will support improved care responsiveness, safety and healthcare outcomes for the millions of Queenslanders served by the state's 124 hospitals, 70 primary health centers and clinics, 17 aged care facilities and 33 extreme remote multi-purpose health services. Queensland Health performs more than 20,000 tests per day in 36 public pathology, forensic and scientific laboratories....The contract includes Sunquest's full end-to-end enterprise laboratory information system for all pathology disciplines including chemistry, hematology, microbiology, histopathology, cytology, blood transfusion and molecular....Sunquest demonstrates support for patient safety and communication with existing systems After being named Vendor of Choice from a field of seven vendors, ahead of the main contract Sunquest was required to create a working prototype to demonstrate key processes and achieve sign-off from a variety of stakeholders. The prototype, delivered in a prompt six weeks, successfully demonstrated interoperability with Queensland Health's existing systems showing Sunquest can meet Queensland's needs.

For the purposes of this note, I will refer to the Sunquest LIS that will provide lab computing in 124 hospitals and other facilities in Queensland as a "health system LIS" or HS-LIS. The press release refers to an "enterprise LIS" which I think is subject to misinterpretation because of the ambiguity of the term enterprise. This new contract strikes me as a potentially important step in the evolution of the classic LIS which has most often deployed in a single hospital or across several hospitals. We are now in the midst of an era with the emergence of huge health systems in the U.S., the leading one with 76 hospitals (see: Healthcare Fast Facts – Top 30 Largest Hospital Systems in America). It might make sense to me for some of these very large health systems to install a single LIS to support the labs functioning in all of the hospitals comprising the large health system.

I believe that many of these large health systems will be seeking in the future to establish multiple "laboratories of excellence" within the system as a means to insource sophisticated testing like genomic and molecular (see: Intermountain Precision Genomics to develop hereditary cancer gene panels). To my mind, this is a far superior policy to the dependence on external reference labs to provide esoteric testing. As these "laboratories of excellence" proliferate in the mega-health systems, it would also seem to make sense for the future to install a "health system LIS" or HS-LIS. This single LIS could then effeciently manage laboratory test ordering, specimen transport, and results reporting, such as will occur in the Queensland project, across all of the labs in the single health system. This will be particularly important with the adoption of digital pathology technology where slide preparation and scanning could take place in one processing lab but with the images transferred to the various surgical pathology specialists scattered in all of the hospitals in the system.

One-Click Healthcare with Amazon; Narrow Networks Yield Savings and Quality

The recent announcement that a trio of powerful companies, Amazon, Berkshire Hathaway and JPMorgan were entering the healthcare market has caused major reverberations on Wall Street and other sectors of the economy (see: Three Major Corporations Will Form Healthcare Company for Their Employees). The announcement has caused speculation about their actual business plan with some suggesting that the company would deploy new technology to disrupt this large part of the US economy. A recent article further suggested that the "Amazonification" of healthcare could start by bringing one-click "shopping" to healthcare (see: The Amazonification of Healthcare starts now). Below is an excerpt from the article:

So why was Amazon’s “one click purchase” so innovative? It’s so simple that it might not sound like a big deal, but IT IS A BIG DEAL. Amazon isn’t about buying books online, although that’s where they started. It’s really about Consumer Financial Engagement where the Consumer is in control. What most don’t realize is that the Retailer who sells through Amazon also benefits from this consumer focus. When you put all the retailers together in one place, say hello to checking out with ONE vendor, ONE receipt and visibility to everything that’s being delivered to your front door. Consumers loved it for it’s simplicity and convenience. Retailers loved it for the fact that they were there in front of the consumers they wanted and Amazon facilitated everything! In fact, most sell more via Amazon than their very own websites. What if a company could provide a similar experience for you and your patients? With “ONE click” that benefited Patients and Providers? This requires us to “Think like Amazon” in healthcare....For the patient, it would be the end of multiple bills from multiple providers for one single visit to the Hospital. Patients could also say goodbye to unexpected collection letters arriving because they forgot to pay a bill that they didn’t know was past due. A huge positive shift would occur because someone finally put the needs of the patient and provider into one solution.

We all know by now how one-click technology brings simplicity to the purchase of goods and services for Amazon customers. On-line shopping becomes truly frictionless and this is one of the explanations for its success. For Amazon Prime customers, one-click shopping is offered for a yearly membership fee (see: About Amazon Prime). In terms of the purchase of healthcare services, the adoption of a one-click strategy would imply access only to a narrow network to simplify shopping and payment for healthcare (see: Employers May Adopt ‘Narrow Networks’ of Health Care Providers). This means that the choice of providers would be limited under a health insurance plan that would presumably offered to the employees of the three companies. Narrow networks have been the source of complaints in the past in terms of restriction of consumer choice.

It's important to understand that one of the reasons that Amazon's one-click is so popular with consumers is that Amazon brings a wealth of information to the attention of the consumer intending to buy goods or searches including detailed product descriptions and ratings by consumers who have brought that product. I think that if this wealth of information could likewise be brought to the attention of the healthcare consumers by Amazon and its partners plus an assurance of quality and lower cost, consumers would probably tolerate some limits on their freedom of choice in terms of healthcare providers. 

Equifax Releases Credit Locking App That May Not Work; Try Credit Freeze

Equifax is giving software a bad name. First there was the huge database breach of the company in the Fall of 2017 (see: Massive Equifax Data Breach Could Affect Half of the U.S. Population). Not only was this a major database security mishap but the company did not endear itself to consumers in terms of the remedies proposed to correct the problem. It also brought to light the fact that some big and often anonymous companies like Equifax can be the cause of many bad days for consumers through no fault of their own. Now comes news that the company has released a faulty app that is designed to allow consumers to lock access to their credit files from a mobile phone but doesn't seem to work (see: New Service, Same Old Equifax: Credit Locking App Freezes Up Your Money). Below is an excerpt from the article. Its long and detailed and refer to it for a more comprehensive view of the problem.

Amid that mess [of the security breach] came a promise from Equifax that it would create a simple app that allowed people to “lock” their credit files without all the hassle and without a fee....It was supposed to be simple: You download the app and swipe the lock to the right, which restricts access to your file. [There were multiple problems with the app.]....That’s when we told Equifax. About 90 minutes later, a spokeswoman said the company had identified the issue and resolved it. Except that it hadn’t. The locking mechanism still wouldn’t lock. A company spokeswoman said Equifax had not experienced widespread issues with the service, but, as with any new product, there had been isolated problems they were working to resolve.....Equifax’s new app offers a lock instead of a freeze. Locks works similarly to freezes — both restrict access to your credit file — but it should be easier to unlock your credit file since you can do it from your phone with a swipe, and doesn’t require a 10-digit pin or a fee. What is not clear, however, is what disadvantages may come with locks. Many state laws exist that govern freezes, offering consumers protection. By creating locks, the companies avoid them.....So, after I tried to lock my husband’s file five times with no luck, I changed course and obtained what we’ve been telling people to get for years: a freeze. It took all of a minute on Equifax’s website. Maybe in a year or two, Equifax will have its act locked up once and for all.

What I find most interesting about Equifax is that it's both a record storage and a software company with enormous responsibilities and potentially huge liabilities, almost all of it outside of the control of consumers. And in spite of its importance, it seems to lack basic expertise in its core businesses. I am sure that it's not alone in this regard compared to similar companies but it has certainly vaulted into the eye of the public with disastrous results. Get ready to hear similar stories like this in the future. Hospitals come to my mind as institutions that acts as stewards for critically important data but may be relatively incompetent in terns of data security. For example, hospitals seem to be one of the major targets for ransomware attacks (see: WHY HOSPITALS ARE THE PERFECT TARGETS FOR RANSOMWARE).

Intermountain Precision Genomics to Develop Hereditary Cancer Gene Panels

The emerging healthcare model which is dominated by a small number of very large health systems will be characterized, in part, by in-house, sophisticated genomic and molecular lab testing by these systems. This is because these large health systems will have the capital to invest in their own "laboratories of excellence" within their system. Such is the case with Intermountain Healthcare which has its own in-house genomics laboratory called Intermountain Precision Genomics. Intermountain Health is one of the giant health systems with 37,000 employees, 22 hospitals, and more than 185 clinics. Here is the mission statement for this laboratory copied from its web site:

At Intermountain Precision Genomics in-house laboratory, experts analyze the DNA and genetic makeup of a cancer patient's tumor, enabling detection of the individual genes with errors in a person's cancer to determine treatment options. The testing is proprietary to Intermountain Healthcare, but access to it is available to oncologists anywhere. The testing serves patients with late-stage cancer who have failed in a traditional treatment method.

Intermountain Precision Genomics has just announced a plan to develop hereditary cancer gene panels (see: Intermountain Precision Genomics to develop hereditary cancer gene panels). Below is an excerpt from the article describing this new test offering:

Intermountain Precision Genomics announced...it will develop hereditary cancer gene panels. IPG...is poised to validate and launch several tests to identify disease-causing genetic variants associated with hereditary cancer syndromes.....The move follows a recent article in the Journal of Clinical Oncology that reveals an unmet need for genetic testing in women with a history of breast and ovarian cancer. The JOC article, "National Estimates of Genetic Testing in Women with a History of Breast or Ovarian Cancer," shows that fewer than one in five women with a history of breast cancer or ovarian cancer who meet specific National Comprehensive Cancer Network criteria have undergone genetic testing. Moreover, the journal notes, most have never discussed testing with a healthcare provider...."Genetic testing may be used to identify individuals previously diagnosed with cancer as well as healthy individuals who have hereditary cancer gene mutations," added Brent Hafen, who directs cancer genetic counseling for Intermountain. He added that genetic counseling in association with genetic testing allows individuals with an increased cancer risk to obtain more frequent screenings at younger ages, which leads to earlier detection and treatment.

The field of predictive genetic testing is blossoming with 23andMe as one of the pioneers in the field. The FDA is now allowing 23andMe to market tests that assess genetic risks for the following ten diseases or conditions (see: FDA Approves Marketing Of Consumer Genetic Tests For Some Conditions):

• Parkinson's disease, a nervous system disorder impacting movement
• Late-onset Alzheimer's disease, a progressive brain disorder that destroys memory and thinking skills
• Celiac disease, a disorder resulting in the inability to digest gluten
• Alpha-1 antitrypsin deficiency, a disorder that raises the risk of lung and liver disease
• Early-onset primary dystonia, a movement disorder involving involuntary muscle contractions and other uncontrolled movements
• Factor XI deficiency, a blood clotting disorder
• Gaucher disease type 1, an organ and tissue disorder
• Glucose-6-phosphate dehydrogenase deficiency, also known as G6PD, a red blood cell condition
• Hereditary hemochromatosis, an iron overload disorder
• Hereditary thrombophilia, a blood clot disorder

So, to summarize, parallel to the testing and surveillance of patient with suspected current malignant neoplasms, we now have labs providing genomic testing to identify disease-causing genetic variants associated with hereditary cancer syndromes. Not only will such testing be financially remunerative for the performing labs, it will also serve patients by allowing those with the genetic predisposition to cancer to monitor their health more closely.

Medical Chatbot Improves Patient Response Rate for Flu Shot Reminders

One of the continuing challenges in healthcare is developing techniques for communicating with patients in an efficient and effective way. The goal of such a conversation may be to remind them about an appointment or perhaps persuade them to take some action regarding their health. A recent article addressed a chatbot campaign launched by a physician office to increase patient response to flu shots (see: Chatbot campaign for flu shots bolsters patient response rate by 30%). A chatbot is a computer program which conducts a conversation via auditory or textual methods (see: Chatbot) Such programs are often designed to convincingly simulate how a human would behave as a conversational partner, thereby passing the Turing test. Below is an excerpt from the article about the chatbot:

A number of vendors are offering chatbots for healthcare, notably Babylon Health, Buoy Health, Catalia Health, Florence, Memora Health, SapientX, SimplifiMed and Your.MD, among others. Chatbots can be used in a number of different ways. One is to triage patients. In this scenario, the patient tells the bot about his or her symptoms and the bot responds with further options. Another way bots can be used is for administrative purposes, such as scheduling and communicating with patients....[One physician] decided...[to use]...a product from SimplifiMed specifically to help facilitate communication between patients and clinicians. A key example of when his practice used this function was its annual flu initiative. During flu season the practice typically sent out pamphlets and emails to remind patients to get their shots....[The] response rate, in fact, jumped from around one percent when the practice used other channels to 30 percent with texting. The time it took patients to respond was also much faster than usual. ....The [physician's] practice has recently switched over to athenahealth so the chatbot can now integrate with the EMR system. In the future he said the practice will expand the chatbot use to some of the triage purposes.

The article does not go into any detail about how the chatbot software was integrated into the physician's practice but I think there are a couple of ways it might have been used. One path is an app for patients that is installed on their smart phones and can deliver medical advice. Another chatbot option might occur when a patient calls the physician's office for an appointment. Following such an interaction, a suggestion about the need for a flu shot can be initiated by the chatbot. I have been impressed by the improvement in AI technology such that an interaction by a patient with a chatbot is becoming less arduous and artificial. I was also impressed by the number of medical chatbot vendors that were referenced in the article. Looks like a booming industry.

Inspirata Acquires Omnyx from GE Healthcare, Achieving an End-to-End Solution

The business model of Inspirata is relatively unique compared to other companies connected to digital pathology. The company seeks to enhance the digital pathology workflow of its clients presumably pathology departments and consulting firms. Here is a summary of the company goals copied from the company web page (WELCOME TO INSPIRATA):

We...help cancer institutions overcome the financial barriers to adoption using our unique business and delivery model where we make the upfront capital investment in the hardware, software and storage needed to enable a cancer institution to move to a fully automated digital pathology workflow inclusive of the on premise resources needed to operate the scanning lab to convert glass slides to digital images. At the end of the engagement, the institution owns the technology assets and can hire the personnel or renew Inspirata’s contract to continue the managed services model.

Inspirata recently acquired GE Healthcare's Omnyx (see: Inspirata Acquires Digital Pathology Company Omnyx, Enabling Delivery of an IVD Device for Primary Diagnosis in Europe and Canada). Below is an excerpt from the article announcing the purchase:

Cancer informatics and digital pathology workflow solution provider Inspirata...has acquired Pittsburgh, PA-based Omnyx from GE Healthcare. Omnyx was an early innovator in bringing brilliant software to pathology departments around the world....[According to] Inspirata CEO Satish Sanan, “It brings us the last mile to reach our goal of having an end-to-end integrated pathology solution with a scanner-agnostic whole slide image viewer and image management system. It also gives us a fully supported IVD device cleared for primary digital diagnosis in Europe and Canada, and it expands our customer base and geographic footprint across those countries.”....“Our short-term plan is to rapidly combine the advantages of our digital pathology software platform and the Dynamyx platform by converging them onto a shared, state-of-the-art technology stack,” continues Sanan. 

The history of Omnyx, launched originally as a partnership with UPMC, is complicated. Here are a few of the details from an article on the topic from December, 2016 (see: Omnyx ends UPMC affiliation): 

Digital pathology company Omnyx LLC will be folded into GE Healthcare at the end of the month, ending an eight-year partnership with Pittsburgh hospital system giant UPMC to commercialize a nascent technology....UPMC and GE Healthcare formed Omnyx in 2008 as 50-50 owners with the promise of contributing a combined $40 million to the venture. UPMC and GE Healthcare predicted that Omnyx would capture 25 percent or $500 million of an eventual $2 billion market.

The acquisition of the Omnyx software by Inspirata makes good sense. Note in the second excerpt above that CEO Satish Sanan emphasizes the goal for his company of developing an "integrated pathology solution with a scanner-agnostic whole slide image viewer and image management system." Inspirata will continue to work primarily in the digital pathology software space, enabling the customer to purchase scanners form other companies. Also note the reference to the acquisitor of a "a fully supported IVD device cleared for primary digital diagnosis in Europe and Canada." The recent FDA digital pathology approval for Philips was restricted to that system for primary diagnosis (see: FDA Approves the Philips Digital Pathology WSI Solution for Primary Diagnosis). However, it is likely that approval of digital pathology systems for primary diagnosis from other vendors will follow in rapid succession.

Pathology Informatics Webinar on Precision Medicine; February 20 at 1:00 p.m. ET

You are all invited to participate in an upcoming free webinar entitled: The Challenges of Enabling Precision Medicine Diagnostics. This is part of a continuing series of presentations sponsored by the Association for Pathology Informatics (API) and Sunquest Information Systems. The webinar will take place on Tuesday, February 20, at 1:00 p.m. ET. You can register at this link to reserve your spot. The recent surge in interest for precision medicine diagnostics has many healthcare facilities and laboratories facing a number of operational and clinical challenges, including volume of data produced, data interpretation, and workflow complexity. In this webinar, you will learn how informatics can be applied to address some of these challenges, enabling a more efficient pursuit of precision medicine.

The speaker for the webinar will be Nabil Hafez, Senior Director of Product Management, Precision Medicine, at Sunquest. Nabil brings extensive experience in product management, genomics, diagnostics, and informatics to Sunquest. Prior to accepting his position at Sunquest, he was Product Director, Neurology, at Quest Diagnostics, where he oversaw the national neurology diagnostic testing product portfolio including routine testing, cytogenetics, and advanced molecular genetics and immunology. He pioneered and launched Quest’s first digital diagnostic test. Nabil holds an MBA from Duke University, an MS in Bioinformatics from Brandeis University, and a BS in Biology from Binghamton University. 

Fitbit Bands Collect Data Describing Six Billion Nights of Sleep

We are entering a new era when billions of data points relating to health are being collected via health wearables such as Fitbit bands. A recent article revealed some fascinating information about the sleep patterns of many people in the U.S. (see: What Fitbit's 6 billion nights of sleep data reveals about us). Below is an excerpt from the article. It's chock full of interesting data including graphs so read the whole thing if you are interested.

Most of Fitibit’s bands...have built-in heart-rate monitors, which produce much more accurate sleep-measurement results than earlier bands. These bands track your sleep automatically, in your own bed, on your normal schedule, under normal conditions. Since Fitbit began tracking sleep stages in March 2017, it has collected data from 6 billion nights of its customers’ sleep.... The measurements include not just how long you sleep, but what stages of sleep you experience....Women sleep 25 minutes longer a night than men. They average six hours and 50 minutes of sleep a night, whereas men get only six hours and 26 minutes. Neither group gets anywhere close to the recommended eight hours a night. Women get about 25 minutes more sleep a night than men. Women also get about 10 minutes more REM sleep than men every night, too — a gap that widens after age 50.....The news for women isn’t all good, though: They’re 40% more likely to suffer from insomnia — trouble falling asleep — than men....[W]e get less deep sleep as we age. When you’re 20, you’re getting half an hour more deep sleep a night than when you’re 70. We get less and less of the good sleep as we age....Northerners go to bed five minutes earlier than Southerners. They wake up earlier, too. That may seem like a very small difference, but on the scale of billions of data points, it’s significant....The average American goes to bed at 11:21 p.m. 

This is only the beginning of our journey involving the huge amount of health data that will be collected by wearable health devices in the future. The current Fitbits will look primitive a few years hence when accurate vital signs will be collected continuously for a huge swath of the population. Many more of us will be wearing these devicess in the future because many of them will be distributed free by health insurance plans (see: Wearable Health Monitoring Devices: a Means to Lower Insurance Costs?; Health Insurance Company Pays Its Policy Holders to Stay Fit; Apple Watch "Gifted" to Insurance Policy Holders; Any Gotcha's with the Deal?). For privacy advocates, this may look like a nightmare. For technology and data enthusiasts, it will be a fascinating time.