ARUP Emerges as a Commercialization Leader at the U

Inside ARUP. Photo credit: Dan Croft, ARUP.

ARUP Emerges as a Commercialization Leader at the U

A culture conducive to innovation and translational research has led to four promising U spinouts emerging from this lab in recent years

ARUP isn’t just about processing your blood work. Innovation, research, collaboration, and commercialization have become an important part of this large laboratory’s DNA. In the last five years alone, four promising U-spinout companies have emerged from ARUP initiatives and collaborations with groups on campus, and dozens of invention disclosures have come from its researchers, both faculty and staff.

Supporting Laboratory Innovation

Because ARUP is a nonprofit enterprise, it has certain obligations it must meet. While ARUP’s for-profit competitors such as LabCorp and Quest Diagnostics distribute their profits to their shareholders each year, the money left over at ARUP after expenses must, by law, be reinvested back into the organization. According to Noriko Kusukawa, vice president and director of innovation and strategic investments at ARUP, the lab purposefully chooses to distribute a sizable portion of these reinvested funds to research and development. “We do this because one of our primary missions is to support the mission of the University of Utah,” she explains. As a result of this focus, “…education, training, and research are very important to us.”

According to Mark Astill, vice president of research and development at ARUP, this support results in approximately 150 peer-reviewed publications by ARUP faculty and staff each year. What sets this research apart from many other departments on campus, however, is that most of it is translational in nature. “ARUP’s research and development has a small ‘r’ and a capital ‘D’,” Astill explains. “We don’t do a lot of basic research here, important as it is. Rather, our focus is on developing pragmatic solutions to real-world problems.”

This research focus on solving real-world issues lends itself to practical discoveries that are more easily commercialized than other types of research. As a result of this, ARUP set up an internal patent committee to routinely review inventions so they are vetted for real-life applicability and so that feedback from ARUP’s industry partners can be sought early in the process. Kusukawa explains that when one of these inventions meets certain criteria, primarily when it is: relevant to what ARUP does, is likely to benefit the organization, and is patentable, the lab often chooses to support it further, both with funding of some sort as well as with commercial mentoring.

A Pragmatic Approach

ARUP’s translational research focus arises for two reasons. First, because ARUP faculty and research staff are heavily involved in the many tests performed at the laboratory, they are often interested in finding ways of making them more efficient. Second, because many of the faculty routinely work with clinicians to manage patients, or in some cases see patients themselves, they have a strong interest in bettering patient care. These two foci have led directly to four U spinouts emerging in recent years from ARUP research, each determined to both improve laboratory science and provide better patient care.

4DQC

Frederick Strathmann, assistant professor of pathology and inventor of 4DQC’s technology. Photo Credit: Peta Owens-Liston, ARUP.

4DQC (Fourth Dimensional Quality Control) is a recent U-spinout based on the efforts of Frederick Strathmann, assistant professor of pathology. Strathmann has designed software that is focused on laboratory-wide data capture and real time metric presentation in a dashboard format, sort of a DOMO for the laboratory science world. Routine tasks that medical technologists perform when troubleshooting issues are also automated by the software, thus allowing lab managers to see potential problems before they arise.

The goal of 4DQC is to lead a change from retrospective data review processes that dominate current laboratory quality assessments to real time, prospective analyses that use automated quality metrics and predictive analytics. This, Strathamnn believes, should result in less “do over” tests for patients and more tests being able to be run on existing equipment each day. The company is currently planning a soft launch of its software within ARUP this fall.

Techcyte

Mohamed Salama, professor of pathology and co-inventor of Techcyte’s technology. Photo Credit: Peta Owens-Liston, ARUP.

Like 4DQC, U-spinout Techcyte also seeks to improve current laboratory methods. Each day, millions of common tests such as a complete blood count or a urine test are ordered by physicians and processed by advanced machines. These machines are programmed to flag samples that deviate from a normal range. Flagged tests often require further examination. When this is the case, a small portion of the sample being tested is smeared onto a slide (e.g., blood, urine, feces, etc.) and sent to a pathologist to review under a microscope. These pathologists must manually count cell types to either confirm the machine’s findings or contradict them. If, for example, a blood test has revealed that a patient has an abnormally high white blood cell count, the pathologist must manually count the number and types of white blood cells on that sample. “This manual process is tedious for pathologists,” explains Mohamed Salama, professor of pathology and a co-inventor behind Techcyte’s technology.

Believing that there must be a way to utilize technology to do this type of counting for pathologists faster and better, Salama decided to team up with Tolga Tasdizen, an associate professor of electrical and computer engineering at the SCI Institute, along with one of Tasdizen’s students. Together, the team created software that automatically classifies the contents of slides using advanced deep learning algorithms. When the software is launched, all Techcyte’s clients will need to do is log on to Techcyte’s website and digitize a slide by scanning it under a microscope scanner. The slide will then be automatically uploaded to Techcyte’s servers where its contents will be rapidly pre-classified and identified. One of Techcyte’s major goals is to provide a tool that supports pathologists and laboratory professionals with work flow efficiency.

According to Ralph Yarro, the company’s CEO, Techcyte will be launching a minimum viable product (MVP) of its offerings in October of this year.

IDbyDNA

Screenshot from Taxonomer

Although diagnostic tests have become far more effective and technologically advanced in recent years, many of these tests are limited by the fact that they are designed to check for a small number of diseases. When faced with the presence of a possible infectious disease such as malaria or tuberculosis, physicians must check a patient’s symptoms, match those symptoms to a known infectious disease, and then run a test for it. If that test comes up negative, they must run a test for another disease, and so on until the source of the infection is found.

Taking advantage of recent gains in next generation sequencing (processes that sequence DNA and RNA much more quickly and cheaply than previously done) and big data (the ability to quickly process large amounts of complex information), a team of researchers at the U have developed a revolutionary new software tool that rapidly reads DNA and RNA sequences from biological samples, and determines which infectious agents are present in a patient’s bodily fluids. This software tool, called Taxonomer, is the core technology behind U-spinout IDbyDNA. It was developed by a large multidisciplinary team from ARUP, Human Genetics, the USTAR Center for Genetic Discovery, Biomedical Informatics, Pediatric Infectious Diseases, and representatives from the Centers for Disease Control and Prevention (CDC). According to Mark Yandell, co-inventor and professor of human genetics, “Taxonomer can detect known and even unexpected pathogens in patient samples all at once.”

Robert Schlaberg, assistant professor of pathology and co-inventor of IDbyDNA’s technology. Photo Credit: Peta Owens-Liston, ARUP.

Taxonomer will also be useful in diagnosing the exact type of pathogen that has caused a patient’s disease. “Pneumonia, sepsis, and encephalitis can all be caused by a very large number of pathogens,” explains co-inventor Robert Schlaberg, assistant professor of pathology. “Identifying the pathogen responsible will enable physicians to target them with the appropriate treatment.”

Schlaberg says that the company is preparing for launch of a Taxonomer-based diagnostic test in collaboration with ARUP in the fall of 2016. Taxonomer is available at www.taxonomer.com.

AvanSci Bio

AvanSci Bio’s MilliSect™ Instrument

The recent growth in genomic testing of tumors over the last 10 years is allowing doctors to determine which gene mutations are involved in a patient’s cancer and which are not. Such information is important because some gene mutations are more likely to respond to a particular drug than others. This type of testing is one of the primary reasons behind the growth of personalized cancer treatment plans that oncologists are preparing for their patients more frequently. However, nearly all of these tests, known as molecular tumor tests, require that specific cells of interest be dissected out from a patient’s tissue sample (usually cancerous tumor cells). Such samples, or biopsies, are far more invasive to collect from patients than simple procedures such as blood tests. Some biopsies require surgery, and nearly all require some kind of anesthesia be used. Understanding this, Katherine Geiersbach, former assistant professor of pathology at the U, was always frustrated when she had to request a new biopsy be done on a patient because the cancerous tissue content on the original biopsy sample was too small for a molecular test to be run. She soon realized, however, that the issue wasn’t the samples; it was in how the cancerous content is collected for analysis. Most tissue for molecular tests is acquired by hand using a scalpel. This method sometimes doesn’t allow a pathologist to precisely collect enough pure sample for molecular testing, particularly when the amount of tissue is small to begin with. A laser method also exists to collect precision samples, but these instruments can cost up to $500,000 and can be difficult to use.

Geiersbach knew that there had to be a more precise yet cost-effective method for precisely extracting pure amounts of cancerous tissue from biopsies. When outside technology developers Nils Adey and Rob Parry of Salt Lake City-based AvanSci Bio heard about this issue from Geiersbach, they decided to team up with her, Mark Herrmann, who was with ARUP at the time, and the Software Development Center at the U to solve it. The result was a tool called the MilliSect™ Instrument that was initially sold by the U-spinout. This technology, now owned by Roche Diagnostics, is able to extract tissue samples as small as 250 microns across (a human hair is about 75 microns across by comparison), far more precise than hand scraping samples produce. MilliSect is also automated, computer-controlled, hands-free, and much less expensive than laser methods. It is saving pathologists time and, more importantly, resulting in less patient biopsies having to be redone.

The AvanSci Bio Team (left to right): Rob Parry, Derek Bosh, Mike Worthen, Nils Adey, Dale Emery, and Shelly Kaufman

Synergizing With the U

Astill is quick to point out that none of the U spinouts that have emerged from ARUP research could have happened if it wasn’t for the alliances it has developed with other groups on campus. “Because laboratory medicine covers so many different fields, it is essential that we forge strong partnerships with colleagues across campus to effectively do and translate our research,” he explains. 4DQC, for instance, worked with the U’s Software Development Center (SDC) and a student team from the Lassonde New Venture Development Center, Techcyte teamed up with colleagues from the SCI Institute to produce its software program, inventors from multiple departments formed IDbyDNA, and AvanSci Bio’s instrument required the expertise of the U’s SDC as well as outside experts. This synergistic effect has led ARUP to become both a leader in laboratory science as well as in technology commercialization.

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