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A roundup of instrumentation, software and other tools and technology news

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Putting money into a 3D platelet bank, bringing six-month results down to six seconds, speed-reading the microbiome, assessing new drug candidates, validating comprehensive two-dimensional gas chromatography mass spectrometry for metabolite biomarker discovery and pairing up for central nervous system (CNS) trials. That’s what’s on tap for our November roundup of hardware and software in life-sciences research and pharma/biotech R&D.
NIBIB awards KIYATEC $225,000 to develop 3D platelet bank
GREENVILLE, S.C.—On Sept. 30, KIYATEC announced that it had been awarded a $225,000 Small Business Innovation Research (SBIR) Phase I grant from the National Institute of Biomedical Imaging and Bioengineering (NIBIB), one of the 27 institutes and centers that comprise the National Institutes of Health (NIH). Over the course of the six-month SBIR award, KIYATEC will develop 3D microbioreactors useful for the in-vitro production of platelets and advance its technology around bone marrow models.
Bone marrow has important implications for the company’s focus in 3D cancer assays, especially with respect to immuno-oncology models combining cancer and the human immune system. In collaboration with Tufts University’s biomaterial scaffold design and fabrication expertise, KIYATEC will develop a perfusion bioreactor system containing a live bone marrow mimetic capable of generating clinically relevant quantities of platelets from initial bone marrow precursor cells and then characterize their morphology and function.
The NIBIB grant will further KIYATEC’s mission to create clinically relevant 3D microenvironments useful for clinical diagnostics, translational research and clinical therapies. The end goal would be the eventual commercialization of the technology platform in order to provide the market with highly functional, donor-free platelets in addition to 3D cancer assays incorporating components of the bone marrow niche.
“This grant is further recognition of KIYATEC’s industry-leading expertise in 3D modeling of the human condition and its ability to combine innovations in biology and engineering to develop clinically meaningful ex-vivo 3D platforms,” said Dr. Howland E. Crosswell, KIYATEC’s chief medical officer and the project’s principal investigator. “Ultimately, we want to positively impact patients and, if successful, this approach would reduce the demand for platelet donation by generating renewable sources of donor-free human platelets, all in vitro.
IO Informatics enthuses about AstraZeneca’s SIEVE at ISWC
BERKELEY, Calif.—Robert Stanley, CEO of IO Informatics (IOI), recently presented the results of IOI’s continuing collaboration with global pharma giant AstraZeneca (AZ) at the 14th Annual International Semantic Web Conference (ISWC) in Bethlehem, Pa., saying: “AstraZeneca’s SIEVE system, building on IOI’s Sentient software and services for data curation, integration and search, has been successfully applied to improve retrieval and analysis of valuable but previously underutilized historical clinical trials data at AstraZeneca.”
“SIEVE provides a web-based environment suitable for cross-study analysis,” Stanley continued. “The environment aligns data across clinical data including treatments, various molecular assessments and outcomes. The new SIEVE integrated datasets support over-arching goals for biomarker identification and qualification, trial design, concomitant medication analysis, translational and precision medicine.”
IOI’s Knowledge Explorer software was used by IOI in collaboration with AZ to explore the content of these records as linked data networks using formal Worldwide Web Consortium semantic standards. The team has analyzed and integrated over 42,000 trials records, identified by unique subjectIDs. Over 36,000 records contained valid data, each including a unique trial, patient and at least one row of laboratory data. IO integrated this complex and widely diverse data under a semantic data model, or “ontology,” with automated import and curation functions to meet SIEVE requirements. The data was harmonized by the application of machine reasoning or “inference,” with growing data integration and curation rules. The resulting dataset was aligned with AZ data dictionaries as well as with public ontologies and thesauri to ensure long-term interoperability with data from other sources within AZ. The integrated and curated data was then connected to IOI’s Web Query software to support rich scientific searching, reporting and analysis.
“Our semantic technology solves difficult integration and curation problems that were prohibitively time-consuming and challenging using older methods,” said Bill Hayden, IOI’s global director of business development, “but new levels of research and business efficiency and power are the outcomes that matter.”
How efficient? Well, whether hyperbole or not, it is striking that AZ’s lead person for the SIEVE Project reportedly stated: “Questions that used to take my team six months to answer...are now answered in six seconds.”
“This example of how semantic technology can and does allow for better data integration and knowledge harvesting opens up unlimited possible uses including aiding to solve challenges in personalized medicine and big data within the pharmaceutical industry,” Stanley said.
UCSD researchers team up with Illumina to speed-read your microbiome
SAN DIEGO—The human microbiome, or the total collection of bacteria, viruses and other microorganisms living in and on your body, has been linked to a variety of health and disease states, including obesity, allergies, asthma and a rapidly growing list of other conditions. But as researchers try to sort out the complex relationship between microbial populations and human health and use that information to diagnose or treat disease, they are generating a deluge of microbial sequence data that first needs to be organized and analyzed.
To this end, University of California, San Diego (UCSD) School of Medicine’s Dr. Rob Knight and his team built a microbiome analysis platform called QIIME (pronounced “chime” and short for “Quantitative Insights Into Microbial Ecology”). This software will now be more readily accessible to hundreds of thousands of researchers around the world through BaseSpace, a cloud-based app store offered by Illumina, which develops life-sciences tools for the analysis of genetic variation.
“Previously, we relied on personal contacts and scientific publications to spread the word about QIIME, and then users needed to download several different software packages to their own computers. Users also needed some technical programming skills to use QIIME,” said Knight, professor of pediatrics and computer science and engineering. “By working with Illumina, not only will many more researchers now be able to access QIIME from the cloud, the BaseSpace interface will make it much easier for non-technical researchers to analyze their data. This advancement will significantly ease the bottleneck in a variety of human and environmental microbiome studies.”
Two high-profile microbiome studies that rely on QIIME are the Human Microbiome Project, a National Institutes of Health-led initiative akin to the Human Genome Project, and the American Gut Project, a crowdsourced, crowdfunded project in which Knight’s team is sequencing as many human microbiome samples as possible, from anyone who wants to participate.
“QIIME has proven to be a widely successful open-source project—the original paper our group published on it in 2010 has been cited by more than 3,000 other papers since,” said Yoshiki Vázquez-Baeza, an incoming UCSD Computer Science and Engineering graduate student in Knight’s lab. “This collaboration, among many other things, will help us expand our user base and increase the availability of our methods.”
“BaseSpace is a cloud solution for data repository and analysis options that help streamline the processing of the seemingly ubiquitous genomic and metagenomic sequence data that researchers generate every day,” said Jay Patel, associate product manager of BaseSpace applications at Illumina. “QIIME is a highly utilized tool in metagenomics research and we are excited to make it part of the Illumina ecosystem.”
Japanese agency selects Certara’s Phoenix WinNonlin Software
PRINCETON, N.J.—Certara, a  global biosimulation technology-enabled drug development company, announced recently  that the Japan Agency for Medical Research and Development (AMED) has selected Certara’s Phoenix WinNonlin software for pharmacokinetic/pharmacodynamic (PK/PD) modeling and non-compartmental analysis of new drug candidates. AMED was launched on April 1, 2015, and fulfills a similar role to the National Institutes of Health in the United States.
“Considered the gold standard for PK/PD and non-compartmental analysis, Phoenix WinNonlin is being used by more than 6,500 researchers at more than 1,500 biopharm companies, academic institutions and global regulatory agencies,” said Certara CEO Dr. Edmundo Muniz. “In fact, Phoenix WinNonlin is relied upon by 100 percent of leading pharma companies, according to survey results published in the January 2015 IQ Consortia report on preclinical PK/PD modeling. We are delighted that AMED chose to start working with Certara right away as the Agency expands its drug development analysis capabilities.”
Prime Minister Shinzo Abe is reportedly counting on AMED to move drugs from the bench into the clinic and onto the market. AMED is expected to employ Phoenix WinNonlin to create PK profiles and assess bioavailability for new drug candidates in its preclinical program. These data will help AMED’s domestic and international biopharmaceutical partners to identify which molecules hold the most therapeutic potential and should be progressed into clinical trials. AMED is currently testing about 200,000 samples provided by 10 biopharmaceutical companies. However, it plans to open the program to additional biopharmaceutical partners shortly. Its initial focus is on the development of drugs for cancer and infectious diseases. AMED will flag promising molecules for its partners and request that they develop them further.
GCxGC-MS validated for metabolomics profiling, biomarker discovery
KANNAPOLILS, N.C.—Scientists at the David H. Murdock Research Institute (DHMRI) in North Carolina recently validated the use of comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) for metabolite biomarker discovery.
“GC x GC-MS is an approach to biomarker research that tends to be underused,” commented Dr. Kevin Knagge, group leader of the DHMRI Analytical Sciences Laboratory (ASL), which includes metabolomics, nuclear magnetic resonance imaging and proteomics. “The advantage we found is that it increases the number of compounds that can be seen, greatly improving global metabolic profiling.”
DHMRI scientists tested 109 human serum samples with GCxGC-MS and compared them to the standard approach of chromatography time-of-flight mass spectrometry (GC-MS). Using GCxGC-MS, more than twice as many metabolites were identified. In addition, the GCxGC-MS analysis identified 34 metabolites with statistically significant differences compared to 23 in the GC-MS analysis when associated to controls. The study results are detailed in the Journal of Proteome Research in the paper entitled “Comparison of GC-MS and GCxGC-MS in the Analysis of Human Serum Samples for Biomarker Discovery.”
“Combining the new software program and the technology that we have on our instrument allowed us to do more elaborate data analysis and data collections, which then increased the resolution and separation,” Knagge said. “We want more metabolomics data for our global metabolomics profiling and for the studies our collaborators bring to us, and this new methodology does that.”
Beyond serum, GCxGC-MS can profile metabolites in urine or tissue samples as well as plant materials. DHMRI is currently using GCxGC-MS for metabolomics profiling and biomarker research related to the prevention and treatment of chronic diseases.
CluePoints partners with Bracket for CNS trials
CAMBRIDGE, Mass.—CluePoints, a software provider of risk-based monitoring (RBM) solutions for clinical trials, has announced a partnership with Bracket Global, a leading provider of technologies and services designed to drive superior clinical outcome results. The exclusive partnership will see CluePoints’ RBM software offered in combination with Bracket’s Blinded Data Analytics and Rater Training and Quality Assurance oversight program for psychiatry and neurology trials. Bringing together CluePoints’ and Bracket’s expertise and solutions is expected to enhance the impact of the services that each company delivers to sponsors, improving the integrity and quality of clinical data.
“We are delighted to announce our partnership with CluePoints, a company which is leading the way in software that can support the practical implementation of RBM techniques in today’s trials,” said David Daniel, senior vice president and chief medical officer for Bracket Global. “Integrating CluePoints software into Bracket’s Electronic Clinical Outcomes Assessment-based data quality monitoring programs provides a level of efficiency and sophistication in de-risking CNS studies that has not previously been possible.”
CluePoints CEO Franҫois Torche said: “CluePoints' experience of de-risking over 50 studies using our unique CSM solution, along with Bracket’s world-leading expertise in delivering quality assurance systems, provides us with a unique opportunity to deliver combined services that achieve the most detailed insight into clinical data for sponsors. Working together we will support CNS trials in improving data quality and integrity using independent, objective statistical methodology.”

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