On the cutting edge

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

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MINNEAPOLIS—Late last year, Advanced Cell Diagnostics (ACD), a Bio-Techne brand, celebrated a milestone in the adoption of its RNAscope in-situ hybridization (ISH) technology. Reaching 1,000 publications and increasing to an average of more than one publication per day, papers using RNAscope now feature regularly in top-tier journals, the company notes, marking this as “clear evidence that scientists are applying RNAscope ISH as a robust and sensitive assay that yields the high-quality data necessary for cutting-edge studies.”
A recent surge—400 publications featuring RNAscope in 2017 alone—included a notable increase in pharmaceutical and biotechnology industries. Authors of recent publications include researchers at Bayer, Merck and Eli Lilly.
Reflecting confidence in the assay, ACD says its ISH technology is also becoming a primary assay used in research rather than a secondary confirmatory assay, citing as an example that a recent Nature publication, “Stromal R-spondin orchestrates gastric epithelial stem cells and gland homeostasis,” used more than 40 RNAscope probes to elucidate the mechanism by which epithelial cells regulate and shape their environment.
In addition to the growing number of industrial publications in immuno-oncology, cancer, gene therapy and many orphan diseases development programs, RNAscope is also being used in new areas of academic research, ACD notes. These fields include neuroscience, metabolic diseases and virology and infectious disease research, which have recently seen fast growth alongside RNAscope’s established presence in oncology and stem cell research.
Dr. Yuling Luo, president and general manager of ACD, commented: “We’re very proud of having our customers achieve the 1,000-paper milestone so rapidly, with over 900 papers in the last three years alone. The fact that RNAscope adoption is expanding into new industries and areas of research, as well as becoming a core assay in biopharmaceutical research and diagnostic development, demonstrates the robustness, sensitivity and reliability of the assay. It also shows that RNAscope is playing a significant role in advancing numerous research areas and on its way to being a gold standard method in labs.”

Real-world evidence solutions for Pfizer in cardiovascular
BASEL, Switzerland & BOSTON—BC Platforms, a world leader in genomic data management and analytics, announced in February that Pfizer Finland will be using its technology solutions and research platform, including BCRQUEST.COM, to study data in cardiovascular diseases. The services will be used to analyze anonymized data from Turku University Hospital and other healthcare providers to generate real-world evidence in atrial fibrillation patients. Microsoft will provide the cloud infrastructure for indexing and accessing the information globally through the Microsoft Azure cloud platform.
“Cardiovascular diseases are the leading cause of global mortality in the world and the incidence is rising due to an aging population. The diseases are complex, and therefore we need data to fully understand and provide the best treatment outcomes for patients,” noted Jaakko Parkkinen, country medical director at Pfizer. “We believe that combining our expertise in treatment of cardiovascular diseases with BC Platforms’ advanced genomic and clinical data management solutions through BCRQUEST.COM, we can gather and analyze important real-world evidence to generate optimal patient outcomes.”
Samu Kurki, lead scientist at BC Platforms, commented: “Pfizer is one of the leaders in providing treatment solutions for patients suffering from cardiovascular diseases, and we are delighted that they have chosen to collaborate with us to support the generation of real-world evidence in this space to better understand the complexities of the disease. These types of projects are ideal for leveraging data from innovative healthcare systems to support clinical research and outcomes.”

Broad Institute releases open-source GATK4 software
CAMBRIDGE, Mass.—Early this year, the Broad Institute of MIT and Harvard released version 4.0 of the Genome Analysis Toolkit (GATK), the institute’s flagship genome variant discovery package for analysis of high-throughput sequencing data. GATK4 is fully open-source and is available at no cost for academic and commercial research on local computing infrastructure, and is also designed for deployment on cloud environments. The reengineered GATK solves key bottlenecks, including an analysis step where GATK4 can analyze types of genomic sequence data 15 times faster than GATK3, while increasing input capacity by a factor of five.
The toolkit is developed by a team of software engineers and data scientists at the Broad Institute’s Data Sciences Platform, who work directly with genomics researchers to ensure the GATK stays ahead of increasing demands for accuracy, speed and complexity in genomics research.
GATK4 reportedly offers significant research advantages over earlier versions, which focused on germline short variant discovery only. GATK4 is the first and only open-source software package that covers all major variant classes (SNPs, indels, copy number and structural variation) for both germline and cancer, and for genomes and targeted sequencing assays. In addition, GATK4 includes tools that take advantage of machine learning, including neural network algorithms, which improve the accuracy in discovery of variants.
Over the last 12 months, software engineers at the Intel-Broad Center for Genomic Data Engineering have also incorporated major performance optimizations into GATK4.
“We completely reengineered GATK4 to optimize speed, scale and flexibility, while maintaining the best practices pipelines and high quality of data output that have become the standard for genomics research around the world,” said Eric Banks, senior director of the Data Sciences Platform. “Already, GATK4 has been put to the test internally at the Broad Institute for six months—including by processing the 24 terabytes of sequence data our genomics platform produces and moves to the cloud every day.”

Automated early development trial data management platform
LINCOLN, Neb.—Celerion recently announced a new core capability for the growing market of early clinical development: the integration of ClinQuick, Celerion’s proprietary electronic data acquisition system, with TrialMaster, OmniComm’s electronic data capture solution, to provide a fully automated clinical trial data management platform.
The dynamic exchange of information between late preclinical efforts and early-stage clinical trials is critical to accelerating the transition from first-in-human through to proof-of-concept patient studies, Celerion notes in touting the new solution.
Celerion uses TrialMaster as the preferred electronic data capture (EDC) system for data capture on multisite studies, and ClinQuick to capture bar-coded data for studies conducted in Celerion clinics. Integrating ClinQuick into TrialMaster automates Celerion’s data acquisition system and provides consistent data management and reporting capabilities in one centralized database. It facilitates consistency of data collection across clinical sites, ensuring accurate and high-quality information.
This integrated solution provides a comprehensive data management platform to access ClinQuick’s bar-coded data, and enable dynamic risk monitoring, robust query management, ad hoc reporting and data extraction in portable industry formats. It has also been incorporated into Celexus, Celerion’s client portal for real-time access to all clinical study data.
“Merging our proprietary electronic data acquisition system with an electronic data capture system is a revolutionary advancement that has not been seen before in early clinical research,” said Dr. Michelle Combs, vice president of data management and biometrics for Celerion. “This automated solution minimizes the need for manual data entry and delivers a centralized data management platform that meets growing client expectations for speed and transparency.”

Thermo and Illumina provide broader access to Ion AmpliSeq technology
CARLSBAD, Calif. & SAN DIEGO—Thermo Fisher Scientific and Illumina Inc. in January signed a commercial agreement that enables Illumina to sell Ion AmpliSeq technology to researchers who conduct scientific studies on Illumina’s next-generation sequencing (NGS) platforms. The best-in-class amplicon technology is highly effective in capturing DNA and RNA from minute amounts of samples for application in multiple areas of research.
Under the agreement, Thermo Fisher will provide Illumina with Ion AmpliSeq technology for research use. Illumina will sell the product directly to its customers under the name AmpliSeq for Illumina. Thermo Fisher will continue to sell Ion AmpliSeq chemistry for both in-vitro diagnostic and research-use-only applications to Ion Torrent NGS customers, and retains the right to make the technology available on other next-generation sequencing platforms.
“Thermo Fisher expects standardization of the AmpliSeq technology will have a profound impact on disease research and encourage greater collaboration among the NGS community,” said Joydeep Goswami, president of clinical next-generation sequencing and oncology for Thermo Fisher Scientific. “Through this agreement, a much larger base of research customers can now leverage Ion AmpliSeq technology’s benefits, while Thermo Fisher continues its commitment to Ion Torrent targeted sequencing solutions for the research market and accelerates its focus and forward momentum in the clinical space.”
“This partnership represents a significant step forward enabling a high performing, flexible amplicon chemistry for use on Illumina’s market-leading portfolio of sequencing systems,” said Mark Van Oene, chief commercial officer for Illumina. “By expanding access to AmpliSeq chemistry to existing customers, we are enabling them to do even more with their systems.”

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