10x Genomics, Genestack, HudsonAlpha, And More: News From June 2020

June 25, 2020 | June featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including 10x Genomics, Genestack, HudsonAlpha, and more.

10x Genomics unveiled the first 45 members selected for participation in its Visium Clinical Translational Research Network (CTRN). Members selected are focused on research in oncology, immuno-oncology, neuroscience, infectious disease, inflammation and fibrosis, COVID-19 and more. The 10x Genomics Visium CTRN was established to improve and accelerate workflows related to assessing the spatial cellular relationship in clinical translational research studies. Visium has the potential to aid in many clinical translational research applications, including biomarker and drug target discovery, engineered immune cell therapy and clinical trial development. “The technologies powering today’s research have led to discoveries that would have been unprecedented ten years ago, but the tools that help translate genomic research to a clinical setting haven’t always kept pace,” Michael Schnall-Levin, SVP R&D and Founding Scientist at 10x Genomics, said in a press release. “By establishing the Visium Clinical Translational Research Network, we can help accelerate the clinical translational process by bridging the gap between scientific discoveries and patient care solutions.” The first 45 members of 10x Genomics’ Visium CTRN were selected from 185 total applications and represent a diverse range of studies that are taking place around the world. The 10x Genomics CTRN will connect researchers across 39 global institutions, including: Barcelona Supercomputing Center; Cancer Research Centre of Lyon (CRCL); Centre de Recherche des Cordeliers (Inserm, Sorbonne Université, Université de Paris); Duke University; Garvan Institute of Medical Research; GSK; Hospital Italiano Buenos Aires, IMTIB; Humanitas Research Hospital; Institut Imagine; Johns Hopkins Medical Institutions; Josep Carreras Leukaemia Research Institute; Lieber Institute for Brain Development; Ludwig-Maximilians University Munich; Mass General Cancer Center; Nanjing Drum Tower Hospital; Queensland University of Technology; RIKEN Center for Biosystems Dynamics Research; RIKEN Center for Integrative Medical Sciences; Sylvester Comprehensive Cancer Center and Bascom Palmer Eye Institute, University of Miami Miller School of Medicine; and University of Michigan Rogel Cancer Center. Press release

Genestack announced that its flagship multi-omics data catalogue, curation and integrative search product, Omics Data Manager (ODM), has been licensed and implemented by AstraZeneca. Genestack's ODM is an enabling technology providing a central hub for organizing and querying multi-omics data from multiple sites, including transcriptomics and proteomics. Curation tools, such as ODM, will enable AstraZeneca scientists to ensure the metadata for studies, samples and data files is accurate, complete and consistent with their data model. ODM's flexible APIs will integrate into AstraZeneca's existing IT architecture and allow cross-study and cross-omics queries. The tool will allow AstraZeneca to fully utilize past, present and future omics datasets by making data findable, accessible, interoperable and re-usable (FAIR). "ODM is our latest product and it builds on years of close work between our domain experts and those at global biopharmaceutical companies,” Misha Kapushesky, Genestack’s CEO, said in a press release. “We're proud of the modern technology stack, flexible multi-omics data and metadata models and APIs, as well as our focus on great user experience. We believe firmly that modern enterprise data strategy is not just about software, but also about the right team and an agile, collaborative, long-term approach." In an official statement, Claus Bendtsen, Executive Director Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, wrote: "Our collaboration with Genestack helps build a single data platform for many of our scientists to query omics data from a large number of studies across R&D. Omics Data Manager will allow our scientists and bioinformaticians to fully harness omics data for faster and more relevant drug discovery and translational research." Press release

The Muscogee (Creek) Nation (MCN), the HudsonAlpha Institute for Biotechnology and HudsonAlpha Health Alliance, have begun a collaboration to bring health and education programs with a focus on genetics and genomics to the tribe. The integration of genomic information in precision medicine is rapidly advancing health care, as an individual’s genome carries important information about disease risks, potential responses to therapy, and appropriate medications. By building programs that integrate genomics into the Muscogee (Creek) Nation Department of Health (MCNDH), its citizens and patients will gain access to these advances. In keeping with tribal leadership’s commitment to improving access to quality and advanced education programs, the collaboration will also provide MCN students and educators access to the latest in genomic science educational tools and classroom support, as well as opportunities to explore careers in biotechnology and genomic medicine through a variety of workforce programs. The MCN genomic health program, through a collaboration with the Health Alliance, will involve the implementation of comprehensive clinical genetic testing to citizens receiving care at MCNDH. This will include clinical decision support for MCNDH physicians, access to the Health Alliance’s Genome Gateway portal for electronic delivery of genetic test results, and test-specific education for patients and physicians. The program will be managed with strict adherence to the tribe’s privacy standards, quality protocols and supervision for the purpose of improving health outcomes for MCN citizens. “This exciting program creates a critical bridge between the Muscogee (Creek) Nation and the advanced genomic science and education programs at the HudsonAlpha Institute,” said Devin Absher, Director of Genomic Health at HudsonAlpha, in a press release. “We think this program will serve as a new collaborative model that will give MCN a leadership position in Native American health initiatives, empowering their citizens to participate in the biotechnology revolution, while maintaining tribal autonomy.” Press release

Bright Computing announced that the San Diego Supercomputer Center (SDSC) at the University of California San Diego will be using Bright Cluster Manager to manage the facility's newest supercomputer, called “Expanse”. The Bright Cluster Manager software platform will enable Expanse to balance and manage resource diversity across virtually all domains of their science and engineering users, maximizing resource utilization and increasing workload efficiency for research scientists across the country and beyond. Expanse will enter production in the fall of 2020 and be available to tens-of-thousands of researchers across the U.S. through the National Science Foundation's Extreme Science and Engineering Discovery Environment. Bright Cluster Manager will provide comprehensive management of the Expanse system, enabling SDSC to administer its HPC resources as a single entity, provisioning the hardware, operating systems, and workload managers from a single unified web interface. Bright will also provide SDSC with access to: Bright Autoscaler, which will enable Expanse to operate as both an HPC cluster and a Kubernetes cluster, supporting heterogeneous computing environments that combine Expanse with remote instruments, data sources, and edge devices; and Cloud Bursting, which will support SDSC's expansion into the public cloud, enabling users to access the vast computational and data resources via direct scheduler integration with Expanse. Press release

Seattle Children's Research Institute and global biotechnology leader CSL Behring announced a strategic alliance to develop stem cell gene therapies for primary immunodeficiency diseases. Initially, the alliance will focus on the development of treatment options for patients with two rare, life-threatening primary immunodeficiency diseases—Wiskott-Aldrich Syndrome and X-linked Agammaglobulinemia. These are two of more than 400 identified primary immunodeficiency diseases in which a part of the body's immune system is missing or functions improperly. "CSL Behring will collaborate with Seattle Children's experts to apply our novel gene therapy technology to their research pipeline, with an aim to address unmet needs for people living with certain rare primary immunodeficiency diseases," said Bill Mezzanotte, Executive Vice President, Head of Research and Development for CSL Behring, in a press release. "Expanding our gene therapy portfolio into an area of immunology well known to CSL exemplifies how we are strategically growing our capabilities in this strategic scientific platform and are collaborating with world class institutions to access innovation with the potential to vastly improve patients' lives." CSL Behring researchers, working with researchers from Seattle Children's Research Institute, will investigate applying the proprietary platform technologies, Select+ and Cytegrity, to several pre-clinical gene therapy programs. These technologies, which have broad applications in ex vivo stem cell gene therapy, are designed to address some of the major challenges associated with the commercialization of stem cell therapy, including the ability to manufacture consistent, high-quality products, and to improve engraftment, efficacy and tolerability. Press release

Metabolon and DNA Genotek have collaborated to bring OMNImet·GUT, the first device for in-home collection and ambient-temperature storage and shipping of fecal samples for metabolomics, to the research market. "For years, our customers from across biopharma, academia and population health have been asking for a validated, ambient-temperature solution to study metabolites in human feces," said Luke Miller, VP Laboratory Operations, Metabolon, in a press release. "When DNA Genotek approached us to validate their new in-home technology, we knew it would help to unlock a new realm of functional insights for microbiome research as well as other areas of health, wellness and disease research." In the past, the only option to study metabolites in feces required immediate freezing and cold chain shipping of the sample. Understanding the barriers this created for patient at-home collection, DNA Genotek collaborated with Metabolon for validation of the collection tubes and the stabilization chemistry necessary to protect the intricate nature of metabolites in feces and ensure sample integrity. Metabolomics is uniquely positioned to provide a readout of the small molecule metabolites, which serve as the "language" for communication between microbiota and the host, and between microbial populations. Metabolon will offer its industry-leading metabolomics analysis and short chain fatty acid analysis on samples collected using OMNImet·GUT. Press release

A Purdue University data science and machine learning innovator wants to help organizations and users get the most for their money when it comes to cloud-based databases. Her same technology may help self-driving vehicles operate more safely on the road when latency is the primary concern. Somali Chaterji, a Purdue assistant professor of agricultural and biological engineering who directs the Innovatory for Cells and Neural Machines [ICAN], and her team created a technology called OPTIMUSCLOUD. The system is designed to help achieve cost and performance efficiency for cloud-hosted databases, rightsizing resources to benefit both the cloud vendors who do not have to aggressively over-provision their cloud-hosted servers for fail-safe operations and to the clients because the data center savings can be passed on them. "It also may help researchers who are crunching their research data on remote data centers, compounded by the remote working conditions during the pandemic, where throughput is the priority," Chaterji said in a statement. "This technology originated from a desire to increase the throughput of data pipelines to crunch microbiome or metagenomics data." The Purdue technology works with the three major cloud database providers: Amazon's AWS, Google Cloud, and Microsoft Azure. Chaterji said it would work with other more specialized cloud providers such as Digital Ocean and FloydHub, with some engineering effort. Press release

After years of development, engineering and enhancement, researchers at St. Jude Children’s Research Hospital have made publicly available a software system that enables better detection of gene fusions. The system, called CICERO, offers additional insights into cancers, as well as new targets for drug treatments. The latest version of CICERO was published in Genome Biology. “In both pediatric and adult cancers, gene fusions can be valuable targets for drug treatment,” said Jinghui Zhang, St. Jude Department of Computational Biology chair, in an official statement. “In many pediatric cancers, they are the initiating genomic alterations that drives the tumorigenesis of a cancer, which means that drugs targeting that gene fusion can effectively treat the cancer.” Press release

CILcare announced a strategic partnership with the start-up Vertidiag, a company specialized in balance disorders. By combining their know-how, CILcare and Vertidiag can propose a complete service offering to identify and develop therapeutic solutions for people suffering from ear diseases including hearing loss, tinnitus, otitis and vertigo. CILcare has developed its foundations on unique expertise in testing the efficacy and safety of drugs, gene & cell therapy, and implantable devices that target hearing loss, tinnitus and otitis. CILcare’s team is mainly composed of doctors, engineers, and experts in otology and neurosciences. The company operates worldwide from its facilities in the South of France and in Lexington, MA, USA, where CILcare partners with CBSET, a not-for-profit CRO linked to MIT, and specialized in translational sciences. CILcare has a portfolio of over 50 sponsors in the USA, Europe and Asia, and is recognized worldwide as the reference CRO partner for external innovation in hearing and otic disorders. Vertidiag finds its origins from a world-renowned academic team, which has more than 50 years of experience in understanding the molecular mechanisms underlying the pathogenesis of vestibular disorders. Vertidiag has developed a technical platform to induce controlled vestibular disorders and to measure their functional impacts. This platform uses behavioral pharmacology, along with a battery of cellular and molecular biology tools that support the understanding of the mechanisms of action of potential drug candidates. “Both Vertidiag and CILcare have a sense of urgency in defining and delivering solutions to Biotech, Pharma, Medtech companies and Academics, with drug candidates that have the potential to become treatments for patients in the near future. We know that working together will benefit this cause. Our teams share the same values of scientific and operational excellence; they trust each other and are naturally working together towards a common goal,” Nicolas Chanut, Vertidiag’s CEO, said in an official statement. Press release