Congenica, PerkinElmer, Illumina, And More: News From September 2017

September 25, 2017

September 25, 2017 | September featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including Congenica, PerkinElmer, Illumina, and more.

Cambridge Semantics announced the release of Anzo Smart Data Lake (ASDL) 4.0, its flagship platform product that builds a semantic layer at scale on all enterprise data and empowers users to extract powerful insights at record speed. Incorporating several new technical advancements designed to deliver a generational shift over current data lake, data management and data analytics offerings. ASDL 4.0 offers an end-to-end, enterprise-scale open platform that creates a single semantic layer of an organization’s structured and unstructured data. The platform is designed to break down the IT barriers that can cost enterprises millions of dollars in lost opportunities by slowing down or blocking data access. Press release

Congenica announced a new customer partnership with the Coimbra Paediatric Hospital (CPH). Through this partnership, the hospital has licensed Congenica’s Sapientia software platform to perform analysis of whole-exome sequencing data and produce diagnostic reports for its In2Genome project. The €1.2 million ($1.4 million) project funded by Portugal2020, Compete 2020, and European Structural and Investment, aims to revolutionize the diagnosis of rare genetic diseases through insights gained from population-wide genomic data. Initiated by The Medical Genetics Unit of CHUC, which is housed in CPH, the In2Genome project is a multidisciplinary consortium collaborating with Portuguese companies Coimbra Genomics and Genoinseq by Biocant. The project, which commenced in July 2017, is expected to run for two years. Press release

PerkinElmer announced an innovative collaboration with In-Depth Genomics (IDG) to support IDG’s Whole Genome Sequencing (WGS) Diagnostic Program that will bring genetic diagnosis to patients across a wide range of neurological conditions including rare/orphan disorders. This collaboration will help pave the pathway towards improved diagnoses and treatments. IDG, which will offer its program to any U.S. physician, will also be funding the initiative at no cost to the patient, thereby providing universal access to the latest diagnostic technology. The program plans to ultimately sequence 100,000 genomes of patients who suffer from rare and undiagnosed conditions. This program will leverage the large network of neurologists that IDG’s leadership has previously worked with to screen approximately 2,500 patients through a gene panel. IDG is actively seeking pharmaceutical and biotech partners who share the vision of transforming the landscape of diagnoses and therapies. PerkinElmer will provide clinical WGS, interpretation services, and diagnostic report generation to IDG. IDG will use the de-identified genomic and clinical data to support R&D in hundreds of rare neurological conditions. Press release

PerkinElmer also expanded its Whole Genome Sequencing (WGS) services to families that preserve their cord blood and cord tissue with ViaCord. This launch follows the Company’s recent introduction of its clinical WGS services. Parents that choose ViaCord, PerkinElmer’s cord blood and cord tissue preservation business, now have the opportunity to benefit from a physician-ordered WGS test of their child’s DNA via a simple saliva test. The test examines a broad range of disease-related genes and provides diagnostic findings contributing to pediatric onset diseases. Additionally, the test reports on pharmacogenetic variants used to optimize certain drug selection. “WGS is another great opportunity for families to identify and prepare for important health concerns, positioning themselves to benefit from the fast moving area of personalized medicine,” said Morey Kraus, chief scientific officer, ViaCord, in a press release. “We have seen tremendous progress using cord blood stem cells to treat disease, and I expect families who make such health conscious decisions to benefit from WGS as well.  Additionally, with the rapid progress we’ve seen with regenerative medicine and gene editing, insights from WGS may be used in the future, in combination with a family’s cord blood and cord tissue, to optimize the design of a treatment plan. This is a very exciting next new step in advancing personalized medicine.” Press release

Advanced Analytical Technologies (AATI) and Illumina recently entered into an agreement to support collaborations and co-marketing activities involving AATI’s Fragment Analyzer Automated CE Systems for quality control (QC) analysis of nucleic acids in Illumina next-generation sequencing (NGS) workflows. The Fragment Analyzer accelerates NGS library preparation with simultaneous qualification and quantification of DNA and RNA. AATI’s systems provide a scalable method, tested by Illumina, for accurate analysis of a broad range of sample types in Illumina NGS library prep workflows, including genomic DNA, RNA, cell-free liquid biopsy, single-cell isolates, and prepared libraries before sequencing. Assessing nucleic acid quality is essential for the success of NGS applications. The identification of DNA and RNA samples likely to produce suboptimal libraries that yield poor sequencing performance due to degradation, fragmentation, or low purity can be achieved by verifying the integrity of samples before library preparation. Similarly, accurate quality and quantity analysis of prepared DNA libraries can be used to optimize cluster generation during sequencing, resulting in cost and time savings while maximizing both sequencing data quality and output. “The Fragment Analyzer systems give our customers new options to streamline the analysis of nucleic acid isolates and prepared libraries,” says Kevin Meldrum, Senior Director of Product Marketing at Illumina, in a press release. “We look forward to working with AATI to provide robust QC solutions, especially as NGS sample numbers grow and multiplexing techniques are empowered by our high-capacity NGS platforms.” Press release

PSSC Labs announced its work with Biosoft Integrators to provide powerful, turn-key HPC Cluster solutions for researchers in the biotech and genetic research fields. Biosoft Integrators (BSI) works with researchers around the world to integrate laboratory technology platforms. With extensive experience in laboratory settings, the company’s founders realized that often equipment and software are poorly integrated and lack the functionality to work with each other, requiring researchers to manually transfer work and data between software and equipment. BSI provides researchers with greater efficiency and management by providing tools which unify the laboratory and laboratory informatics. BSI combines knowledge, experience and technology platforms to the biotechnology marketplace including the manually tracked lab to the fully automated and integrated consumer genomics facility. PSSC Labs will work with BSI to create turn-key high performance computing (HPC) clusters, servers, and storage solutions. PSSC Labs has already delivered several hundred computing platforms for worldwide genomics and bioinformatics research. Utilizing the PowerWulf HPC Cluster as a base solution platform, PSSC Labs and BSI can customize individual components for a specific end user’s research goals. Press release

The National Heart, Lung, and Blood Institute (NHLBI) awarded Exotect a $224,576 STTR grant to further the development of novel therapeutics for the treatment of pathological conditions affected by airway mucus hypersecretion. These pathological conditions include chronic bronchitis, cystic fibrosis, bronchiectasis, chronic obstructive pulmonary disease (COPD), and asthma. In partnership with the University of Texas MD Anderson Cancer Center, the grant will be used by Exotect to generate derivatives of the company’s current promising candidates and test for improved solubility, target affinity, pharmacodynamics, and toxicity with the ultimate goal of selecting a potential molecule for clinical development. The concept for Exotect’s program is based on research from Burton Dickey, Professor and Chair of the Department of Pulmonary Medicine at the University of Texas MD Anderson Cancer Center.  Collaborators include Michael Tuvim, Professor and Director of Laboratory Research, and Roberto Adachi, Associate Professor. Dickey, Tuvim, and Adachi will continue to remain engaged in the development of the therapeutic technology with Exotect. “The goal of our program is to identify drugs that prevent rapid mucin secretion that can block airways, while preserving baseline secretion that is required to keep airways clear” said Dickey in a press release. “We were surprised to find that genetic modulation of Syt2 had such a profound effect on stimulated mucus secretion and are excited to develop small molecule inhibitors that target this protein.” Press release

Synthego announced the appointment of Sir Andrew Witty to the Synthego advisory board. Witty was also recently appointed to the board of directors at G1 Therapeutics and UnitedHealth Group. Witty is Chancellor of the University of Nottingham in England and recently served on the board of directors at GSK while CEO from 2008 to April, 2017. He brings more than 30 years of biopharma experience ranging from product management and business development, to strategic partnerships, including significant international experience serving in a number of senior roles in Europe and Asia while at GSK. He has also been advisor to several governments around the world. "Synthego's vision for automating biological research will revolutionize the industry by accelerating application development and enabling machine learning based insights. Their recent rapid advances of the CRISPR field highlight their ability to execute on deep technology with a multidisciplinary, informatics-first approach," said Sir Andrew Witty in a press release. "I look forward to contributing to the company's success as the business extends further into the genome engineering market." "Andrew's broad experience in the biopharmaceutical space will help us unlock the full value of our platform and grow in key areas of the industry. This is part of the next step in bringing Synthego's bioinformatics and experimental expertise to new applications and markets," said Paul Dabrowski, CEO of Synthego, in a written statement. "Andrew's appointment strengthens the company's position as a leader in genome engineering solutions, we are privileged to have him join our advisory board." Press release

Synpromics announced a new research partnership with Solid Biosciences. Under the terms of the agreement, Synpromics will provide Solid Biosciences access to a set of key muscle-selective promoter candidates to be used in the development of new treatment options for Duchenne muscular dystrophy (DMD). The use of Synpromics’ synthetic promoters will enable the enhancement of Solid Biosciences’ investigational gene therapy candidates for the treatment of DMD. These muscle-selective promoters have been designed using Synpromics’ PromPT technology and bioinformatics expertise, and will be evaluated by Solid Biosciences for optimal product specific gene control. Press release

Feng Zhang has been announced as the recipient of the 2017 $500,000 Lemelson-MIT Prize, the largest cash prize for invention in the United States. Zhang is a core member of the Broad Institute of MIT and Harvard, an investigator at the McGovern Institute for Brain Research, James and Patricia Poitras Professor in Neuroscience at MIT, and associate professor in the departments of Brain and Cognitive Sciences and Biological Engineering at MIT. Zhang and his team were first to develop and demonstrate successful methods for using an engineered CRISPR-Cas9 system to edit genomes in living mouse and human cells and have turned CRISPR technology into a practical and shareable collection of tools for robust gene editing and epigenomic manipulation. CRISPR has been harnessed by Zhang and his team as a groundbreaking gene-editing tool that is simple and versatile to use. A key tenet of Zhang’s is to encourage further development and research through open sharing of tools and scientific collaboration. Zhang believes that wide use of CRISPR-based tools will further our understanding of biology, allowing scientists to identify genetic differences that contribute to diseases and, eventually, provide the basis for new therapeutic techniques. “We are thrilled to honor Zhang, who we commend for his advancements in genetics, and more importantly, his willingness to share his discoveries to advance the work of others around the world,” said Dorothy Lemelson, chair of The Lemelson Foundation, in a press release. “Zhang’s work is inspiring a new generation of inventors to tackle the biggest problems of our time.” Press release

Lonza has introduced the CytoSMART 2 System, an updated version of Lonza’s popular CytoSMART System for live cell imaging. The CytoSMART 2 Device features an advanced optical system and more powerful camera unit, which enables researchers to capture higher-resolution images of their cell cultures. Images taken can be digitally enlarged two-fold to display more cellular detail for enhanced monitoring of cell cultures, migration assays and differentiation experiments. Lonza’s CytoSMART 2 System is easy to set up and can take time-lapse recordings without having to remove cultures from the incubator. Since fluctuations in the surrounding environment can affect cellular behavior, capturing images from inside the incubator with the CytoSMART 2 Device allows the cells to be exposed to constant conditions throughout the duration of an experiment. Press release

AYOXXA announced the introduction of its advanced low-volume beads-on-a-chip multiplex protein analysis system. The LUNARISTM system can be readily integrated into any laboratory routine and is optimized to provide easy-to-use, standardized workflow from sample to result. The LUNARISTM system combines the advantages of a bead-based multiplexing approach and the reliability and scalability of a plate-based format with the simplicity of image-based analysis. The system is comprised of a dedicated reader, automated analysis software, and a growing portfolio of LUNARIS multiplex protein assay kits for the detection and quantification of soluble inflammation and immune-response markers. Based on an innovative plate design, antibody-coated beads are pre-deposited in spatially separated micro-cavities on the planar LUNARISTM BioChip. This variable bead-array format allows straightforward assay development, flexible workflow and permits sample archiving for remote analysis, decoupling experimental execution from readout. This allows for batch execution and supports readout at AYOXXA´s own and other qualified service labs, better matching the design and execution process of typical translational studies. Press release

Cofactor Genomics announced $18M in financing led by Menlo Ventures with major participation from existing investor Data Collective (DCVC) and new investor Ascension Ventures, and participation from existing and new investors iSelect, Y Combinator, Wilson Sonsini Goodrich & Rosati, and Stanford. The company welcomes Mark Siegel (Menlo Ventures), Matt Ocko (DCVC), and John Kuelper (Ascension Ventures) to its board of directors. “This financing—which includes leading investors who have grown hugely successful companies spanning the data science, biotech, and healthcare verticals—is enormous validation of the platform that we’ve built and reflects excitement for Cofactor’s next phase of growth where we intend to package this expertise in discrete applications that can be easily adopted by research labs and clinical practices throughout the nation” Jarret Glasscock, CEO of Cofactor, said in a press release. The investment comes on the heels of Cofactor securing CAP/CLIA accreditation of its platform in order to process clinical-grade formalin-fixed paraffin embedded (FFPE) patient samples, as well as the validation and launch of two initial products: Pinnacle and Paragon. Pinnacle examines nearly 600 RNA biomarkers known to be associated with response to targeted therapeutics, while Paragon is an RNA-based immunophenotyping assay with broad applications to the field of Immuno-Oncology and beyond. Mark Siegel, Managing Director of Menlo Ventures, commented; “RNA is the unwritten chapter in the book of personalized oncology care. We at Menlo are happy to be supporting the growth of Cofactor and their team with decades of genomics experience as they leverage their powerful technology to write this new chapter.” Press release

Researchers at Philip Morris International (PMI) have successfully connected human tissues from the lung and liver in a novel multi-organ-on-a-chip (MOC) in vitro model for toxicity testing. The lung-liver MOC has the potential to reduce the necessity for animal testing in the toxicological assessment of airborne toxins, facilitate the discovery of important mechanisms underlying diseases, and further the development of safer and more effective therapeutics. Details of the lung-liver MOC have been presented at the recent World Congress on Alternatives and Animal Use in the Life Sciences in Seattle, Washington, USA. The growth of human tissue in two-dimensional models is now frequently replaced with three-dimensional (3D) modelling, which more accurately represents human biology. Microengineering now also enables the incorporation of small devices into 3D models to reproduce the complex microenvironments of specific organs. These are often referred to as organs-on-chips (OoCs). However, OoCs can only represent a single organ, and therefore cannot be used to study the many organ-to-organ interactions observed in the human body. The lung-liver MOC aims to address this by creating an accurate model of the lung and liver combined. “Adding relevant liver tissues to in vitro models of the lung is essential for the thorough toxicological assessment of airborne compounds,” said David Bovard, Post-Doctoral Fellow, Systems Toxicology, PMI, in a press release. “While these compounds are absorbed through the lung, the true toxicity of some will only be realized following their metabolization by the liver. Combining lung and liver tissues effectively is very challenging, and we are delighted to have reached this important milestone. We can now begin to envisage an in vitro toxicity testing strategy that accurately represents the complexity of the human body and the interplay between organs, without the need for animal testing.” Press release

Gecko Biomedical (“Gecko”) announced that it has received CE Mark approval for its SETALUM Sealant, allowing the company to market its technology in Europe. The SETALUM Sealant is a biocompatible, bioresorbable and on-demand activated sealant usable in wet and dynamic environments as an add-on to sutures during vascular surgery. The polymer is applied to tissue in-situ and activated using a proprietary light activation pen. The technology at the foundation of the SETALUM Sealant was developed at The Massachusetts Institute of Technology, Harvard Medical School, and Brigham and Women’s Hospital. SETALUM Sealant is the most recent successful example of bio-inspired technology in medicine, and is based on the adhesive mechanisms found in nature that work in wet and dynamic environments. The grant of the CE Mark for the vascular sealant is the first regulatory validation of the safety and performance of Gecko Biomedical’s scalable and innovative polymer platform. Press release

iXpressGenes (iXG) has been awarded a $1,000,000 Phase II Department of Defense (DoD) Small Business Innovation contract to develop extremophile-derived antibiotics to protect soldiers from biowarfare agents and “superbugs.” Selection was based on achievements during the Phase I project to now continue development and maturation of discovered antibiotic candidates. iXG, a biotechnology company located on the HudsonAlpha Institute for Biotechnology campus, specializes in protein crystallization, microbiome and structure-based drug discovery. iXG has developed a rare environmental DNA library from extremophilic environmental samples, collected from hot springs, thermal vents, and permafrost. Extremophilic organisms are those that thrive in extreme physical or chemical conditions that are hostile to most life on earth. Using next generation sequencing technology and bioinformatics tools, researchers discovered a high prevalence (>60%) of novel organisms and biosynthetic pathway types within environmental DNA samples from extreme cold (permafrost) and hot (hot springs) environments. A high throughput platform, Extremophilic Microbiome Antimicrobial Discovery (EMAD), was created during the Phase I effort. Press release

The Center for Clinical Data Science (CCDS) in Boston received the world’s first purpose-built AI supercomputer called NVIDIA DGX Systems with Volta. Soon, radiologists in the Boston-area will have AI “assistants” to help them quickly and accurately diagnose disease from MRIs, CAT scans, X-rays and more. Article