The Jackson Laboratory, Benchling, Genomenon, And More: News From January 2020

January 30, 2020

January 30, 2020 | January featured exciting new, products, and partnerships from around the bio-IT community from innovating companies, organizations, and universities, including the Jackson Laboratory, Benchling, Genomenon, and more.

With the goal of identifying advanced treatment approaches for children with genetic orthopedic conditions, Shriners Hospitals for Children and The Jackson Laboratory (JAX) have entered into a research affiliation agreement. The agreement is part of Shriners Hospitals for Children’s new Genomics Institute. Based at its headquarters in Tampa, Florida, the Genomics Institute is focused on finding the genetic causes of orthopedic conditions and disabilities such as clubfoot, scoliosis, and osteogenesis imperfecta, and easing – and, in some cases, perhaps even ending – the potential for a lifetime of medical care and personal struggle. As part of this agreement, Shriners Hospitals will perform next-generation sequencing on DNA samples obtained from families at its 22 hospitals and outpatient locations in North America and from its international network of outreach clinics. Investigators at JAX will provide expertise on genomic data analysis, specialized knowledge bases and algorithms, as well as the microbiome. JAX will also aim to develop mouse models carrying the same genetic variations as patients with these rare pediatric diseases, providing impactful research platforms for discovering new treatments and important clinical information. Press release

The Mark Foundation for Cancer Research announced the creation of The Mark Foundation Center for Advanced Genomics and Imaging at the Johns Hopkins University (JHU), which will receive initial funding of $5 million over 2 years. Bringing together the tools of astronomy image analysis, pathology, computer science, cancer genomics, and immunogenomics to solve problems in oncology, the new center will find innovative solutions that can expand the number of cancer patients who benefit from immunotherapy. Scientists from The Mark Foundation will collaborate with JHU researchers as part of a joint steering committee that will review scientific progress and facilitate the success of the center. “It takes a village of diverse disciplines and areas of expertise to confront the vast challenges presented by cancer, and the work of this center is the perfect embodiment of this reality,” said Michele Cleary, CEO of The Mark Foundation, in a press release. “One focus of the center is especially imaginative, as it involves developing a new platform that takes a model used in astronomical nighttime sky analysis and turns it into one that can be used to analyze cancer tumors.” The Mark Foundation Center for Advanced Genomics and Imaging will be led by Drew Pardoll, Director of the Bloomberg-Kimmel Institute for Cancer Immunotherapy and co-Director of the Cancer Immunology Program at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, together with Janis Taube, Professor of Dermatology and Pathology and Director of the Division of Dermatopathology and co-Director of the Tumor Microenvironment Laboratory of the Bloomberg-Kimmel Institute for Cancer Immunotherapy. Press release

Benchling announced the launch of Benchling for Lab Automation, a new solution to help life sciences companies maximize lab automation investments. The offering provides a centralized environment for researchers to design, document and run up to 10,000 samples in a single experiment and digitally track the results of each sample. By connecting liquid handlers, analytical instruments, and other equipment to Benchling’s cloud platform, researchers can analyze experimental results and processes at scale, achieving deep biointelligence and unlocking new insights to accelerate breakthroughs. “We built Benchling for Lab Automation to help scientists create the laboratory of tomorrow with the equipment of today. Now, researchers can do more experiments in a shorter amount of time, saving ten hours per experimental run and unlocking the full potential of their lab automation investments,” Saji Wickramasekara, CEO and Co-Founder of Benchling, said in a press release. “By uniting hardware and software, we’re helping the modern scientist harness the power of biointelligence – complete traceability for every experimental sample, result, and process – to uncover deeper insights and achieve breakthroughs faster than ever before.” Life science companies are investing heavily in lab automation to enable high-throughput workflows, but existing lab automation software is rigid and can’t adapt to meet the highly iterative, dynamic needs of modern life science. This creates bottlenecks in data aggregation and prevents sample traceability. Benchling for Lab Automation addresses the limitations of current lab automation solutions by giving scientists a flexible, seamless interface between the Benchling platform and lab robotics, unlocking biointelligence, improving scientist productivity, and keeping pace with evolving R&D processes. Press release

Genomenon announced that over 175,000 recently documented genetic variants (DNA mutations) have been added to the Mastermind Genomic Search Engine in the 4th quarter of 2019, for a cumulative total of more than 5.9 million genetic variants. This number reflects the rapidly accelerating pace of genomic discovery. “Mastermind automatically reads the titles and abstracts of every scientific medical paper published, over 30 million!” Genomenon wrote in 2019 for their Best of Show award-winning entry. “The full text of papers with genomic information is then indexed to develop the most comprehensive view of the genomic landscape. To date, Mastermind has indexed the text of over 6.2 million genetic publications and covers over 4.1 million variants.” Press release

Beiersdorf and Insilico Medicine announced that they are entering a collaboration to jointly discover novel, safe bioactive ingredients for a specific skin indication at an unparalleled pace, that will serve as the basis for developing appropriate skincare products. “As part of our Open Innovation culture, we are always looking for new technologies and partners with strengths that complement ours. We are delighted to now be working with Insilico Medicine as a veritable expert when it comes to artificial intelligence. We are able to evaluate new active ingredients significantly more quickly and more efficiently by simulating biological effects in silico. This enables us to cater even better to the consumers’ as yet unmet skincare needs,” May Shana’a, Senior Corporate Vice President, Research and Development, at Beiersdorf, said in a press release. Press release

MOgene announced it has selected Fluidigm’s Advanta assays and microfluidics-based Juno system to expand its next-generation sequencing (NGS) services portfolio. Using Fluidigm’s recently released Advanta RNA-Seq NGS Library Prep Kit as well as the Advanta RNA Fusions and Solid Tumor NGS Library Prep Assays, MOgene will increase the scale of its RNA sequencing services offering and introduce new high-value NGS assays for detection of RNA fusions and genetic mutations in cancer. “Our mission at MOgene is to provide best-in-class next-generation sequencing services to research, pharma, biotech and government institutions,” said Craig Morley, CEO of MOgene. “Harnessing decades of experience providing comprehensive, highly customized and data-driven genomic solutions, we take a consultative approach to deliver on basic, translational and clinical research project goals for our clients.” The Advanta assays, when used with Juno microfluidic systems, provide high-quality NGS results with as little as 10 nanograms of total RNA input. Additionally, they enable faster turnaround times, leading to a more efficient NGS library preparation process. Press release

LexaGene announced it has expanded its number of validated tests for antibiotic resistance and has completed testing different superbug isolates provided by the Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA) Antibiotic Resistance (AR) Isolate Bank. In a press release, Jack Regan, LexaGene’s CEO and Founder stated, “Antibiotic resistance is a big problem.  People are dying every day due to the lack of high-quality, rapid diagnostics at the point of care that can both identify the cause of an infection and determine whether it is resistant to common antibiotics. To address this shortcoming, LexaGene has developed a fully automated, molecular-based diagnostic that can provide these answers in an hour – rather than the typical 3-day turnaround time for a sample shipped to a reference laboratory. To evaluate our newly developed assays, we tested them against the most dangerous antibiotic-resistant bugs we could get our hands on and have been thrilled with the data – as we successfully detected 100% of the targeted genetic sequences.” Press release

Scientists from the National University of Singapore (NUS) are working as members of an international team to produce a first-of-its-kind ultra-high resolution 3D comprehensive map of the human brain’s neural network. The effort involves teams from Singapore, Japan, South Korea and Taiwan. Australia and China have also expressed interest to be part of the project. Initiated at NUS, the Singapore team, comprising researchers from the local scientific community, will use synchrotrons—extremely powerful x-ray sources—to trace the complex and intricate networks that cover the brain. Associate Professor Low Chian Ming from the NUS Yong Loo Lin School of Medicine’s Department of Pharmacology and Department of Anaesthesia is a co-founding member of this international consortium, and leads the team from Singapore. The team will work to construct the map of the human brain and coordinate the data management for this endeavor. The work will link the synchrotron facilities in the Asia Pacific region under a collaboration called Synchrotron for Neuroscience - Asia Pacific Strategic Enterprise (SYNAPSE), which is expected to involve more than 1,000 researchers. Launched at the NUS Shaw Foundation Alumni House Auditorium, the founding members of the initiative signed a Memorandum of Understanding (MOU) committing to work together to complete their brain map project by 2024. Press release

A new research center which aims to revolutionize medical research and drug development using microengineered Organs-on-Chips has opened at Queen Mary University of London. Organs-on-Chips models have seen significant advancement recently, Bio-IT World reported. Theses models contain tiny hollow channels lined by living human cells that recreate the microenvironment experienced by cells within the human body. As miniaturized living systems with human cells, Organs-on-Chips can predict human response with greater precision and detail than today's cell culture or animal-based testing, and can be used in a laboratory to test drugs and understand how the body works. The new Queen Mary - Emulate Organs-on-Chips Centre will use Organs-on-Chips to recreate the human biology of different organs by incorporating the appropriate types of cells and tissues cultured under continuous fluid flow and mechanical forces, such as cyclic breathing and peristalsis, which create the microenvironment experience by cells in the body. Queen Mary has established the Centre in partnership with Emulate, a U.S.-based company that is on the leading-edge with a portfolio of Organs-on-Chips products and lab-ready systems for use by researchers worldwide. The Centre will provide access to Emulate's Organs-on-Chips technology to enable researchers to develop organ models of their design for use in a wide variety of experiments and drug development programs. It will also provide opportunities for collaboration with Emulate and support for commercialization and translational impact. Press release

Personal Genome Diagnostics (PGDx) is partnering with Eisai to develop a comprehensive liquid biopsy biomarker discovery solution for oncology, to be used by Eisai researchers at their Tsukuba Research Laboratory. The goal of this collaboration is to create a kitted NGS product that will enable researchers and biopharma companies to conduct biomarker discovery work using non-invasive blood samples collected from patients in clinical trials. By delivering comprehensive genomic insights from the samples, researchers may generate clinical data repositories to gain deep insights into the molecular evolution of tumors throughout the treatment course without the need for invasive, and resource-intensive, serial tissue biopsies. Using DNA isolated from patient blood samples, the automated NGS solution will detect somatic alterations across more than 500 genes in cancer and drug-resistance related pathways. The profiling assay will report single nucleotide variants (SNVs), insertion/deletions, copy number alterations, rearrangements, and genomic signatures, including microsatellite instability (MSI) and tumor mutation burden. A key advantage of this solution will be the ability to provide comprehensive genomic profiling data in clinical trials where tissue is not available, and it will enable investigators to evaluate drug response dynamics and emerging mechanisms of treatment resistance. “We are always striving to evolve and expand our liquid biopsy capabilities and believe that many innovations and insights will be discovered by interrogating blood samples using the new solution we are developing with Eisai,” John Simmons, Vice President of Translational Medicine, PGDx, said in a press release. “Our goal is to create the tools that will provide critical oncology insights that researchers and biopharma companies need to speed the process for developing new therapies for cancer patients.” Press release