CRISPR Patents, Oxford Nanopore, Komodo Dragons, And More: News From July 2019

July 31, 2019

July 31, 2019 | July featured news, products, and partnerships from around the bio-IT community including CRISPR patents, Oxford Nanopore, the first high-resolution sequence of the Komodo dragon, and more.

The US Patent and Trademark Office awarded two new patents to the University of California (UC), University of Vienna, and Dr. Emmanuelle Charpentier covering methods of the CRISPR-Cas9 gene-editing technology. US Patent 10,358,658 covers CRISPR methods for targeting and binding, modifying or cleaving a target DNA using single-molecule guide RNAs. US Patent 10,358,659 covers CRISPR methods for targeting and binding, modifying or cleaving a target DNA with a Cas9 protein that contains a mutation in a RuvC and/or HNH domain and a single-molecule guide RNA. These two patents join numerous related CRISPR-Cas9 patents that have issued to UC in prior weeks. Over the next several weeks, five additional applications are expected to issue as patents, which will grow UC's portfolio to 15 total patents. The portfolio covers various compositions and methods that allow for targeting and editing genes in any setting, including within plant, animal, and human cells, as well as modulating transcription. Additional CRISPR-Cas9 patents in this team's portfolio include 10,000,772; 10,113,167; 10,227,611; 10,266,850; 10,301,651; 10,308,961; 10,337,029; and 10,351,878. These patents remain unchallenged and are not a part of the PTAB's recent interference declaration between 10 UC patent applications and multiple previously issued Broad Institute patents and one application, which jeopardizes essentially all of the Broad's CRISPR patents involving eukaryotic cells. Press release

Oxford Nanopore has started high-tech, automated manufacturing processes at its new factory in Oxford, UK. The MinION building is a bespoke, state-of-the-art, high-tech manufacturing facility that brings new, highly automated production processes to the manufacturing of consumable flow cells for Oxford Nanopore’s novel, real-time DNA/RNA sequencing devices.  Full, end-to-end production will be phased in over the coming months. The factory, located on the Harwell Campus in Oxford, will support a significantly increased production capability, exceeding 1 million flow cells/year in 4-5 years. Inside the 34,500 sq. ft. MinION building, Oxford Nanopore has invested in new high-volume, automated manufacturing processes. This is designed to achieve greater levels of production control and product homogeneity, at a scale that will ensure the company can meet future, increased demand. The factory will manufacture consumable flow cells for the MinION, GridION, PromethION and Flongle devices, as well as for future novel devices such as SmidgION (a smartphone sequencer) and Plongle ("plate Flongle", for high sample number, small/rapid tests). The factory is also designed to scale up manufacturing of current and future preparation kits that accompany the consumable flow cells, as well as new lines such as Ubik – a rugged, power-free sample extraction and preparation device. Press release

Janssen announced a collaboration with the UC Berkeley and the University of California, San Francisco (UCSF), with the goal of inspiring data-driven approaches to improve health and develop the next generation of leaders in healthcare data sciences. This program will be the first of its kind in the San Francisco Bay Area, which serves as a hub of both tech and biotech industries and is home to two of the world's top universities. The agreement was facilitated by Johnson & Johnson Innovation. "We're at an inflection point where the health, technology and consumer industries are converging in new and potentially life-saving ways," Mathai Mammen, Global Head at Janssen, said in a press release. "This fellowship program aims to bring together data scientists, large biomedical datasets and expertise from both industry and academia to find innovative new ways of improving healthcare and bringing meaningful solutions to people in need." The parties will collaborate to create and establish a data science health innovation fellowship program, run by UCSF and UC Berkeley, working with product and platform teams within Janssen. The program will recruit serial cohorts of up to five outstanding data scientists from industry or academia to conduct innovative research in areas of unmet patient need. Fellows will have access to computer science, engineering, and statistics expertise and technology innovation at UC Berkeley and clinical expertise and data at UCSF, which they will use with other health and biological datasets to safely and respectfully conduct research projects over two years with mentorship from Janssen, UCSF and UC Berkeley. Press release

Rafael Pharmaceuticals has entered into an out-licensing agreement with Ono Pharmaceutical. The exclusive license agreement is for the development and commercialization of CPI-613 (devimistat), Rafael’s first-in-class clinical lead compound, which targets cancer metabolism enzymes, as well as its other related compounds. Under the terms of the agreement, Rafael will receive a one-time upfront payment of approximately $12.9 million and up to an additional approximately $150.3 million if certain development and commercial milestones are achieved. Rafael will also receive low-double digit royalties based on net sales of the products in Japan, South Korea, Taiwan and ASEAN (Association of Southeast Asian Nations) countries. ONO will have exclusive rights to develop and commercialize the Products for all indications in ONO’s territory. Rafael continuously retains all exclusive rights to develop and commercialize the Products outside of ONO’s territory. Press release

A new study from researchers at the Gladstone Institutes, in a close collaboration with scientists at UC San Francisco (UCSF) and Zoo Atlanta, provides the first high-resolution sequence of the Komodo dragon, as well as insight into how it evolved. The study, published in Nature, details how the team studied the DNA of two Komodo dragons from Zoo Atlanta named Slasher and Rinca, whose blood samples were obtained as part of their scheduled annual check-ups. "This project was a great opportunity for us to learn more about Komodo dragons using the newest and best technologies, and then be able to contribute our findings toward the general knowledge of lizard biology," Joszeph R. Mendelson III, a herpetologist and evolutionary vertebrate biologist, and the director of research at Zoo Atlanta, said in an official statement. The study, also released on BioRxiv as a preprint with a data repository, provides an extremely high-quality sequence of the Komodo dragon genome, which can now be used as a reference in efforts to sequence other vertebrate genomes. Full article

GigaScience and River Valley Technologies announced a new partnership to deliver a research publishing process that is extremely rapid, low-cost, and modular. As a pioneer of open data and open science publishing, GigaScience brings editorial expertise in publishing research that includes all components of the research process: data, source code, workflows, and more. River Valley Technologies, with 30 years of expertise in publishing production, delivers an end-to-end publishing solution, including manuscript submission, content management and hosting, using its collaborative online platforms. The collaboration is developing a publishing process that, in addition to providing on-the-fly article production, will create more interactive articles that can be versioned and forked. The collaboration's first product will be the launch of a new scientific research journal, GigaByte, in 2020, which will allow extremely rapid publication of short articles focused on non-complex data sets and rapidly evolving research computational tools and technologies. The articles in this journal will be able to be versioned and forked to allow researchers to add new data and information to an article over time without having to completely rewrite the article. Press release

Certara announced that it has formed a new practice area called Certara Global Health (CGH) to focus its technological expertise on helping to achieve equity in health for all people worldwide. CGH is a new product development innovation practice inspired by Certara's drug development and scientific due diligence work for the Bill & Melinda Gates Foundation. "Certara Global Health will bring together talent, technology, software, systems and processes to accelerate the development of medicines for those that need them most," Craig Rayner, SVP and Co-Lead of CGH, said in a press release. "Working closely with the foundation and other leaders in the global health sector, CGH will focus on creating novel and impactful drug development, regulatory science and patient access approaches that will deliver effective and affordable therapies to populations in need around the world. A triple bottom line practice across the global health product development ecosystem." CGH will leverage Certara's cross-functional, interdisciplinary global scientific staff to create a 'sandbox of innovation.' CGH will employ:

  • New quantitative drug development methodologies, such as model-informed translational medicine, innovative clinical trial designs, human infection models, quantitative systems pharmacology (QSP) and toxicology, and the full range of proven pharmacometrics capabilities (PK/PD, PBPK, etc.) to accelerate the drug development process;
  • Novel regulatory science approaches to create precedents for increasing certainty in decision-making and expediting the regulatory review;
  • New Chemistry, Manufacturing and Control (CMC) talent to tackle the toughest CMC challenges in delivering quality medicine to low-middle income countries;
  • Innovation in accelerating access to medicine for global populations, leveraging new epidemiological models, real-world evidence, pharmacology-to-payer prototyping, early deployment approaches, and tools to support product distribution and access. CGH staff will also use new technologies and modalities to improve health literacy, clinical trial participation, medical adherence behavior, infection surveillance and real-world data collection globally.
  • Apply modeling and simulation in an integrated drug development environment to propel drug discovery and lead optimization. For example, using QSP alongside modern screening approaches to improve hit-to-lead, lead candidate selection, and first-in-human dosing strategy;
  • Support due diligence of assets, stage-gate decisions and portfolio management to identify and triage optimal drugs for select populations;  
  • Develop technologies, software and processes across all areas to codify best practices, increase quality and support/enable best outcomes. Press release

Congenica announced it has renamed its software platform Congenica and expanded its capabilities to include Copy Number Variant (CNV) calling for exome and gene panel sequencing. The latest software version will continue to streamline and enhance genomic clinical interpretation and help to reduce time to diagnosis in healthcare systems globally. As part of the latest release of Congenica, a complete CNV module has been delivered, enabling calling and analysis of CNVs, single-nucleotide variants (SNVs) and Indels in one place, through a simple to implement and streamlined workflow. David Atkins, CEO of Congenica, said in a press release: "Empowering healthcare professionals to make important clinical decisions that transform the lives of patients is at the heart of everything we do at Congenica. That's why we've changed the trade name of our software platform to make it synonymous with our company name and values. We collect a wealth of health information, amounting to trillions of data points, then interpret and understand every detail. Already, a diagnosis that could have taken years, can now happen in a matter of hours, providing patients with quick and accurate answers to previously unanswerable questions. Ultimately, we want to enable disease prediction and empower people to maintain wellness and lead fuller lives." The news coincides with the launch of a new company website and logo, which better reflects Congenica's commitment to enabling genomic medicine and delivering life-changing answers for patients. Press release

Philip Morris International (PMI) is opening the doors on scientific transparency and reproducibility with the creation of an open online platform for sharing data, software, and scientific protocols. Called INTERVALS, the platform has been built to address the current scientific reproducibility crisis and gather in a single place scientific data relating to modified risk tobacco products (MRTPs), also known as Reduced-Risk Products (RRPs). Open to scientists from both academia and industry, and designed to enable third-party collaboration and analysis, INTERVALS follows the FAIR Guiding Principles for data sharing, i.e., data should be Findable, Accessible, Interoperable, and Reusable. Scientists are encouraged to add their own independent research to INTERVALS, thereby contributing to transparency in the field and increasing the visibility of their work. "Across the life-sciences, we see consistently low rates of the reproducibility of scientific research," said Stéphanie Boué, Scientific Data Transparency, PMI, in a press release. "Sharing data in a way that enables reanalysis and reuse is not yet done in a systematic manner, despite the fact that doing so would clearly benefit the scientific community and society in general. This is particularly true where the quality of science may be questioned due to the affiliations of researchers, funding sources, or research topics. Tobacco harm reduction is one such area, and INTERVALS is a crucial resource to ensure full transparency and reproducibility of the scientific research being conducted in the field." INTERVALS includes full, standardized, and extensively annotated datasets from a number of clinical and pre-clinical studies that PMI has conducted as part of the assessment of its MRTPs. These range from large in vivo inhalation studies, to the novel in vitro studies using three-dimensional human tissue cultures, to clinical studies investigating the pharmacokinetics of different nicotine delivery systems. The platform provides detailed information on study protocols and interoperable data files that allow independent reanalysis of key findings, meta-analyses, and efficient data reuse. Alongside raw data, rich metadata are also provided to describe experiments, data production, data processing, and additional relevant information. Each study, protocol, and dataset are assigned a unique DOI, making them easily findable and citable. Press release

Jounce Therapeutics announced an update on its strategic collaboration with Celgene, originally established in July 2016. Under the terms of a new license agreement, Celgene has licensed worldwide rights to JTX-8064, a highly-selective, potential first-in-class antibody that targets the LILRB2 receptor on macrophages. Jounce retains full worldwide rights to its pipeline beyond JTX-8064, including vopratelimab, JTX-4014, and all discovery programs, as Jounce and Celgene have also entered into a mutual agreement to terminate their original strategic collaboration agreement. Under the terms of the new license agreement for JTX-8064, Jounce receives a $50.0 million non-refundable license fee and is eligible to receive from Celgene up to $480 million in development, regulatory and commercial milestone payments, as well as royalties on potential worldwide sales. Celgene will be responsible for all development and commercialization of JTX-8064. Press release


Eagle Genomics announced that its new office at JLABS in Manhattan, New York City, opened its doors on Thursday, July 25. As part of the New York Genome Center community, the new residency space at JLABS places Eagle Genomics at the heart of genomics research in New York, alongside 29 other companies with a focus on biotech and life sciences innovation. Eagle Genomics' e[automateddatascientist] is the platform behind the brains solving the world's life sciences challenges. Enabling rapid improvement of productivity and accelerating time to insight and product delivery, Eagle Genomics' conversational learning software platform has the ability to handle data at a genomic and microbiomic scale. "We are delighted to be expanding our presence in the US and to be joining the innovative community at JLABS," said Anthony Finbow, Chief Executive Officer at Eagle Genomics, in an official statement. "Having a home at the heart of genomics research in New York, closer to many of our customers, will allow us to develop unique connections and a greater understanding of the challenges facing international life sciences researchers, which will help to drive forward the capabilities of our platform."