Oxford Nanopore Targets Diagnostics, New Products from Vizgen, Agilent, More

April 27, 2023 | Ginkgo Bioworks acquires an adeno-associated virus capsid discovery and engineering platform; Oxford Nanopore Technologies and bioMérieux SA have teamed up bring nanopore sequencing to the infectious disease diagnostics market, and the emergency of Large Language Models ops. Plus, new products from Metabolon, Cytiva, Vizgen, Agilent, and more.

Elsevier has launched EmBiology, a research tool that visualizes a comprehensive landscape of biological relationships, empowering researchers to gain a rapid understanding of disease biology and focus on critical evidence. Powered by Elsevier’s Biology Knowledge Graph, EmBiology draws on a broad and deep database of multiple sources, including over 7.2 million full text journal articles from high impact Elsevier and third-party publishers, 34.5 million abstracts and 430,000 clinical trials. EmBiology surfaces relationship information, including directionality and effect, for a wide range of subject areas including expression, biomarkers, and regulation. Elsevier automates data curation with customized Machine Learning (ML) technology that transforms unstructured text into structured information. The resulting knowledge graph includes 1.4 million entities connected by 15.7 million relationships to enable deep insights from a broad range of literature, with more added weekly, so researchers can be confident they are always viewing the latest concepts and terms. Results are displayed in a Sankey diagram that visually facilitates understanding of disease development, progression, and drug responsiveness, whatever the researchers’ level of data skills. Users can also apply filters to narrow down their research question and rapidly confirm their experimental hypotheses for new drug targets, biomarkers, and drug repurposing projects. Press release.

Comet, a platform for managing, visualizing and optimizing models from training runs to production monitoring, today announced a new suite of tools designed to revolutionize the workflow surrounding Large Language Models (LLMs). These tools mark the beginning of a new market category, known as LLMOps. With Comet's MLOps platform and cutting-edge LLMOps tools, organizations can effectively manage their LLMs and enhance their performance in a fraction of the time. The new suite of tools serves three primary functions:

Prompt Playground: Comet’s Prompt Playground allows Prompt Engineers to iterate quickly with different Prompt Templates and understand the impact on different contexts.

Prompt History: This debugging tool keeps track of prompts, responses and chains to track experimentation and decision-making through chain visualization tools.

Prompt Usage Tracker: Now teams can track usage at a project and experiment level to help understand prompt usage at a very granular level. Press release.

Cytiva launches X-platform bioreactors to simplify single-use upstream bioprocessing operations. X-platform bioreactors, initially available in 50 and 200 L sizes, are provided with Figurate automation solution software and can increase process efficiency through ergonomic improvements, production capability, and simplified supply chain operations. The bioreactors also work with the Cytiva Bioreactor Scaler to determine the optimal target settings for scaling without trial and error. As well as mAbs, the X-platform can be used to manufacture cell and gene therapies as well as viral vectors. The majority of mAbs approved by the FDA in 2022 use Cytiva technologies in their manufacture. Press release.

Oxford Nanopore Technologies and bioMérieux SA have teamed up to improve health outcomes globally by exploring selected opportunities to bring nanopore sequencing to the infectious disease diagnostics market. The companies are jointly exploring selected opportunities to advance patient care by providing access to nanopore-based clinical research and in vitro diagnostic (IVD) solutions. Initial areas of collaboration will include a test for determining antibiotic resistance of tuberculosis; an assay to identify pathogens in normally sterile clinical samples; and validating Oxford Nanopore’s sequencing platform with BIOMÉRIEUX EPISEQ CS application for rapid infection outbreak monitoring in patient-care settings. Press release.

Vizgen has launched the MERSCOPE PanCancer Pathways Panel. The PanCancer Pathways Panel features a list of genes targeting canonical signaling pathways of cancer and is constructed using recognized oncology databases including OncoKB, MutSig, the Cancer Genome Atlas, and Hallmarks of Cancer to ensure inclusion of critical cancer genes. The Panel provides a key tool for researchers to study tumor behavior at cellular and subcellular levels across multiple different types of cancers. The PanCancer Pathways Panel features characterization of major oncology signaling pathways including RAS/RTK, PI3K, NOTCH, MYC, Cell Cycle, HIPPO; inclusion of cell type markers to identify healthy and disease states; and compatibility across multiple cancer types. Press release.

New research presented at this year’s European Congress of Clinical Microbiology & Infectious Diseases in Copenhagen, Denmark, by the Barcelona Institute for Global Health, Spain, has identified several gold-based compounds with the potential to treat multidrug-resistant “superbugs.” Gold is known to have antibacterial properties, making gold metalloantibiotics—compounds with a gold ion at their core—an exciting potential new approach. Gold complexes stop enzymes from working, disrupt the function of the bacterial membrane, and damage DNA. Crucially, this multimodal mechanism should prevent antimicrobial resistance from developing. Press release.

Ginkgo Bioworks has announced the acquisition of StrideBio's adeno-associated virus (AAV) capsid discovery and engineering platform assets with a secondary close scheduled upon the transfer of certain additional in-license agreements to Ginkgo. Ginkgo will incorporate these capabilities and IP into its end-to-end AAV gene therapy development platform, allowing Ginkgo's customers to leverage new tools to effectively target many different tissue types, and potentially to improve the safety profile of their future gene therapies. Ginkgo is also receiving StrideBio's existing library of capsids, which includes advanced candidates extensively tested in large animal models, and which are now available for licensing and broader partnership. Additionally, Ginkgo receives the IP and data for StrideBio's lead preclinical asset for Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), a rare genetic heart disease, which Ginkgo plans to sell or outlicense to a commercial partner. The acquisition is focused on the enabling platform IP of StrideBio and does not include any real estate. One employee of StrideBio will transfer to Ginkgo as part of the transaction, joining Ginkgo's mammalian engineering team. Press release.

Agilent Technologies has launched the Agilent SureSelect Cancer CGP Assay designed for somatic variant profiling for a broad range of solid tumor types. The pan-cancer assay design is based on an NGS panel comprising 679 genes globally curated from leading cancer databases and in partnership with key clinical cancer researchers. The assay workflow is efficient, automatable, and flexible, making tumor molecular profiling more accessible to the broad clinical research community. The biomarkers include key classes of somatic variants (SNVs, CNVs, indels, translocations, de novo gene fusions), along with the immuno-oncology biomarkers TMB (tumor mutational burden), and MSI (microsatellite instability) to aid clinical and translational researchers in investigating potential cancer therapeutics. Based on Agilent’s industry-leading library prep and target enrichment chemistry, this high-performance assay provides up-to-date, globally curated biomarker content for comprehensive molecular profiling of solid tumors, supports as low as 10 ng of input, and incorporates walkaway automation to improve lab efficiency and productivity. The workflow incorporates flexible data analysis options, including Alissa Interpret for tertiary analysis and reporting, customer bioinformatics pipelines, and third-party software. Press release.

Metabolon has launched its Bile Acids and Short Chain Fatty Acids Targeted Panels that measure microbially-derived metabolites of biological significance to identify biomarkers for the prediction and early detection of disease areas, including oncology, neurology, liver, diabetes, and gastrointestinal, and gut health. Together, this new suite of panels targets dozens of microbially-derived metabolites across multiple pathways, including bile acid metabolism, sulfur metabolism, nitrogen metabolism, and vitamin B metabolism to advance pre-clinical and clinical research efforts. Metabolon’s Short Chain Fatty Acids Targeted Panel measures nine metabolites and can be used to track biomarkers and enhance biological understanding across preclinical and clinical research. Metabolon’s Bile Acids Targeted Panel measures 21 metabolites and has been designed specifically to advance pre-clinical research identifying bile-acid related biomarkers in digestive, metabolic, and neurological health. Press release.

Absci Corporation and M2GEN have announced a partnership to create new cancer medicines and bring them to market at unprecedented speed. Absci’s generative AI drug creation platform will tap into M2GEN’s clinical and molecular data set, ORIEN AVATAR (AVATAR), to accelerate the creation of therapeutics for a range of malignancies and patient profiles, bringing AI drug creation to the fight against cancer. A key challenge in creating effective cancer treatments is finding specific antigens that can be targeted by immunotherapies. M2GEN’s AVATAR database represents a valuable resource for discovering such antigens. Absci will use its reverse immunology technology to first search the database for antibodies from patients with exceptional immune responses, then computationally re-assemble antigen-antibody pairs as promising starting points for drug development. Press release.

Akili Labs and BGI Genomics agreed upon a technology transfer agreement to provide the Southern region of Africa with clinical-grade sequencing solutions. Improving genetic sequencing services' cost and turnaround time will play a major role in expanding precision medicine-driven healthcare in Africa. The partnership will supply the first truly Africa-based service to meet client needs and process samples locally in full compliance with regional data protection laws. With the continent home to the world's most diverse genomics data, local talent must have the tools and resources to develop localized genomics sequencing capabilities focusing on improving health outcomes. Press release.

The University of Tartu, Estonia, was selected by the European Medicines Agency as one of the data partners of the DARWIN EU network. This is a first step towards the common use of health data in Europe to support public health, medicines regulation, and safety based on evidence from data collected in the routine provision of healthcare. Joining the DARWIN EU data network is a great recognition of the work that has been done and a good opportunity for Estonia to cooperate internationally in the health field. As a result of the accession, Estonia's health data will be integrated into a wider network of real-world data and evidence-based conclusions on the use, safety, and efficacy of medicines will influence patient care across Europe. The inclusion in the DARWIN EU network has also been facilitated by the Estonian Biobank's unique database, which brings together genetic and health data from over 200 000 Estonians. Press release.