NVIDIA’s Synthetic Brain Images, Genomic Research Diversity, New Products – Bio-IT World

August 3, 2021 | Kings College London uses NVIDIA’s Cambridge-1 supercomputer to build synthetic brain images, Singapore researcher detect SARS-CoV-2 in wastewater, American Heart Association Issues statement on genomic research diversity, and biobank acquisitions. Plus new products from 10x Genomics, Paradigm4, Thermo Fisher, SciBite, and more.

Immunai, a New York and Tel Aviv-based biotech company, has acquired the Swiss bioinformatics company Nebion. Nebion’s technology platform and database extend Immunai’s target discovery and drug development capabilities. In addition, Immunai has brought on several key executives, including Board Member Robert Langer, Chief Science Officer Jacques Banchereau, and Chief Business Officer Mark Jacobstein. The company has raised more than $90M in capital to-date to build its drug discovery platform. The Nebion team brings 13 years of experience curating public gene expression datasets and developing intuitive discovery tools that help researchers learn from the transcriptome. Incorporating Nebion’s deeply curated public datasets will expand AMICA, Immunai’s Annotated Multiomic Immunological Cell Atlas, already the largest such database in the world. This data will improve Immunai’s machine learning models, enabling the platform to find drug targets from aggregated public data sets and providing validation data for targets found through other methods. Nebion’s single-cell data integration approaches represent a unique asset for high-resolution target identification and in-silico validation of candidate genes. Immunai’s partners will have access to more robust and granular insights, improving the quality of their drug discovery and development process. Press release.

Researchers from the Antimicrobial Resistance (AMR) Interdisciplinary Research Group (IRG) at Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, alongside collaborators from Biobot Analytics, Nanyang Technological University (NTU) and Massachusetts Institute of Technology (MIT), have successfully developed an innovative, open-source molecular detection method that is able to detect and quantify the B.1.1.7 (Alpha) variant of SARS-CoV-2. The breakthrough paves the way for rapid, inexpensive surveillance of other SARS-CoV-2 variants in wastewater and is published in Ecotoxicology and Public Health. Paper.

The American Heart Association, in the Association’s journal Circulation: Genomic and Precision Medicine, has published a new scientific statement on eliminating barriers to genomic research participation. Genomic studies have produced advances in how to calculate and reduce heart-disease risk, however, the benefits don’t necessarily apply to people from historically marginalized racial and ethnic groups and Indigenous populations. Efforts must be made to eliminate barriers to increase their participation in genomic research, according to the statement. The statement highlights a need to create new, high-quality, human reference genomes representing more diverse groups of people. This means more people from diverse ethnicities and ancestry are needed to participate in medical research. Paper.

King’s College London is using Cambridge-1 to build AI models that are able to generate synthetic brain images by learning from tens of thousands of MRI brain scans taken of patients of various ages and with a variety of diseases. The work will enable scientists to differentiate healthy brains from those that are diseased, giving them a more nuanced understanding of what diseases look like and possibly enabling earlier and more accurate diagnoses. The use of synthetic data has the additional benefit that it can ensure patient privacy since the images were AI generated. This also allows King’s to open the research to the broader U.K. healthcare community. The AI model was developed by King’s and NVIDIA data scientists and engineers. It is one of several projects taking place on Cambridge-1, the U.K.’s most powerful supercomputer, with 80 NVIDIA DGX A100 systems integrating NVIDIA A100 GPUs, BlueField-2 DPUs and NVIDIA HDR InfiniBand networking. King’s College London intends to share its synthetic data model with the greater research and startup community. Press release.

PerkinElmer plans to acquire BioLegend, a leading, global provider of life science antibodies and reagents, for approximately $5.25 billion in a combination of cash and stock, subject to certain adjustments. BioLegend provides its academic and biopharmaceutical customers with best-in-class antibodies and reagents in high-growth areas such as cytometry, proteogenomics, multiplex assays, recombinant proteins, magnetic cell separation and bioprocessing. The transaction will be the largest in PerkinElmer’s history and is expected to close by the end of the 2021 calendar year, subject to regulatory approvals and other customary closing conditions. Privately-held BioLegend has more than 700 employees based primarily in the U.S., with estimated 2022 revenues of $380 million. Upon joining PerkinElmer, BioLegend will expand PerkinElmer’s existing life science franchise into new segments, and its state-of-the-art campus in San Diego, California will become PerkinElmer’s global Center of Excellence (CoE) for research reagent content development for the combined company. The combination is expected to be accretive to PerkinElmer’s existing revenue growth and margin profile and provide an estimated $0.30 of adjusted earnings per share accretion in the first full year following close and greater than $0.50 in the second year following close. The combined company will generate immediate revenue synergies which are expected to reach $100 million annually by the fifth year following the transaction close and no significant cost synergies are planned. Press release.

OKRA.ai has announced a collaboration with the AWS for Health initiative from Amazon Web Services (AWS) to help rapidly up-skill pharmaceutical companies that are looking to harness technology to engage with physicians and lower the costs of commercializing new treatments. AWS for Health is a new initiative featuring services and solutions from AWS and AWS Partners, built specifically for healthcare, biopharma, and genomics. The initiative makes it easier for health customers to select the right tools and partners for their highest-priority workloads across the health communities. Historically, the process of delivering value to physicians and patients has been highly inefficient, based on rigid rules and limited data. However, with the commercial brain built by OKRA.ai, life science companies have been able to connect vast amounts of data and make significant improvements in engaging and communicating with doctors, with agility and scale. The collaboration between OKRA.ai and AWS enables companies to roll out solutions quickly, internationally, and integrated within their existing infrastructure. Press release.

Paradigm4 has launched its REVEAL: Multi-Omics app, allowing researchers to undertake advanced, cross-study analyses and enable quick searches for genes and proteins across all integrated public reference and proprietary datasets. It is built on top of Paradigm4’s SciDB next generation analytics platform, designed for rapid data slicing that enables scientific data modelling, storage, and population-scale computation. The REVEAL: Multi-Omics app provides biopharmaceutical developers the ability to interrogate ‘omics datasets in a rapid, scalable and cost-effective way, giving them broad insights into disease biology, pathology and the ability to test and support hypotheses from multiple studies. It combines a simple load that captures rich metadata, allowing users to construct a select data based on experimental details, pipeline analyses, biosample details and annotation fields. Press release.

Thermo Fisher Scientific has announced a new suite of Ion Torrent Oncomine immune repertoire assays designed to detect potentially malignant clones of T-cells and B-cells, which play a key role in the immune response system. Using proprietary Ion AmpliSeq technology, the new pan-clonality assays target multiple parts of the B- and T-cell immune receptors using a single reaction with ultra-high sensitivity, thereby increasing the probability of malignant clone detection and decreasing the time to results. One of the challenges of current NGS-based immune repertoire analysis has been the need to run multiple secondary tests due to the high test-failure rates of a typical single NGS assay. The new Oncomine pan-clonality assays overcome this challenge by uniquely targeting multiple parts of the receptor to reduce the need for secondary tests and increase the probability that a single assay can detect a potentially malignant clone. Press release

Thermo Fisher Scientific has also released a set of solutions to support adeno-associated viral (AAV) manufacturing. A new media panel, gene kit, and advanced purification resins help reduce manufacturing costs while increasing the viability of gene therapies as treatment options for patients. The Gibco Viral Vector HEK Media Panel covers a broad variety of HEK293 cell types and is not tied to specific transfection reagents or techniques. Its ready-to-use formulations will help AAV developers identify an optimal formulation for their target cell line. The easy-to-use Applied Biosystems resDNASEQ Quantitative Plasmid DNA – Kanamycin Resistance Gene Kit offers an all-in-one solution for precise and rapid measurement of residual plasmid DNA. It includes a highly sensitive multiplex qPCR assay with all reagents and optimized sample prep options for a streamlined workflow that delivers results in under five hours. Finally, Thermo Scientific POROS CaptureSelect AAV affinity purification resins, the newest in a portfolio of viral vector solutions, can significantly improve downstream processing of viral vectors by reducing purification steps and offering scalability to maximize process consistency, efficiency and productivity. Standard purification processes require multiple chromatographic or centrifugation steps, which results in low yields and long process development timelines. Press release.

Summa Equity Fund II has acquired Axion BioSystems, a US life science tools business specializing in the development, production, and marketing of MEA (Microelectrode Arrays) and impedance technologies. Its tools are used to understand cell behavior and function in real-time, for applications including cell and gene therapy (CGT). Founded in 2008 in Atlanta, Georgia, Axion BioSystems originally developed its technology from a graduate research project at Georgia Tech. Now operating across North America, EMEA and APAC, the company has placed more than 500 systems to date and has grown to more than 60 full-time employees. Press release

BioIVT has acquired Tissue Solutions and Valley Biomedical Products & Services. Tissue Solutions is a virtual biobank based in Glasgow, UK, providing medical researchers with high quality human tissue and other biological materials for use in drug discovery, target identification and validation, assay development and validation, and biomarker and companion diagnostic development, primarily supporting research into oncology, blood disorders, and central nervous system, inflammatory, autoimmune, cardiovascular, infectious, and metabolic diseases. All BioIVT’s and Tissue Solutions’ biospecimens are fully consented, collected under institutional review board (IRB) oversight, and provided with the donor’s age, gender, race, disease confirmation, medications, comorbidities, and laboratory results. Press release. Valley Biomedical Products & Services, Inc. located in Winchester, VA, was founded in 1986 and provides specialized biological products and services for the biotechnology, research and development, and clinical diagnostics markets. It operates three business units, focused on developing research products and cell culture sera; manufacturing human and animal source blood products to client specifications; and producing non-biological liquid reagents. BioIVT’s cell and gene therapy clients will be able to use Valley Biomedical’s human AB serum for their drug discovery and development work, and its IVD clients will be able to employ Valley Biomedical’s biological matrices as quality control matrices for their manufacturing processes. Press release.

MMS has been selected by Health Data Research UK (HDR UK)—the UK’s national institute for health data science—as a partner to support the International COVID-19 Data Alliance (ICODA) initiative. During the pilot phase of the project, MMS will provide flexible service levels based on the capability of each contributor to transform their data to ICODA standards. The MMS biometrics and data science team will provide simple guidance to the full range of data services and data mapping as needed. After the pilot completes, MMS data scientists will use learnings to develop tools to further enable contributors such as open-source code and training that academic researchers can use to transform their own data. Additionally, later phases of the engagement may include data mapping and incorporation of real-world health data. Press release.

Cresset, provider of software for molecule discovery and design, has released Flare V5, its comprehensive molecule design platform. This release of Flare incorporates the advanced ligand-based methods validated through years of use in Forge with its established structure-based science. The integration enables chemists to discover novel molecules more efficiently and effectively. Significant enhancements have also been made to increase the speed and automation of Free Energy Perturbation (FEP) calculations, enabling single compounds to be predicted in as little as 30 minutes. New analysis methods have been added to help understand the behavior of water within the target active site. Press release.

Cellares Corporation has announced that Poseida Therapeutics, a clinical-stage biopharmaceutical company using proprietary genetic engineering platform technologies to create cell and gene therapeutics with the capacity to cure, has joined its Early Access Partnership Program (EAPP). Poseida is the third organization to participate in Cellares’ EAPP, following industry partner PACT Pharma and academic partner Fred Hutchinson Cancer Research Center. Cellares initiated the EAPP in 2020 to provide participants with visibility and early access to Cellares’ Cell Shuttle, a next generation cell therapy manufacturing platform enabling closed, automated, and scalable production of cell therapies. By entering the program, Poseida is helping advance the Cell Shuttle’s development, range of use, and applicability via insight and experience with respect to manufacturing workflows for a variety of autologous and allogeneic cell therapies. Poseida currently has two autologous CAR-T product candidates in the clinic, including P-BCMA-101, for patients with relapsed/refractory multiple myeloma, and P-PSMA-101, for patients with metastatic castrate-resistant prostate cancer. The company, which completed an initial public offering in July 2020, also has off-the-shelf versions of both therapies in development, and is exploring TCR-T, anti-c-kit CAR-T, induced pluripotent stem cells (iPSCs), and genetically modified hematopoietic stem cells (HSCs) and NK cells. Immunotherapy pioneer and distinguished oncologist Carl June, M.D., an advisor to Cellares who helped guide the development of the Cell Shuttle, recently joined Poseida’s Immuno-Oncology Scientific Advisory Board. Press release

10x Genomics has launched its Chromium X Series, a next-generation platform for single cell analysis. The new Series comprises the Chromium X, the company’s most powerful instrument yet that delivers routine million cell experiments down to two cents per cell, an industry first. It also includes the Chromium iX, an instrument capable of running experiments for tens of thousands of cells seamlessly upgradable to the X as scientists expand their research projects. The Chromium X Series is compatible with all of the company’s existing low throughput and standard single cell assays and is supported by the 10x Genomics Cloud Analysis offering for data management, analysis and collaboration. The Chromium X series is available now for pre-order and is expected to ship in early August. Press release.

Twist Bioscience Corporation has acquired iGenomX, a company offering multiplex library preparation tools for next-generation sequencing (NGS) workflows. The acquisition is expected to enhance Twist’s capabilities to support multiplex sequencing preparations across multiple markets and to accelerate Twist’s conversion of customers from static microarray platforms to genotyping by sequencing workflows. iGenomX was founded in 2012 to develop and commercialize a high-throughput rapid library preparation that facilitates large sample volume with a simple workflow at enabling price points. The resulting commercial library construction maximizes laboratory capacity for many applications including population genetics, agrigenomics, microbiome and synthetic biology. The total purchase consideration was $35 million, including an initial $500,000 cash payment and $29.5 million in Twist stock, as well as a contingency consideration of $5 million in Twist shares upon completion of certain milestones, no sooner than six months post-close. Press release

Akoya Biosciences announced partnerships with Nikon, CrestOptics, and Andor to enable the development of new spatial biology applications, through the recently announced I2 Network. Akoya is the first spatial biology provider to publicly team up with multiple imaging companies to foster an ecosystem of novel innovations and applications on its platform. Through these strategic relationships, Akoya and its microscopy partners are paving the way for collaboration on new spatial biology applications. Press release.

SciBite has unveiled a Software-as-a-Service (SaaS) version of TERMite, SciBite’s named entity recognition engine, and its CENtree ontology management platform. Researchers can use the new cloud-hosted TERMite and CENtree as part of their digital workplace, offering greater flexibility to enable them to work from multiple locations and settings. SciBite uses Elsevier’s well-established cloud hosting tooling and processes, supported by a dedicated SciBite-Elsevier IT team, who proactively track and maintain this service. The SaaS offering provides continuous monitoring to ensure maximal uptime as well as following the Elsevier 10-step security policy, providing a trusted and secure environment for its hosted solutions. With the new SaaS versions of TERMite and CENtree, customers will see productivity exponentially increase through less procurement time, with lower overall and bundled hardware, maintenance, and administration costs; rapid implementation of products once purchased, with seamless upgrades; and flexible access to a secure environment from multiple locations and settings. Press release

Waters Corporation is expanding its joint work with the Bioprocessing Technology Institute (BTI), a research institute of Singapore’s Agency for Science, Technology and Research (A*STAR). Among their new collaborative projects, Waters and BTI have started work on applying analytics that can rapidly identify and visualize complex molecules within glycomics and metabolomics data to help ensure overall safety, accuracy, and speed of biologics manufacturing. Their goal is to eliminate a major bottleneck in the characterization of biopharmaceuticals, namely the identification and quantitation of complex biomolecules such as released N- and O- glycans and metabolites that influence therapeutic function. As part of the project, Waters will contribute scientific expertise and the use of Waters instruments including the SYNAPT series mass spectrometry system along with a BioAccord LC-MS System. The SYNAPT instrument features ion mobility mass spectrometry technology to provide complete characterization of complex compounds and molecules. The BioAccord system can be used to monitor product quality attributes in real time that can affect efficacy and safety of innovator drugs and biosimilars. Press release

MicroGen Diagnostics has acquired its RTL Genomics partner lab to expand expertise and capacity in non-clinical primary research. For over a decade, RTL Genomics has focused on Next-Generation Sequencing, assay design, library preparation, bioinformatics and biostatistics for research purposes. Its client partners include government agencies and Fortune 500 businesses in all 50 states and 30 countries worldwide. Since 2008, MicroGenDX has been perfecting a mature bioinformatics pipeline for its targeted 16S and ITS NGS clinical testing, which has allowed the company to become the industry leader in highly accurate, rapid-turnaround, low-cost molecular diagnostics. The carefully curated MicroGenDX reference database now contains over 50,000 microbial species. With the addition of RTL Genomics lab resources and experienced staff, MicroGenDX and RTL Genomics aim to replicate the same bioinformatics success with whole genome sequencing. MicroGenDX’s acquisition of RTL Genomics is a reunion. Both labs were originally separate divisions of the same company, Southwest Regional PCR, and both are located in Lubbock, Tex. In 2017, MicroGenDX and RTL Genomics separated into two independent businesses. Press release.