Sequencing Project for Developmental Differences, New Data Management Tools, Hyperscale Storage, More

May 3, 2021

May 3, 2021 | NIH grant tackles COVID-19 disparities, St. Jude launches historic expansion, Illumina all in on African Pathogen Genomics Initiative, and new platforms and services to ease drug and vaccine development. Plus: new storage from VAST Data, and new solutions for tracking research papers and patents.   

National Institutes of Health is funding $29 million in additional grants for the NIH Community Engagement Alliance (CEAL) Against COVID-19 Disparities. This funding was supported by the American Rescue Plan. The awards will provide $15 million to 11 teams already conducting research and outreach to help strengthen COVID-19 vaccine confidence and access, as well as testing and treatment, in communities of color. An additional $14 million will fund 10 new research teams to extend the reach of COVID-19 community-engaged research and outreach. Press release. 

Illumina, GeneDx (a wholly owned subsidiary of BioReference Laboratories) and The University of Washington are collaborating to study early detection of developmental differences in children. The project, SeqFirst, will provide early access to whole-genome sequencing (WGS) to 100 children suspected of having developmental differences at the point of diagnosis. Scientists anticipate this will lead to earlier, more rapid diagnoses, as well as lowering health care costs and improving subsequent treatment for these children. Illumina will support the study by providing advanced sequencing reagents and GeneDx will perform state-of-the-art diagnostic WGS. Press release

Scientists from Virginia Tech and City of Hope aim to improve therapy for deadly brain cancer with a $3.75M grant from the National Institute of Neurological Disorders and Stroke. They will study how fluid flow affects CAR-T cell therapy on brain cancer. The group believes the complex way fluid flows through glioblastoma tumors holds the key to the therapy’s success. They believe they can use that flow to improve chimeric antigen receptor T cell therapy (CAR-T) and help more patients survive. Press release. 

St. Jude Children’s Research Hospital is launching the largest strategic investment in its nearly 60-year history, committing $11.5 billion during the next six years to accelerate research and treatment globally for children with catastrophic diseases. The Six-Year St. Jude Strategic Plan focuses on the expansion of patient care and clinical and laboratory-based research related to pediatric catastrophic illnesses, including work in cancer, blood disorders, neurological diseases and infectious diseases. The plan calls for an additional 1,400 jobs; the expenditure of $1.9 billion in new construction, renovation and capital needs; and the development of new research areas. Press release.

Illumina has committed $60 million in sequencing capabilities to a global pathogen genomics initiative, in partnership with the Bill & Melinda Gates Foundation and other public and private entities. The initiative expands on the Africa Pathogen Genomics Initiative (Africa PGI) announced in October 2020, and will help create a comprehensive pathogen genomic network around the world, building critical public health capabilities in areas of need. Illumina will donate next-generation sequencing (NGS) platforms, reagents, and training support worth approximately US $60 million over five years. The expanded scope will begin with a focus on South Asia, equipping national public health institutions with better public health tools, bringing us closer to the vision of an early warning system for global pathogens. Press release. 

Paradigm4 unveiled its scalable solution for efficiently working with the Allotrope Data Format (ADF). Addressing the vital economic challenge of uncovering new critical quality attributes (CQAs), Paradigm4’s REVEAL Analytical Development app enables data analysts to bring together chemistry, and manufacturing and controls (CMC) data ranging from viscosity and imaging, to particle size, into a platform that can facilitate fast, retrospective analysis and modelling with minimal compute resources. The app is built on top of Paradigm4’s novel computational database engine, SciDB, which is purpose-built to handle large-scale heterogeneous scientific data. By allowing computation on data within the database itself, the REVEAL app simplifies compliance. REVEAL Analytical Development complements the ADF through incorporation of its features into an array-native scientific database management platform, mitigating the challenges posed by in-memory processing of large datasets stored in files. The app also enables data selection and computation from imported ADF files using Python and R APIs. Press release.

Aigenpulse has rolled out an update to its CytoML Experiment Suite, its automated, end-to-end, machine learning solution specifically aimed at streamlining and automating cytometry analysis at scale and replacing manual gating processes. The latest release of the Suite (v5.2) introduces new unbiased analysis features and has an easy-to-use interface with no need for difficult installation or program scripting. Users can perform automated analyses in an unbiased manner for exploratory use cases, including FlowSOM and Phenograph for algorithm-based clustering, and use powerful dimensionality reduction methods such as tSNE and UMAP to visualize connected data. The batch processing tool enables a range of parameters to be simultaneously explored to assist scientists in finding the best representation of their data. Press release.

DNA Script has announced a partnership with Moderna to develop a prototype for rapid mobile manufacturing of vaccines and therapeutics as part of the Defense Advanced Research Projects Agency's (DARPA) Nucleic Acids On-Demand World-Wide (NOW) Program. The partnership will employ DNA Script's novel enzymatic synthesis platform to quickly generate high-fidelity nucleic acids without the use of hazardous chemical solvents to power Moderna's existing manufacturing technology for the rapid production of messenger RNA therapeutics and vaccines. As part of the agreement, DNA Script will receive up to $5 million in grant funding from DARPA. Press release.

Mission Bio has launched its Pharma Assay Development (PAD) services. The PAD Team will provide customers with early access to services based on the latest new technological innovations, in addition to services on Mission Bio’s existing products to implement Single Cell Multiomics capabilities into discovery, translational and clinical research efforts. Mission Bio has appointed Harsha Kavuri to head up the PAD Team as General Manager, affirming its strategic focus to service the dynamic needs of customers working in areas like hematology and cell and gene therapy. Press release.

BC Platforms (BCP) has announced a new strategic partnership with US-based company TripleBlind to help drive the development of privacy and intellectual property rights (IPR) preserving “federated AI” for its Global Data Partner Network. The partnership will enhance BCP’s contribution to the Finnish-led PRIVASA (Privacy Preserving AI for Synthetic and Anonymous Health Data) consortium. The two-year PRIVASA project aims to promote access to, and sharing of, anonymized health data to accelerate product development by Finnish health technology companies operating in international markets. BCP will be contributing federated AI learning approaches to train machine learning algorithms without the need to exchange actual data. This method will enable BCP to address data governance and privacy requirements, as individual-level data never needs to leave its institution of origin. BCP’s partnership with TripleBlind will further improve this federated AI concept by ensuring IPR protection, encrypting analyses and results using its proprietary cryptographic technology. Press release.

BCP has also announced the launch of the new Cohort Discovery (CD) search functionality on the Health Data Research (HDR UK) Innovation Gateway (The Gateway) – powered by BC|RQUEST technology in partnership with HDR UK. The CD functionality enables global researchers to discover, assess, and request access to datasets by searching for specific cohorts or demographic groups across multiple datasets. CD facilitates access to data in a fast, secure, de-identified and ethical way through Trusted Research Environments: safe and secure locations from which researchers can access and analyze data, without needing to move the data around. The function will be rolled out across all the 640 datasets on The Gateway, with COVID datasets being prioritized initially. Press release.

DeepDyve has launched DeepDyve Digital Library, the industry’s first fully integrated platform aimed at helping research organizations discover, access, and manage research papers. The Digital Library is a one-stop platform designed for small to medium-sized teams and organizations needing easy and affordable solutions for reading and organizing scientific papers without the need for an IT staff. DeepDyve delivers copyright-compliant content in partnership with the world’s leading academic publishers, including Springer Nature, Wiley-Blackwell, Oxford University Press, New England Journal of Medicine and many more. The Digital Library provides a fully integrated suite of workflow and collaboration tools to make research easy and affordable for an entire organization. The platform allows teams to search, organize, and access the full text of five million open access articles and 20 million premium rentable papers from over 20,000 journals. In addition, researchers are able to purchase and download any paper from its comprehensive collection of 100 million citations available in the reference database. The Digital Library supports automatic de-duplication of purchases, so if one team member has already bought a paper, it will be available to all plan members, avoiding repeat charges and reducing waste. Press release.

QIAGEN has launched QIAseq DIRECT SARS-CoV-2 Kit, a viral genome enrichment and library preparation solution that significantly reduces library turnaround times and plastics use compared with ARTIC project protocols, the primer-based approaches for next-generation sequencing that are considered the gold standard in NGS-based characterization of SARS-CoV-2 genomes. QIAseq DIRECT SARS-CoV-2 supports sample multiplexing with up to 768 Dual Molecular Indices—unique markers tagged to molecules in a sample to eliminate errors from downstream analysis—in a library preparation workflow from extracted viral RNA that reduces turnaround time to as little as four hours. This also increases the number of samples per sequencer to over 6,000 samples on the highest-throughput instruments. The kit also cuts plastics usage by 50%, drastically reduces hands-on time, requires no fragmentation or ligation reactions and can be readily automated with robotic liquid handlers. The viral enrichment approach delivers superior uniformity of coverage across the SARS-CoV-2 genome as well as deeper sequencing performance compared with the most widely used amplicon-based options. Press release.

Digitate has announced the availability of ignio AIOps for Azure in the Microsoft Azure Marketplace. ignio AIOps for Azure is an AI-driven software that consolidates and builds the context of an Azure subscription, starting from all its resources and their historical capacity and performance metrices, and leverages AI to mine intelligence and insights, leading to recommendations that will ensure smooth operations. Further, ignio AIOps for Azure judiciously combines the context thus developed along with automated actions to deliver intelligent Azure operations. It acts as an intelligent virtual expert that detects and assesses the deviation in system behavior, triages and resolves the incidents, predicts the future state and prescribes actions proactively to ensure simple and smooth Azure Cloud operations. Press release.

VAST Data has launched Gemini, the enterprise storage appliance model reinvented for the age of hyperscale. This offering, which disaggregates the business of hardware and software, allows VAST to sell managed software on hardware that customers can buy at cost as integrated appliances that ship directly from the manufacturer. With Gemini, VAST has solved many of the greatest hurdles associated with pure software and pure appliance models enabling customers to buy like hyperscale cloud operators without the heavy lifting commonly associated with building always-on, massively scalable clouds of low-cost flash infrastructure. The new offering provides customers all of the benefits of a software-defined business model in terms of flexibility and cost advantage, but at the same time preserves the simple and multigenerational cluster appliance model that customers have come to love from VAST Data. This event marks the company’s complete transition into a software business and is intended to align VAST’s business objectives precisely with the needs and objectives of its customers. Gemini is a multi-faceted commercial offering that builds on VAST’s Universal Storage concept which industry analyst firm IDC has declared as “the storage architecture of the future.” Press release. 

10x Genomics has launched its Chromium Single Cell Gene Expression Low Throughput (LT) Kit, a new offering designed to put the power of single cell analysis within the reach of more scientists than ever before. The new LT Kit reduces the startup cost for a single experiment, enabling a broader base of scientists to conduct single cell analysis. In addition, scientists now have the ability to use the 10x Genomics Cloud to perform a standard analysis of every sample at no additional cost, accelerating findings in a cost-effective manner. 10x Genomics recently started shipping its Single Cell Gene Expression with CellPlex, making single cell analysis on its standard kits more affordable. The CellPlex solution allows the multiplexing of up to 96 samples in a single chip, giving scientists the ability to drive larger experiments as they scale up from the LT Kit. CellPlex will also integrate into the company’s high throughput kits to be released with Chromium X. Press release.

Oxford Nanopore and Circulomics have launched kits to enable routine sequencing of ultra-long fragments of DNA. The Ultra-Long DNA Sequencing Kit, which has enabled read lengths of up to 4.2 Mb and maximizes the quantity of ultra-long fragments, is now available. In combination with Circulomics Nanobind Kits, the Oxford Nanopore Ultra-Long DNA Sequencing Kit is designed to maximize the quantity of ultra-long reads and has enabled the continuous sequencing of single DNA fragments of up to 3+ Mb externally and 4+ Mb internally. It’s possible for users to achieve more than 100 reads over 1 Mb per PromethION flow cell run using this approach. The ability to sequence complete ultra-long fragments of DNA with nanopore sequencing provides a totally novel approach to assembly coupled with more comprehensive biological data. Users are able to span large structural variants and highly repetitive regions, whilst gaining information about modifications. Press release. 

Qlucore has released Omics Explorer (QOE) version 3.7, an extensive upgrade adding features in many different areas to strengthen visual analysis support even further. Key features of the new version are ChIP-seq and ATAC-seq analysis support, a new Biomarker workbench coupled with an upgraded statistical framework and significant enhancements to the Genome browser. The Genome browser has new visualization functions plus support for ChIP-seq, ATAC-seq and gene fusions. The Biomarker workbench is optimized for experiments and studies in the areas of drug development and biomarker discovery. Press release. 

NanoString Technologies announced the company has been awarded a Technology Access Program grant with Illumina Accelerator startup, Doloromics, focused on gaining a deeper understanding of chronic pain diseases by spatially characterizing the dorsal root ganglion (DRG). NanoString will partner with at least one startup from each global Illumina Accelerator funding cycle for a GeoMx Digital Spatial Profiler (DSP) Technology Access Program grant. The founders of Doloromics have significant experience in studying chronic pain in human peripheral nerves and have published extensively on the inadequacy of current mouse systems as well as biological differences in pain transmission and receptor expression that exist between men and women. Spatial profiling of the DRG from patient tissues with the Whole Transcriptome Atlas may be highly informative as it would allow a thorough understanding of the transcriptional expression within the DRG and could support discovery and validation of new targets. GeoMx DSP is uniquely positioned to advance this research because it is designed to read-out on Illumina sequencers, leveraging state-of-the-art next generation sequencing and the novel biological insights provided by innovative spatial profiling technology. Press release.

LifeArc and the Medical Research Council (MRC), with support from the Biotechnology and Biological Sciences Research Council (BBSRC), today announce three major investments totaling £18m to create a national network of cutting-edge “Gene Therapy Innovation Hubs”. The £18m funding will support the creation of three dedicated facilities to advance the clinical development of new genetic treatments, with potential to transform care for millions of patients including those with rare and life-threatening genetic diseases. Hubs will be at King’s College London, NHS Blood and Transplant in Bristol and the University of Sheffield. These Innovation Hubs will enable academic-led clinical trials of novel gene therapies to take place, helping the most innovative research to reach patients. Gene therapies offer huge potential as treatments for a wide range of conditions and the UK has a world-class genetics research base – however, to date, academics have found it difficult to get access to the clinical materials, facilities and expertise required to progress gene therapy research into clinical trials. The Hubs will unlock development pathways for these new treatments by offering access to GMP (good manufacturing practice) facilities for clinical trial materials, alongside essential translational support and regulatory advice. The Hubs will operate as a coordinated network, sharing technical skills and resources to enable innovative gene therapy research. Press release.

Elsevier and LexisNexis Legal & Professional are collaborating to strengthen the existing patent coverage in Reaxys, its information solution for chemistry R&D. This integration gives companies and researchers access to the LexisNexis Intellectual Property patent content that powers LexisNexis PatentSight (Patent Analytics) and LexisNexis TotalPatent One (Patent Search) in their existing workflow. Relevant patents for pharma and chemical R&D will be retrieved from 105 patent offices, 141m patent documents, and 56 full-text authorities. The content expansion in Reaxys further cements its position as a comprehensive cheminformatics solution by ensuring companies and researchers do not miss key competitive intelligence insights. Press release.

Integrated DNA Technologies (IDT) has acquired Swift Biosciences, a pioneer in the development of Next-Generation Sequencing (NGS) library preparation genomics kits for academic, translational, and clinical research. IDT is a leader in developing and manufacturing nucleic acid products for academic and commercial research, agriculture, medical diagnostics, pharmaceutical development, and synthetic biology. Swift develops and commercializes NGS Library Prep Kits that maximize data output, provide comprehensive coverage, and reduce sequencing costs. Swift associates and products will transition into IDT while continuing to operate from its existing facilities in Ann Arbor, Michigan. Financial terms of the transaction were not disclosed. Press release. 

Involta has launched its CloudOps Workshop, a powerful consulting tool that empowers customers to more easily design the building blocks of a durable cloud operating model. Involta’s CloudOps Workshop is a consulting engagement that enables customers to leverage Involta’s superior cloud expertise to assess their current state of business and provide critical guidance for navigating potential use cases and understanding opportunities for evolution. As a result, businesses can enjoy more successful cloud preparation and operation in support of their applications, producing a significant increase in cost efficiency, reliability and security. Included in Involta’s CloudOps Workshop offerings are cloud governance, patching, image management, CMDB (Configuration Management Database) integration, operational monitoring, cloud connectivity, roles and responsibilities and infrastructure automation. Additionally, Involta’s cloud specialists deliver valuable CloudOps insights to arm the customer with the knowledge and ability to continue their cloud journey with internal implementation or by leveraging Involta’s managed services offerings. Press release. 

PerkinElmer has launched two solutions to identify SARS-CoV-2 variants. Upon detecting a positive case using a first-tier diagnostic assay, labs can now use second-tier assays like the new PerkinElmer PKamp VariantDetect (RT-PCR) and NEXTFLEX Variant-Seq (NGS) kits to provide further information about mutations in the sample. Both kits are currently intended for research use only. Press release.

PerkinElmer has also completed its acquisition of Oxford Immunotec Global PLC, the second largest company in the latent tuberculosis (TB) market. By bringing Oxford’s expertise and technologies into the PerkinElmer Diagnostics portfolio—including the Oxford T-SPOT.TB test—the combined team is helping to combat two of the most highly infectious disease causes of death worldwide: tuberculosis and COVID-19. Press release.