New Illumina Accelerator Start-Ups, Blood Test for Liver Cancer, Several New Collaborations, Software Offerings, More

March 30, 2022

March 30, 2022 | A genomic network model is used to identify aurora kinase inhibitor-sensitive lung tumors, new Illumina Accelerator start-ups are announced, AI algorithms are being used to improve prostate cancer identification and treatment, and a blood-based DNA methylation test can detect liver cancer. 

Jumpcode Genomics launched its newest product, the CRISPRclean Single Cell RNA Boost Kit. The method leverages Jumpcode’s CRISPR-based technology to remove uninformative sequences from libraries, enhancing single cell experiments and enabling scientists to extract greater insights from genomic data. Benefits of the technology include: the ability to double informative transcriptomic reads while enhancing cell type identification; boost usable data by reallocating 50% of sequencing reads from uninformative sequences to transcripts used for differential analysis; and gain a deeper view of expression profiles of individual cells and increase sensitivity to detect rare cell populations. Press release.

Mount Sinai researchers have developed a novel method to identify aggressive early-stage lung cancers and target drugs known as aurora kinase inhibitors to tumors that are especially likely to respond. The findings, published in Nature Communications on March 24, could lead to great advances in treatment for lung adenocarcinoma, the most common type of lung cancer. The Mount Sinai team used a genomics network model to measure tumor invasiveness—distinguishing aggressive tumors from so-called “indolent” ones, which often cannot be told apart via chest CT scan—and identify those that will respond to aurora kinase inhibitors, molecules that can inhibit gene signature regulators. The research team used a genetically engineered mouse model to define the role of aurora kinases in early progression of the disease. They performed molecular profiling of early-stage lung cancer samples with RNA sequencing and identified signature genes associated with tumor invasiveness. Researchers from Sema4 used novel genomic networking approaches to identify key network regulators and therapeutic drugs to demonstrate that targeting the signaling pathway reduces lung cancer spread and improves survival. They identified and tested aurora kinase inhibitors, including AMG900, as an effective treatment to intercept lung cancer progression in the models. Press release.

Path Presenter, a pioneer in the development of digital pathology software, and 4D Path Inc., developer of a pan-cancer diagnostic and precision oncology platform enabling AI-based biomarker typing and prognostication from H&E images, announced a global partnership to distribute 4D Q-plasia OncoReader Breast within PathPresenter’s new Clinical Workflow Platform, ClinPx. 4D Q-plasia OncoReader Breast provides histopathologists with an adjunct technology to potentially improve diagnostic accuracy of breast cancer features (invasiveness, grade, ki-67 status, etc.) solely from digitized histopathology images obtained via biopsies or resections. Through this partnership, pathologists will have the ability to run the 4D Q-Plasia OncoReader Breast directly within the ClinPx whole slide image viewer. Embedding this AI technology within the ClinPx scanner-agnostic digital pathology workflow solution could accelerate the adoption of AI tools within clinical workflows. The primary purpose of integrating 4D’s proprietary algorithms within the ClinPx platform is to potentially improve the throughput, reliability, and quality of consultations provided by physicians. Additionally, users from pharmaceutical organizations could benefit from the enablement of the standardized central pathology review of certain biomarkers within the context of clinical trials leveraging the ClinPx platform. Press release.

Illumina, Inc. has invested in seven new genomics companies to join the fourth global funding cycle of Illumina Accelerator San Francisco Bay Area and Cambridge, UK. During two six-month funding cycles per year, Illumina Accelerator provides selected startups with access to seed investment, access to Illumina sequencing systems and reagents, business guidance, genomics expertise, and fully operational lab space adjacent to Illumina's campuses in Cambridge, UK or the San Francisco Bay Area. The next global funding cycle application deadline is April 1, 2022. The newest companies to join Illumina Accelerator's global portfolio of genomics startups include 4SR Biosciences Inc., a diagnostics and therapeutics company from University of Chicago using proprietary technology to explore new tRNA-based modalities for disease biomarkers and cancer therapeutics; B4X, INC., a therapeutics and diagnostics company from Atlanta, Georgia utilizing multi-omic big data anchored in genomics to deliver life-saving therapeutics and precision diagnostics to individuals suffering from debilitating diseases of the brain; Cache DNA, Inc., a nucleic acid software and storage company from the Massachusetts Institute of Technology that is on a mission to unlock the information stored in nucleic acids through its breakthrough nucleic acid storage and access technology; CRISP-HR Therapeutics, Inc., a therapeutics company from the San Francisco Bay Area that has developed a proprietary, next-generation CRISPR platform to create novel therapeutics for rare diseases; NonExomics, Inc., a proteogenomics and AI-driven therapeutics company from Cambridge, UK and Greater Boston that is developing a proprietary platform to mine novel drug targets from the dark and uncharacterized regions of the genome; Purpose Health, Inc., a mental wellness company from Northern Virginia that supports consumers on their mental wellness journey with data-driven insights into the physiological impact of stress on the microbiome and body; and Rethink Bio Private Limited, a synthetic biology company from India focused on harnessing the potential of microalgae to develop sustainable food solutions to benefit the planet and people. Press release.

Lumea, a global leader in integrated digital pathology solutions, and Verily, an Alphabet precision health company, announced a strategic development partnership. The agreement brings together Verily’s cutting edge artificial intelligence (AI) algorithms with Lumea’s comprehensive end-to-end digital pathology platform with the objective to develop products that can diagnose, prognose, and guide prostate cancer therapy selection with improved objectivity and efficiency. The Verily-Lumea collaboration seeks to utilize Lumea’s digital pathology platform and extensive database of pathology cases to enable Verily to validate its Gleason algorithms for prostate cancer developed in partnership with Google Health. It also seeks to integrate Verily’s algorithms into Lumea’s digital pathology platform. Pathologists will then have access to Verily’s AI to assist in identifying and grading prostate cancer within their existing digital workflow. Press release.

Proscia, a leader in digital and computational pathology solutions, announced a multi-year OEM agreement with Siemens Healthineers. Under the agreement, Siemens Healthineers will expand its Enterprise Imaging offering towards the global digital pathology market using Proscia’s Concentriq Dx platform. The agreement with Proscia enables Siemens Healthineers to expand into one of the few remaining areas of healthcare that has just started to experience the full benefits of digitization. Proscia’s Concentriq Dx in combination with Syngo Carbon offers a best-of-breed solution for digitizing pathology operations at scale alongside diagnostic radiology imaging for healthcare enterprises. By entering the rapidly growing digital pathology market with Concentriq, Siemens Healthineers is expanding its position as one of the industry leaders in healthcare with solutions covering the entire clinical pathway, providing a full spectrum of enterprise services across digital, data, and AI. Press release.

PathAI, a global leader in artificial intelligence (AI)-powered technology for pathology, and Cleveland Clinic announced a five-year strategic collaboration that will focus on leveraging PathAI’s quantitative pathology algorithms both to conduct new translational research and for use as clinical diagnostics in multiple disease areas. This collaborative effort combines PathAI’s AI-based platforms with Cleveland Clinic’s clinical expertise and multi-modal data to unlock a broad implementation of next-generation pathology diagnostics. The collaboration will enable the digitization of hundreds of thousands of pathology specimens, creating millions of whole slide images across multiple disease areas. By linking this digital pathology data with clinical and molecular data, Cleveland Clinic and PathAI will have a rich multi-modal dataset to conduct research using PathAI’s technology platform and menu of pathology algorithms. The partnership also will provide educational opportunities for Cleveland Clinic faculty and trainees, with the goal of enabling the development and usage of AI-powered pathology diagnostics to improve patient care. Cleveland Clinic will become an equity holder in PathAI as part of this agreement. Press release.

Proscia, a leader in digital and computational pathology solutions, and Hamamatsu Photonics K.K., a leading provider of whole slide imaging systems, announced a collaboration to accelerate digital pathology adoption at an enterprise scale. The cooperation agreement increases availability of the companies' unified solution that combines Proscia's Concentriq platform and Hamamatsu's NanoZoomer series of whole slide scanners to deliver the full promise of pathology's digital transformation to laboratories. The collaboration expands access to the companies' existing joint solution for scanning, image management, and AI, building upon its market traction to date. Together, Hamamatsu's NanoZoomer scanners and Proscia's AI-enabled Concentriq platform for image and data management provide a unified solution for the end-to-end pathology workflow, delivering seamless interoperability and enhanced customer experience. Users of Hamamatsu's scanners can now seamlessly integrate their images and all other data into an open ecosystem centered around Concentriq, enabling leading laboratories to drive day-to-day operations and practice digital pathology at an enterprise scale. Under the cooperation agreement, customers will also receive support with implementation to derive full value from the joint solution. Press release.

Helio Health, an AI-driven healthcare company focused on commercializing early cancer detection tests from a simple blood draw, announced that Hepatology Communications published positive results from the ENCORE study validating HelioLiver's strong clinical performance in detecting the presence of early hepatocellular carcinoma (HCC), the most common form of liver cancer and the seventh most common cancer worldwide but the second in cancer-related mortality, often due to late diagnosis. In this prospective, blinded, multi-center Phase 2 study, HelioLiver demonstrated high specificity (91%) and high sensitivity (76%) in detecting early-stage (stage I and II) HCC, significantly outperforming other clinically available detection tools such as AFP (57%), GALAD (65%), and ultrasound (47%). When considering HCC overall, HelioLiver performed at an 85% sensitivity with the same 91% specificity. Helio developed its next-generation sequencing platform, ECLIPSE, to identify 77 methylation targets across 28 genes. These DNA markers work in combination with the serum HCC proteins AFP, AFP-L3%, and DCP to enhance the multi-analyte algorithm. Press release.

Fabric Genomics, Inc. announced their selection by the Broad Institute of MIT and Harvard to support the development and implementation of their clinical whole genome sequencing-based offerings. As part of the agreement, Fabric Genomics will provide the AI-based clinical decision support platform used to support the interpretation of clinical whole genomes and generate patient reports. The collaborators will launch the clinical whole genome interpretation service as part of clinical utility studies with a national healthcare system. Fabric’s AI-powered clinical decision support platform includes Fabric ACE and Fabric GEM, two proprietary technologies that support highly accurate variant detection while providing measurable time savings and significantly lower analysis costs. Fabric’s clinical genomics decision-support system for whole genomes, recently published in the New England Journal of Medicine as part of Genomics England’s 100,000 Genomes Project on rare disease diagnosis, uses artificial intelligence to automate analyses of sequencing data, including single nucleotide variants alongside complex structural variants, which has traditionally been a challenge. It utilizes a patient’s clinical information and probabilistic disease matching to identify not only candidate genes but also to prioritize diagnoses. Fabric’s GEM algorithm has been shown in a growing number of peer-reviewed studies to detect more than 90% of disease-causing variants as the top two candidates. Fabric ACE takes sequencing data as an input and uses a forward-chaining inference engine to inform the classification of variants in clinically relevant genes according to criteria established by the American College of Medical Genetics and Association for Molecular Pathology. Ultimately, this allows for more accurate and faster clinical reporting allowing genomic laboratories to scale their testing. Press release.

Tata Consultancy Services (TCS) announced the launch of its Enterprise 5G Edge suite of solutions with Microsoft Azure private mobile edge computing (private MEC). The TCS suite brings together comprehensive capabilities that help enterprises design, integrate, implement, and operate an enterprise 5G edge ecosystem using the Azure private MEC solution and exploit the edge computing advantages for 5G applications. The new offering serves various industry verticals, bringing together enterprise assessment toolkits for edge and 5G readiness, and edge-native solutions ranging from industrial automation, quality detection, loss prevention, real-time video surveillance, autonomous vehicle management, digital farming, remote field assistance, smart factories, assisted living, immersive experiences with virtual and augmented reality, and more. The Enterprise 5G Edge suite combines TCS applications with the Azure private MEC solution to help enterprises gain newfound intelligence at the edge, resulting in new network-aware and responsive application capabilities. The offering brings together TCS’ IP-enabled automation-driven designs, AI-based modeling and simulations, zero touch provisioning and operation of enterprise 5G edge ecosystem and the new edge platform, securely integrated with enterprise infrastructure. Press release.

TetraScience, the R&D Data Cloud company, announced a new collaboration with PerkinElmer’s informatics business to facilitate faster and better scientific decision-making for customers of PerkinElmer’s Signals Research Suite, a leading cloud-based, electronic lab notebook and informatics platform. With the new collaboration, TetraScience will provide PerkinElmer Signals Research Suite customers with vendor-agnostic, configurable, and productized instrument integrations via its Tetra R&D Data Cloud that will enhance data interoperability and reduce time to scientific outcomes. One of the biggest challenges for laboratories performing routine and advanced analysis today is integrating multiple instruments, which produce data in unique formats, into seamless and high-performing workflows. By utilizing the Tetra R&D Data Cloud, the heterogeneous data formats will be engineered and harmonized into “Tetra Data”, a vendor-neutral data model that will create bidirectional data liquidity between Signals Research Suite and connected laboratory instruments. Press release.

PerkinElmer, Inc. announced V21 of its ChemDraw software, featuring the ability to import, animate, and share 3D chemical structures natively in Microsoft PowerPoint with one click. The key enhancement to a tool used by millions of scientists around the world helps chemists create more intelligent research reports quickly and easily—improving information sharing and collaboration and supporting real-time decision making. Using the new ChemDraw V21 software, chemists simply paste a live 3D rendering of their molecule, with its atom and bond color highlights fully retained, natively into the Microsoft PowerPoint application where they can view, rotate, and share the image. Researchers can also save molecules as 3D printable objects. No other chemical drawing application in the industry today provides these intuitive capabilities, which eliminate the need to use specialized software with steep learning curves. Press release.

The Rare Genomics Institute (RG) announced it is receiving support from Amazon Web Services (AWS) to enhance its RareShare website. RareShare is a unique social hub serving hundreds of rare disorder communities since 2008, allowing direct exchange of information among patients, families, research organizations, and healthcare professionals to improve the lives of those affected. AWS helps nonprofits—including those dedicated to health research and patient empowerment—use cloud technology to increase their impact. As part of the collaboration with the Rare Genomics Institute, AWS is providing unrestricted financial support funds for an array of RareShare projects, AWS computing credits, and project implementation support by dedicated AWS technical specialists. The Rare Genomics Institute plans to work with AWS to upgrade the RareShare website, modernizing the underlying software architecture, enhancing its appearance and navigational features, adding better cross-relational search capabilities, and expanding international access by adding language translation functions. With these improvements, current members will be able to more easily navigate through the website’s content, and new visitors will experience an appealing interface that encourages them to explore and become active RareShare members. Press release.

BC Platforms (BCP) announced expansion of its R&D operations in Singapore, which spearheads precision medicine activities in the Asia Pacific region, including China and Japan. The company also announced a research partnership with Singapore Health Services (SingHealth), Singapore’s largest public healthcare group. SingHealth has joined BCP’s BCRQUEST global data network in a research partnership to accelerate the genetic understanding and clinical research of diseases prevalent in Asian cohorts, including cancer and cardiovascular diseases. The core strategy of BCP is to develop privacy and security driven technology for trusted research infrastructure. This will then enable a safe build up cohort of studies representing Asia’s rich multi-ethnicity, which is of value for life science research as well as clinical decision making. The company’s Singapore R&D Centre will support recent Asia-based collaborations including with Japan’s Mitsubishi Space Software, announced Feb 2022, and Thailand’s Bumrungrad International Hospital (BIH), announced October 2021. Press release.

Optibrium Ltd, a leading developer of software for drug discovery, announced the release of the latest version of StarDrop, its comprehensive software platform for small molecule design, optimization, and data analysis. More than 160 organizations currently use StarDrop, including many of the world’s leading pharmaceutical companies. The new release introduces Inspyra, a module that dynamically learns from chemists’ expert knowledge and feedback to guide automated compound design methods, creating a powerful “augmented intelligence” to accelerate the discovery of high-quality drug candidates. The impact of “generative chemistry” algorithms for automated compound design is often limited in practice by a lack of alignment with chemists’ existing workflows and know-how, resulting in irrelevant compound suggestions. StarDrop’s new Inspyra module addresses this limitation by combining exploratory capabilities of automated compound design with chemists’ expertise, helping to focus on the most relevant chemistry spaces and suggest optimization strategies with the highest potential for project success. Press release.

Telit, a global enabler of the Internet of Things (IoT), introduced its new 5G M.2 worldwide module SKUs powered by the fourth-generation Snapdragon X65 and X62 modem-RF systems. The 3GPP Release 16 solutions will enable Telit customers such as device OEMs and systems integrators to support bandwidth-intensive, mission-critical, and latency-sensitive applications such as smart manufacturing/Industry 4.0, telemedicine, 4K/8K streaming video and private 5G networks. 3GPP Release 16 is the latest version of the 5G standard. It includes enhanced features such as ultra-reliable low-latency communication to enable a wide variety of new use cases for industrial IoT, smart manufacturing, robotics, industrial gateways, fixed wireless access, SD-WAN, 4K/8K video streaming, extended reality, gaming, eHealth, private 5G networks, and more. The Snapdragon X65 and X62 are the world’s first announced 3GPP Release 16 5G modem-RF solutions and the world’s first announced 10 Gigabit 5G systems. Customer samples will be available in Q1 2022 with mass production in mid-2022. Press release.

Accenture and Microsoft will assist the Mount Sinai Health System with its transition to the cloud to help enable innovation at a much faster pace. By modernizing its infrastructure, Mount Sinai will be able to reinvest cost-savings and focus on its healthcare mission. Accenture will collaborate with New York City’s largest academic medical system to help devise and securely execute its strategic cloud migration of clinical applications, including its Epic electronic health records system. Microsoft will provide quality assurance throughout this landmark academic center’s Azure migration process. Accenture, together with Avanade, its joint venture with Microsoft, will help lead the development and implementation of the underlying Azure architecture on which the solution is being built. In addition, Accenture will provide hybrid cloud managed services post migration. The managed services will include around-the-clock server management and support for migrated workloads; storage and backup operations; database support; and automation and analytics. Mount Sinai is building on its ongoing innovation efforts using artificial intelligence within clinical care and research. For example, its Mount Sinai Clinical Intelligence Center is focused on finding ways to use digital tools to fight COVID-19. This strategic migration to Microsoft Azure will further expand MSHS’ continued mission to bring AI-enabled products from bench to bedside. Press release.  

Quantabio, a leading provider of robust DNA and RNA amplification reagents for the most demanding molecular testing and life science research applications, announced the commercial availability of the sparQ RNA-Seq HMR Kit, an ultra-fast RNA next-generation sequencing (NGS) library preparation tool with integrated ribosomal RNA (rRNA) and globin mRNA depletion. The new kit enables scientists to generate high-quality stranded transcriptome libraries from challenging FFPE or low-input human, mouse, and rat (HMR) samples in five hours with minimal hands-on time. While promising, RNA-seq technologies can also be challenging due to complicated workflows, read coverage biases, limited transcript diversity, and high sample costs. The new Quantabio sparQ RNA-Seq HMR Kit overcomes many of these issues with a simple, nine-step workflow that only takes five hours compared to the 20-step, seven-hour process with standard technologies. Scientists are able to generate sequencer-ready libraries in a single day with 33% less hands-on time. The proprietary enzymes included in this kit generate high yields of directional transcriptome libraries from a wide variety of degraded sample types, including FFPE, tissue, and blood, along with input amounts ranging from 1 ng to 1 µg. The sparQ RNA-Seq HMR Kit seamlessly integrates efficient rRNA and globin mRNA depletion with stranded library preparation and is optimized for the rapid construction of high-quality RNA libraries for Illumina NGS platforms. The single-day protocol includes three reaction tubes, nine steps, and nine components for sequencer-ready libraries. The kit is available in 24- and 96-reaction configurations, and the initial template is prepared with 1 ng - 1 µg of total human, mouse, or rat input RNA. Press release.

Herophilus, a leading biotechnology company developing neurotherapeutics to cure complex brain diseases, announced the publication of research that describes a new statistical method to identify and analyze the effects of potentially confounding variables on machine learning models for complex biological datasets. The capability of machine learning (ML) to extract scientific insights from high-dimensional datasets is often limited by confounding variables that bias the models. Determining the influence of confounders is particularly challenging for complex bioscience datasets, which tend to be organized in nested hierarchies that prohibit the use of traditional methods such as linear regression to correct for the effects of nuisance variables. Though tools exist to mitigate known confounders, scientists lack a general method to identify which variables in a set of potential confounders require debiasing. In “Hierarchical confounder discovery in the experiment–machine learning cycle,” published in Cell Patterns, the authors define a new nonparametric statistical method for scoring the effect of a potential confounder, called the “Rank-to-Group” (RTG) score. RTG scoring is robust to outlier noise and can identify the source of a confounding effect even in non-linear structures. The method is applicable both to raw data and to the results of ML models. Press release.

PacBio, a leading provider of high-quality, highly accurate sequencing platforms, announced it will be supporting The Hospital for Sick Children (SickKids) in Toronto, Canada in using HiFi whole genome sequencing (HiFi WGS) to potentially identify genetic variants that may be associated with medical and developmental conditions. Samples that will be examined using HiFi WGS were previously sequenced using short-read DNA sequencing technology, but still lack the identification of a disease-causing variant. Even though more than 70 percent of rare disease, autism, and intellectual disability have genetic causes, more than 50 percent lack an identified causative genetic alteration despite the use of microarrays, whole-exome, or short-read whole-genome sequencing (srWGS). SickKids will use HiFi WGS to analyze samples from research participants who are highly suspected to have a genetic condition but have not yet received a diagnosis despite previous genetic testing, including srWGS. The team will explore whether HiFi WGS can detect potential genetic causes for a range of conditions, such as autism spectrum disorder and congenital diseases. Press release.