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Pathology Image Digitization and AI Analysis, New Proteomics Solutions, Improved Diagnostics for Drug Efficacy, AEs

March 30, 2022 | A genomic network model is used to identify aurora kinase inhibitor-sensitive lung tumors, AI seeks to improved prostate cancer diagnosis and prognosis, improved liver cancer detection is achieved with simple blood test, immunohistochemistry analysis standardization, and PacBio and Sick Kids in Toronto are working to identify genetic variants responsible for childhood disease using HiFi WGS.

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 and 4D Path Inc. 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 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.

Thermo Fisher Scientific introduced a new large-volume electroporation system that allows cell therapy developers to more easily move from clinical development to commercial manufacturing. The Gibco CTS Xenon Electroporation System leverages a closed, highly flexible design to facilitate gene modifications without the use of traditional viral vectors. The electroporation approach enables the introduction of a payload into a cell by temporarily increasing cell permeability using an electrical pulse. Unlike existing large-volume cell therapy electroporation solutions on the market, the Gibco CTS Xenon Electroporation System features programmable, flexible electroporation conditions, offering cell therapy developers full control to optimize a variety of hard-to-transfect cell types and payloads. The system may be used as a standalone technology or integrated with the Gibco CTS Rotea Counterflow Centrifugation System as part of a modular, closed, and automated cell therapy manufacturing workflow. The CTS Xenon Electroporation System can transfect up to 2.5e9 cells in 25 mL in a sterile system, enabling rapid and efficient non-viral transfection for clinical manufacturing applications. In addition, it delivers up to 80% cell viability and 90% gene knockout transfection to seamlessly scale from the small-volume Neon Transfection System without the need for re-optimization of electroporation parameters. 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 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 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 and Hamamatsu Photonics K.K. 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 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.

Boston Cell Standards, a company dedicated to ensuring that cancer patients receive accurate diagnosis and treatment, announced its launch of the Consortium for Analytic Standardization in Immunohistochemistry (CASI). The new organization is led by an international panel of pathologists and scientists dedicated to improving patient immunohistochemistry (IHC) test accuracy and reproducibility. Initially funded by a $2 million grant from the National Cancer Institute, the consortium’s mission is to integrate analytic reference standards into IHC, a test format widely used in surgical pathology to evaluate cancers in tissue samples and determine correct treatment. Whereas standard patient blood tests can be analyzed in any lab and yield the same results every time because of international reference standards, no such reference standards exist in IHC, meaning that different labs could—and often do—return different results from the same sample. CASI will conduct studies to determine appropriate analytic sensitivity thresholds for selected IHC tests, publish collected data, and then offer analytic sensitivity recommendations. In addition to guiding routine clinical practice, these recommendations will be intended to facilitate and simplify methodology transfer between laboratories, from published literature, and in clinical trials. Press release.

Biognosys has launched its expanded suite of proteomics platforms that provide pharmaceutical and diagnostics customers with deep biological insights across the entire R&D pipeline, from early-stage discovery to clinical settings. Biognosys has been offering a large variety of mass spectrometry-based proteomics contract research services for more than a decade. By organizing and expanding its portfolio of research applications under three proprietary platforms—TrueDiscovery, TrueTarget, and TrueSignature—Biognosys now makes it easier for its biopharma customers to integrate multiple complementary proteomics solutions across their entire drug discovery and clinical development pipeline. Through TrueSignature, Biognosys develops and runs customizable precision proteomics biomarker panels. TrueDiscovery and TrueTarget build on Biognosys’ existing key offerings for biomarker discovery and drug target identification, respectively. TrueDiscovery is powered by hyper reaction monitoring (HRM) mass spectrometry, an advanced data-independent acquisition (DIA)-based protein quantification technology co-invented and patented by Biognosys. TrueDiscovery is the only proteomics platform that searches the complete proteome to quantify thousands of the most relevant proteins, including an unlimited number of proteoforms. Press release.

New York State Department of Health (NYSDOH) has given conditional approval to KSL Diagnostics in Buffalo, New York, for the EXACT COVID-19 Antibody Test. Access to the EXACT COVID-19 Antibody Test will now be available to physicians and their patients in the United States through AZOVA Inc. The EXACT COVID-19 Antibody Test is an advanced COVID-19 antibody test that provides semi-quantitative measurements of six distinct antibodies produced by the immune system in response to exposure to the SARS CoV-2 virus or to COVID-19 vaccination. The small volume blood sample can be collected in a home or office setting with a fingerstick. A positive test result could indicate the presence of antibodies arising from a prior COVID-19 infection or COVID-19 vaccination. Press release.

AccessDx Laboratory has introduced an expanded pharmacogenomics (PGx) test that improves the quality, availability, and actionability of drug-gene insights within the clinical workflow. The AccessDx PGx Profile is designed to help providers identify potential risks for adverse drug reactions or reduced medication efficacy. Based on years of clinical and diagnostic research, laboratory expertise, and technical refinements, the AccessDx PGx Profile assesses a targeted range of individual genes and genetic variants. Results can help providers evaluate risks associated with an extensive list of medications known to be influenced by genetic variants to optimize treatment. The panel provides deep insights related to specific ethnic indicators, clinical areas, and medical conditions, so it can be leveraged across a broad spectrum of specialties. Primary care providers and cardiologists may consider results from the AccessDx PGx Profile along with clinical information to treat patients with high LDL levels, for example, while oncologists may use these insights to assist in the selection of medications and precise doses for chemotherapy patients. Press release.

Quantabio 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.

PacBio 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.

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