On January 15, 2020 Personal Genome Diagnostics Inc. (PGDx), a leader in cancer genomics, reported that partnering with Eisai Co., Ltd. to develop a comprehensive liquid biopsy biomarker discovery solution for oncology, to be used by Eisai researchers at their Tsukuba Research Laboratory (Press release, Personal Genome Diagnostics, JAN 15, 2020, View Source [SID1234553236]). The goal of this collaboration is to create a kitted NGS product that will enable researchers and biopharma companies to conduct biomarker discovery work using non-invasive blood samples collected from patients in clinical trials. By delivering comprehensive genomic insights from the samples, researchers may generate clinical data repositories to gain deep insights into the molecular evolution of tumors throughout the treatment course without the need for invasive, and resource-intensive, serial tissue biopsies.

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Using DNA isolated from patient blood samples, the automated NGS solution will detect somatic alterations across more than 500 genes in cancer and drug-resistance related pathways. The profiling assay will report single nucleotide variants (SNVs), insertion/deletions, copy number alterations, rearrangements, and genomic signatures, including microsatellite instability (MSI) and tumor mutation burden. A key advantage of this solution will be the ability to provide comprehensive genomic profiling data in clinical trials where tissue is not available, and it will enable investigators to evaluate drug response dynamics and emerging mechanisms of treatment resistance.

"We are always striving to evolve and expand our liquid biopsy capabilities and believe that many innovations and insights will be discovered by interrogating blood samples using the new solution we are developing with Eisai," said, John Simmons, Ph.D., Vice President of Translational Medicine, PGDx. "Our goal is to create the tools that will provide critical oncology insights that researchers and biopharma companies need to speed the process for developing new therapies for cancer patients."

"Partnering with PGDx to develop this solution is part of our Data Driven Drug Discovery & Development (5D drug discovery) initiative to accelerate drug discovery," said Dr. Takashi Owa, Vice President, Chief Medicine Creation and Chief Discovery Officer, Oncology Business Group at Eisai. "Utilizing digital technology, our history in drug development and PGDx’s liquid biopsy expertise, we expect this new solution will help address the complexities of developing new oncology drugs."

During the development process of this new liquid biopsy biomarker discovery solution, PGDx and Eisai will provide opportunities for researchers around the globe to join the collaboration. It is a shared goal and vision of the two companies that this solution will be utilized in clinical trials, as well as become a future standard option in clinical practice.

On January 15, 2020 AUM Biosciences (AUM), a Singapore-headquartered clinical-stage biotechnology company committed to speedily developing affordable cancer therapies, and Cyclica, a Toronto-based biotechnology company leveraging AI and computational biophysics to decentralize drug discovery, reported a partnership under Project Nexus to apply Cyclica’s proprietary drug discovery platform in AUM’s diverse R&D programs for the early-stage discovery of novel cancer therapies (Press release, AUM BioSciences, JAN 15, 2020, View Source [SID1234553237]).

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While there has been remarkable progress over the past few decades, cancer remains a major concern, with one in every six deaths being related to cancer. With the complex nature of cancer, researchers are faced with challenges in developing effective and affordable cancer treatments using classical drug discovery approaches, which ultimately results in barriers to affordability and availability of life-saving medicines for patients in need.

In this strategic partnership, AUM will deploy its drug development expertise, including a biomarker-driven approach, and utilize Cyclica’s integrated AI-augmented and structure-based platform, Ligand Design and Ligand Express, which together will design advanced lead-like molecules that minimize unwanted off-target effects while providing a holistic understanding of a molecule’s activity through integrated systems biology and structural pharmacogenomics.

"The ability to delve deeper into complex medical outcomes enhances the potential for discovery and assessment of novel molecules while in the development stage, which reduces the risk of failure and expedites the process," said Vishal Doshi, CEO of AUM Biosciences. "We are excited about this partnership with Cyclica, which will help us discover the undiscovered to address the needs of patients in Asia."

"Cyclica’s goal is to decentralize the discovery of medicines by partnering with hyper innovative biotechs globally. We are impressed with AUM’s expertise in drug development and our shared passion for tackling disease areas that are among the most intricate and impactful," says Cyclica’s President & CEO, Naheed Kurji.

Cyclica will receive an upfront payment as well as milestone payments upon the completion of specific stages for Project Nexus. AUM will maintain rights for future development and commercialization of drug assets resulting from Project Nexus.

On January 15, 2020 Integrated DNA Technologies (IDT), a leading comprehensive genomics solutions provider, reported an expanded global partnership with SOPHiA GENETICS, a leader in Data-Driven Medicine (Press release, Integrated DNA Technologies, JAN 15, 2020, View Source [SID1234553238]). Together, the superior enrichment products of IDT combined with SOPHiA GENETICS’s universal analytics platform and advanced multimodal solutions, provide powerful solutions for clinical researchers.

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When bundling IDT’s reagents with the SOPHiA Platform, researchers will benefit from sophisticated analysis technology and the collective intelligence of the SOPHiA community. It will help accurately detect and characterize genomic variants and share insights in the healthcare ecosystem. In addition, users can also take advantage of the SOPHiA Set-Up Program which is designed to support the implementation of Next-Generation Sequencing (NGS)-based testing for genetic diseases. The Set-Up Program is an efficient and reliable process that establishes and demonstrates the analytical performance of a test prior to adoption. The inclusion of superior enrichment products from IDT’s NGS portfolio, which meet the highest standards of quality and performance, plays an essential role in bringing accurate and precise solutions to hospitals globally.

Trey Martin, President of IDT commented, "IDT recognizes that analysis and interpretation of NGS data presents challenges to researchers and clinicians, so we are excited to offer the combination of the sophisticated SOPHiA Platform with our Exome v1 and the soon to be released xGen Exome Research Panel v2. This will give labs a complete solution to get the very best exome data available on the market."

Mirna Jarosz, General Manager of NGS at IDT noted, "We are excited to expand our working relationship with SOPHiA GENETICS to further impact clinical genomics research. We share a common goal of providing best-in-class solutions that ultimately help improve people’s lives. By providing a foundation of the most consistent and highest quality reagents, IDT is supporting SOPHiA in the all-important steps of translating data into actionable treatments for patients. Following our recent launch of NGS Discovery Pools for early stage discovery, our partnership with SOPHiA GENETICS further expands our ability to offer solutions for the entire precision medicine journey, from discovery to diagnostics."

IDT and SOPHiA GENETICS have teamed up for a number of years, including the development of a first of its kind In Vitro Diagnostics (IVD) marked SOPHiA Hereditary Cancer Solution in 2016. SOPHiA GENETICS has launched several additional IVD solutions since then, providing simple and fast procedures for healthcare professionals committed to serving patients by bringing clinical diagnostics in-house.

Jurgi Camblong, CEO and co-founder of SOPHiA GENETICS, commented, "Our strong relationship with IDT has enabled us to further accelerate the democratization in clinical genomics and better serve patients around the world. The universal SOPHiA Platform and genomic solutions make us the partner of choice for best-in-class reagent providers to bring end-to-end, highly-accurate and reliable outcomes to their clients. With the combined powers of SOPHiA’s high performance analytical capabilities and the world-class products that IDT has pioneered, many diseases the world currently faces may soon become more manageable and far easier to detect. The future of precision medicine is made brighter with this collaboration."

On January 15, 2019 NanoString Technologies, Inc. (NASDAQ:NSTG), a leading provider of life science tools for translational research, reported the publication of two peer-reviewed studies using the GeoMx Digital Spatial Profiler (DSP) in the journal Nature (Press release, NanoString Technologies, JAN 15, 2020, View Source [SID1234553239]). The two independent papers published by groups at the MD Anderson Cancer Center and Lund University used GeoMx DSP for deep molecular profiling of immune cells critical for understanding response to immunotherapy in patients with metastatic melanoma.

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The first publication, "B-cells and tertiary lymphoid structures (TLS) contribute to immune checkpoint blockade response," from the team of Dr. Jennifer Wargo at The University of Texas MD Anderson Cancer Center in Houston, TX. The study combines data from GeoMx DSP, RNA-sequencing, and mass cytometry to establish the presence of clonally expanded and memory-switched B-cells in patients responding to immune checkpoint blockade. This is the second publication by the Wargo group utilizing DSP, and it follows up observations in the earlier Nature Medicine paper that used the technology to identify B-cells as predictors of response to neoadjuvant immunotherapy (View Source).

B-cells are adaptive immune cells that produce antibodies and mediate T-cell activation. Recently, the presence of B-cells in the tumor microenvironment has been recognized as a prognostic marker for immunotherapy response. However, the mechanisms by which they contribute to anti-tumor immunity are difficult to determine as their phenotype and behavior differ significantly based on location within the tumor. Notably, B-cells can concentrate in specialized lymphoid organs known as tertiary lymphoid structures (TLS). The B-cells, T-cells, and antigen presenting cells comprising the TLS have distinct phenotypes and functions when compared to non-TLS immune cells. Dissection of the roles and mechanisms that these cells play in the tumor immune environment requires the use of spatially driven multiplex technology such as GeoMx DSP.

"The multiplex GeoMx DSP platform enabled us to specifically define the immune phenotype of tumor-infiltrating and TLS-localized B-cells and T-cells in the tumor sample," said Sarah Warren, Ph.D, Senior Director, Translational Science at NanoString. "By exclusively profiling the B-cells and T-cells within the TLS, we gained insights into the specific mechanisms by which these structures influence immunotherapy outcomes."

The second study, "Tertiary lymphoid structures improve melanoma survival and immunotherapy response," led by Dr. Göran Jönsson at the Lund University in Sweden, used the GeoMx DSP platform to conduct high-plex proteomic characterization of B- and T-cells in melanoma tumors with and without Tertiary Lymphoid Structures (TLS).

"We used the GeoMx platform to better understand the mechanism by which the presence of TLS lead to improved outcomes," said Dr. Jönsson. "We found that infiltrating T-cells in tumors without TLS show a dysfunctional molecular phenotype, suggesting that distinct patterns of intratumoral adaptive immune activation may be partly driven by B-cells."

"These concurrent studies demonstrate the ability of GeoMx DSP to deliver unique and impactful biological insights that advance the field on immuno-oncology," said Brad Gray, NanoString’s president and chief executive officer.

The GeoMx Digital Spatial Profiler enables researchers to rapidly and quantitatively characterize tissue morphology with a high-throughput, high-plex RNA and protein profiling system that preserves samples for future analyses. NanoString and its collaborators have published DSP data in 12 peer-reviewed papers and presented DSP data in more than 35 abstracts at major scientific meetings, demonstrating the utility of DSP technology to address a wide range of biological questions in Formalin-Fixed Paraffin-Embedded (FFPE) tissues.

On January 14, 2020 LabCorp (NYSE: LH) reported it will adopt the Ion Torrent Genexus System* and Oncomine Precision Assay* for use in research and development of companion diagnostics as well as other future oncology and precision medicine applications (Press release, LabCorp, JAN 14, 2020, View Source [SID1234553167]). LabCorp will also evaluate the potential for future deployment of the system and test across its network of laboratories and partner facilities. The adoption is enabled through LabCorp’s participation in Thermo Fisher Scientific’s Next-Generation Sequencing Companion Dx Center of Excellence Program (COEP).

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"We are very excited to collaborate with Thermo Fisher and leverage the capabilities of the Genexus system," said Marcia Eisenberg, Ph.D., chief scientific officer of LabCorp Diagnostics. "This streamlined platform, with fast turnaround time and automated workflow, has the potential to bring the power of next-generation sequencing to a broader range of settings and to stimulate significant advances in the future for the diagnosis and treatment of a broad range of cancers."

LabCorp will explore a variety of applications for the Genexus System and the Oncomine Precision Assay, in addition to their immediate use for cancer research and development of new tests. Upon validation, the platform’s automation will be ideal for accelerating access to next-generation sequencing (NGS) testing for clinical trials through LabCorp’s specialty and drug development central laboratories. If cleared or approved for diagnostic use, the system could be made available to smaller LabCorp laboratories, in addition to hospitals and other LabCorp customers, to help expand the reach of efficient, expedient, and cost-effective NGS testing.

Peter Silvester, senior vice president and president of Life Sciences Solutions at Thermo Fisher, said, "Through our valued partnership with LabCorp, we have a pivotal opportunity to expand access to comprehensive genomic profiling. Our goal is to improve the future standard of care by enabling our customers to leverage genomic information in every setting possible."

The Genexus System is the first fully integrated NGS platform that delivers results in a single day. It features a specimen-to-report workflow that enables laboratories to scale their sequencing runs for processing small batches of samples economically. Developed for the Genexus System, the Oncomine Precision Assay is a pan-cancer panel that enables comprehensive genomic profiling from formalin-fixed, paraffin-embedded (FFPE) tissue and liquid biopsy samples. Currently, the Genexus System and Oncomine Precision Assay are being used for research purposes only.

"The Thermo Fisher Genexus System and Oncomine Precision Assay could one day be deployed throughout our central laboratories to accelerate the development of precision medicine applications, including companion diagnostics," said Steve Anderson, Ph.D., chief scientific officer of Covance. "This platform has the potential to help expand access to NGS testing and become pivotal to LabCorp maximizing our unique capabilities in both diagnostics and drug development to benefit customers and, most importantly, patients."

*For research use only. Not for use in diagnostic procedures.