Genetic Cancer Patients Report COVID-19 Crisis Impacts Medical Care

VHL Alliance | April 22, 2020

New research shows patients with von Hippel-Lindau (VHL) disease, a genetic oncological disorder, are experiencing delay and cancellation of important appointments and even surgery due to the COVID-19 public health crisis. For many people with rare diseases, these effects may be life-changing, particularly for otherwise young and healthy patients who may face irreversible damage as a result of delayed treatment. VHL, or von Hippel-Lindau disease, is a genetic disorder characterized by tumors in up to ten areas of the body. Under normal conditions, the VHL gene controls the cell's oxygen sensing mechanism, keeping cancerous tumors at bay. When the gene is missing or mutated, the body's tumor suppressor signaling does not function correctly. The tumors can be benign or cancerous, and appear and grow unpredictably throughout a patient's life.

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MEDICAL

Genetic Leap and Astellas Establish Research Collaboration to Develop RNA-targeted Small Molecules for Oncology Target

Genetic Leap | March 11, 2022

Genetic Leap today announced a research collaboration agreement with Astellas Pharma, Inc. to develop novel RNA-targeted small molecule therapeutic candidates against an undisclosed oncology target. Under the terms of the agreement, Genetic Leap will deploy its platform to discover and validate RNA-targeted small molecules against an undisclosed oncology target selected by Astellas. The agreement provides Astellas with certain rights to intellectual property on candidates discovered and developed under the collaboration that are directed against the program target. Further details of the collaboration were not disclosed. About Genetic Leap Genetic Leap's vision is to lead the next giant leap in human healthcare by developing today the incredible therapeutics of the future. To accomplish this, Genetic Leap built paradigm-shifting AI technologies that find the causal factors in disease and correct these factors with precision RNA therapy that is safe, convenient, and reversible. The company is leveraging its platform to advance a pipeline that spans internal as well as partnered programs, across both novel and known (but traditionally undruggable) targets.

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MEDICAL

PacBio transforms access to the epigenome and streamlines workflows

PacBio | April 23, 2022

PacBio (NASDAQ: PACB), a leading developer of high-quality, highly accurate sequencing solutions, today announced the release of a transformative capability to detect DNA methylation using the Sequel IIe and Sequel II Systems. This extends PacBio’s unique and highly capable HiFi sequencing technology to now include access to the epigenome, a second layer of genomic information often left unexplored due to fundamental limitations of common sequencing technologies. PacBio’s single-molecule approach provides a much more holistic view of molecular behavior during sequencing. Subtle patterns in this rich information allow detection of modified bases in native DNA during standard HiFi sequencing. As a result, scientists gain access to the epigenome with zero additional cost, effort, or complexity. This advance will unlock important new opportunities across a broad range of applications in fundamental and applied biological science. This update also includes a wide range of workflow improvements to enhance customer experience, such as simplified, unified, and accelerated library preparation workflows and consumables, live instrument performance monitoring, and on-instrument analysis support for recombinant adeno-associated virus (rAAV) genome sequencing, a rapidly growing biopharmaceutical application relevant to gene therapy and vaccine development research. With each product release we continue to improve the utility and value of the Sequel II and IIe platform, providing researchers with unique capabilities that differentiate PacBio HiFi sequencing from all other sequencing technologies, Our latest enhancements to the Sequel II and IIe platform, including 5-base sequencing and improved workflows are expected to both simplify the ability to generate high quality data and enable deeper insights into the complexity of the genome.” Christian Henry, President and Chief Executive Officer of PacBio. Multiple tests are currently required to evaluate rare disease cases for sequencing and methylation variation. HiFi sequencing has the potential to change that by measuring both genetic and epigenetic variation across the full genome in a single experiment. We have had success using 5-base HiFi sequencing at Children’s Mercy Kansas City to identify abnormal methylation in repeat expansion cases, and we plan to apply it to all the future genomes we sequence. It is exciting to access another aspect of the genome without needing to change sample handling or sequencing procedures.” Emily Farrow, PhD, CGC, Director of Laboratory Operations at Children’s Mercy Kansas City and Associate Professor of Pediatrics at University of Missouri Kansas City School of Medicine. We found that the CpG methylation patterns detected in tomato and maize genomes using HiFi sequencing are highly concordant to standard bisulfite sequencing but bring power to resolve transposable elements and other sequences that are out of reach with short reads. When combined with the incredible capabilities of HiFi sequencing for genome assembly and variation analysis, this creates an unmatched opportunity for ultra-high-quality genome and epigenome analysis of plant and vertebrate genomes from a single datatype.” Michael Schatz, PhD, Bloomberg Distinguished Professor of Computer Science and Biology at Johns Hopkins University. PacBio’s HiFi sequencing technology offers a comprehensive view of genomes and transcriptomes. But DNA contains much more information subtly encoded as “epigenetic” modifications to DNA bases. This epigenome influences how genes are expressed and plays a major role in determining biological function in both health and disease. Historically, access to the epigenome has been difficult and required sacrifices in read lengths, accuracy, and completeness while adding workflow complexity. By including automatic detection of the key modified base in humans and many other species (5mC in CpG motifs) PacBio sequencing technology provides access to the combined genome and epigenome without sacrificing read lengths, accuracy, or completeness, and without requiring additional workflow steps. Streamlining workflows is a key focus for PacBio, and this latest update makes it easier to perform HiFi sequencing. The company’s new SMRTbell prep kit 3.0 is capable of reducing workflow time for whole-genome sequencing applications by 50 percent or more and reducing required DNA inputs by 40 percent (to three micrograms per human genome). SMRTbell prep kit 3.0 is suitable for a wide range of applications and supports automation and batch processing of samples. PacBio also introduced a new single-reaction sequencing plate and SMRT Cell 8M tray that better enables customers to run samples at their convenience. About PacBio Pacific Biosciences of California, Inc. (NASDAQ: PACB) is empowering life scientists with highly accurate sequencing platforms. The company’s innovative instruments are based on Single Molecule, Real-Time (SMRT®) Sequencing technology, which delivers a comprehensive view of genomes, transcriptomes, and epigenomes, enabling access to the full spectrum of genetic variation in any organism. Cited in thousands of peer-reviewed publications, PacBio® sequencing systems are in use by scientists around the world to drive discovery in human biomedical research, plant and animal sciences, and microbiology.

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Illumina Introduces New Pan-Cancer Companion Diagnostic to Match Patients with Rare Genetic Mutations to Targeted Therapy

Illumina | May 27, 2022

Illumina, Inc. (NASDAQ: ILMN), a global leader in DNA sequencing and array-based technologies, today announced the addition of a companion diagnostic (CDx) indication to its CE-marked in vitro diagnostic TruSight™ Oncology (TSO) Comprehensive (EU) test. This single test kit, recently launched across Europe, assesses multiple tumor genes and biomarkers to reveal the specific molecular profile of a patient's cancer. The CDx pan-cancer indication will allow identification of cancer patients with solid tumors who are positive for neurotrophic tyrosine receptor kinase (NTRK) gene fusions including NTRK1, NTRK2 or NTRK3, and may benefit from targeted therapy with Bayer's VITRAKVI® (larotrectinib), in accordance with the approved therapeutic labeling. TSO Comprehensive (EU) is a comprehensive genomic profiling (CGP) test which combines less prevalent biomarkers with more prevalent ones in the same test, using a single biopsy specimen. This helps maximize the chances of identifying an actionable alteration so that patients can be treated with a targeted therapy or enrolled into a clinical trial based on their unique tumor genomic profile. The addition of this first CDx claim specific to NTRK gene fusions, a rare but highly actionable biomarker, helps provide patients harboring this genetic alteration with an opportunity to benefit from larotrectinib, a genomically matched treatment. This CDx claim, developed in partnership with Bayer, is the first of a series under development, building upon Illumina's broad portfolio of oncology partnerships with industry leaders to advance cancer diagnostics and precision medicine, We continue to focus on unlocking the potential of new biomarkers to identify those most likely to benefit from precision medicines so that no patient is left behind—we don't want anyone to miss the opportunity to have their biomarker detected and gain access to a potentially life-saving therapy." Paula Dowdy, Senior Vice President and General Manager of Illumina for Europe, the Middle East, and Africa. Across most solid cancer tumor types, NTRK gene fusions can have a rare prevalence of 0.1-3% and can be challenging to detect as these genes fuse with many different partners, many of them previously unknown. Most CDx tests are specific to one type of cancer, but the NTRK claim is pan-cancer, enabling TSO Comprehensive (EU) to target multiple solid tumor types and a broad range of known and novel gene fusion partners across all three NTRK genes. This helps maximize the chances of finding actionable information from each patient's biopsy, to inform treatment with larotrectinib. Since it launched four years ago, VITRAKVI has demonstrated high response rates and highly durable responses in adults and children with TRK fusion cancer, The CE marking of Illumina's TSO Comprehensive (EU) assay inclusive of NTRK gene fusion detection for VITRAKVI is an important advance in enabling precision oncology for patients in Europe. Assays that enable precision oncology through comprehensive genomic testing are crucial for informing optimal treatment plans and help to ensure the best possible outcomes for cancer patients. We look forward to continuing to collaborate with Illumina to ensure that more patients are evaluated comprehensively inclusive of NTRK gene fusions." Christine Roth, Member of the Executive Committee of Bayer's Pharmaceuticals Division and Head of Bayer's Oncology Strategic Business Unit. The performance of TSO Comprehensive (EU) with NTRK fu­sions was assessed by analytical and clinical validation studies. Pooled data from three clinical trials, LOXO-TRK-14001 (NCT02122913), NAVIGATE (NCT02576431) and SCOUT (NCT02637687), were used to demonstrate the clinical effectiveness and safety of TSO Comprehensive (EU) in identifying NTRK1, NTRK2 and NTRK3 gene fusion positive patients who may be eligible for treatment with larotrectinib. The primary endpoint was the overall response rate (ORR), measured as the patient presenting either a complete response, a surgical complete response or partial response, to larotrectinib. We were delighted to be the clinical study partner for Illumina in this significant achievement of the first CDx claim for the TSO Comprehensive (EU) panel, TSO Comprehensive (EU) represents a powerful and versatile platform with a broad range of cancer-relevant content, and we recognize its value to our biopharma partners, for the development and delivery of companion diagnostics to further precision medicines." Professor Richard Kennedy, Global VP of Biomarker Development & Medical Director, Almac Diagnostic Services. Illumina has a growing pipeline of CDx claims under development through partnerships with pharmaceutical companies, which will be added to TSO Comprehensive (EU) following appropriate regulatory approvals. These CDx claims will help unlock groundbreaking targeted therapies and immunotherapies to make a difference in the lives of cancer patients. As Illumina continues to expand its broad portfolio of oncology partnerships with industry leaders, the company aims to advance cancer diagnostics and precision medicine. About Bayer Bayer is a global enterprise with core competencies in the life science fields of health care and nutrition. Its products and services are designed to help people and planet thrive by supporting efforts to master the major challenges presented by a growing and aging global population. Bayer is committed to drive sustainable development and generate a positive impact with its businesses. At the same time, the Group aims to increase its earning power and create value through innovation and growth. The Bayer brand stands for trust, reliability and quality throughout the world. In fiscal 2021, the Group employed around 100,000 people and had sales of 44.1 billion euros. R&D expenses before special items amounted to 5.3 billion euros. About Illumina Illumina is improving human health by unlocking the power of the genome. Our focus on innovation has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture and other emerging segments.

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CELL AND GENE THERAPY

Bicycle Therapeutics Announces Continued Clinical Progress and Updates to Management Team

Bicycle Therapeutics | January 06, 2022

Bicycle Therapeutics plc, a biotechnology company pioneering a new and differentiated class of therapeutics based on its proprietary bicyclic peptide technology, announced continued progress in its ongoing Phase I/II clinical trials of BT8009, BT5528 and BT7480. “Last quarter, we reported interim clinical results from ongoing trials of two of our Bicycle toxin conjugates, BT8009 and BT5528, demonstrating preliminary anti-tumor activity in two tumor types, and announced the first patient dosed in the Phase I clinical trial of BT7480, our first tumor-targeted immune cell agonist to enter the clinic. In our trial of BT8009, we are pleased to confirm the preliminary activity and see that these patients remain on trial. We look forward to presenting interim BT8009 Phase I results at a medical meeting and initiating the BT5528 expansion cohorts this year. We are also pleased with our progress advancing BT7480 in the ongoing Phase I clinical trial and look forward to sharing additional details regarding the potential for Bicycles beyond our toxin conjugates as we strive to become a leader in the development of targeted oncology therapeutics.” Kevin Lee, Ph.D., Chief Executive Officer Bicycle Toxin Conjugates® (BTCs) BT8009 and BT5528 In the ongoing Phase I portion of the Phase I/II clinical trial of BT8009, a second-generation BTC™ targeting Nectin-4, four out of 11 patients were previously reported to have a partial response under Response Evaluation Criteria in Solid Tumors version 1.1, including one out of four (25%) in the 2.5mg/m2 dose and three out of seven (43%) at the 5.0 mg/m2 cohorts. All four patients previously reported as responders have since received at least one subsequent scan, and all have been confirmed as ongoing RECIST 1.1 responses. One patient in the 5.0 mg/m2 cohort, who previously was reported to have a partial response with an 89% tumor reduction, has now received two subsequent scans, which each showed that total tumor volume has been reduced by 100%, constituting a confirmed complete response. All four patients previously reported to have a RECIST 1.1 clinical response remain on therapy. The tolerability profile of the 2.5mg/m2 and 5.0 mg/m2 cohorts remains consistent with that previously reported. Dose escalation in the BT8009 Phase I trial remains ongoing, with patients currently being dosed at 7.5mg/m2 weekly or every-other-week. Bicycle intends to present interim Phase I results from the ongoing clinical trial at a medical meeting this year. The Phase I/II trial of BT5528, Bicycle’s second-generation BTC targeting EphA2, is also ongoing, with plans remaining on track to initiate the expansion cohorts this year, with an expected recommended Phase II dose of 6.5mg/m2 every-other-week. Bicycle tumor-targeted immune cell agonist™ (Bicycle TICA™) BT7480 Bicycle also initiated a Phase I clinical trial of BT7480, a novel, fully synthetic Bicycle TICA targeting Nectin-4 and agonizing CD137, in the fourth quarter of 2021, and dose escalation in that trial remains ongoing. BT7480 and other Bicycle TICAs, including a novel NK-cell-engaging molecule, were the subjects of four posters at SITC in November 2021. Management Team Updates Bicycle is also announcing the expansion of and transition in its management team. Michael Skynner, Ph.D., the company’s Chief Operating Officer has been appointed to the newly created position of Chief Technology Officer, effective January 3, 2022, to focus on leading and overseeing the growth of Bicycle’s proprietary phage display discovery platform in oncology, as well as on creating innovative opportunities for the platform outside of oncology. Dr. Skynner joined the company in January 2016 as Vice President, Operations and Discovery and had served as COO since March 2018. Alistair Milnes, who has served as the company’s Vice President, Human Resources and Communications since January 2021, has assumed the COO role. Mr. Milnes previously led human resources and communications at multinational energy and mineral companies. Both Dr. Skynner and Mr. Milnes are based in the United Kingdom. “We are delighted to announce our recent management team appointments, with Mike Skynner becoming our new CTO and Alistair Milnes moving to the COO role. Mike has been an invaluable contributor to Bicycle’s success to date and has led our platform discovery efforts since joining in early 2016. Following recent promising clinical progress, we believe it is time to focus on accelerating the growth of our proprietary oncology pipeline and on identifying innovative ways to potentially capitalize on our unique technology beyond our current therapeutic focus. I am confident that Mike can help us achieve these objectives.” Dr. Lee added, “I am similarly enthusiastic about Alistair’s appointment as COO and believe his operational experience and track record of successfully identifying, recruiting, and retaining key talent at large, multinational companies will be instrumental in helping guide Bicycle through our next phase of growth.” About Bicycle Therapeutics Bicycle Therapeutics is a clinical-stage biopharmaceutical company developing a novel class of medicines, referred to as Bicycles, for diseases that are underserved by existing therapeutics. Bicycles are fully synthetic short peptides constrained with small molecule scaffolds to form two loops that stabilize their structural geometry. This constraint facilitates target binding with high affinity and selectivity, making Bicycles attractive candidates for drug development. Bicycle is evaluating BT5528, a second-generation Bicycle Toxin Conjugate targeting EphA2; BT8009, a second-generation BTC targeting Nectin-4, a well-validated tumor antigen; and BT7480, a Bicycle TICA™ targeting Nectin-4 and agonizing CD137, in company-sponsored Phase I/II trials. In addition, BT1718, a BTC that targets MT1-MMP, is being investigated in an ongoing Phase I/IIa clinical trial sponsored by the Cancer Research UK Centre for Drug Development. Bicycle is headquartered in Cambridge, UK, with many key functions and members of its leadership team located in Lexington, MA.

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