Sponsored by Akoya Biosciences
In this webinar, Dr. Kurt Schalper, director of the Translational Immuno-oncology Laboratory at the Yale Cancer Center, will discuss the immune composition and therapeutic implications in human non-small cell lung cancer (NSCLC), focusing on dominant immune evasion pathways and T-cell dysfunction. He will present results from studies using genomic and spatially resolved analysis of different cell types, targets, and pathways that have shed light on the complexity of tumor/immune cell interactions and their role in sensitivity and resistance to immunostimulatory anti-cancer therapies. He will also discuss the potential application of these concepts for future biomarker development and novel treatment strategies.
- Discuss the role of the tumor microenvironment in tumor progression and therapeutic resistance.
- Learn about the dominant mechanism of immune evasion and immunotherapy response in human NSCLC.
- Understand the current landscape of immunotherapy biomarkers and the contribution of spatially resolved analysis.
Sponsored by Mission Bio
Clonal Heterogeneity in Acute Lymphoblastic Leukemia at Diagnosis and During Chemotherapy Treatment Detected by Single-Cell Sequencing
Acute lymphoblastic leukemia (ALL) is an aggressive leukemia that occurs most frequently in children and is characterized by the presence of few chromosomal rearrangements and additional mutations. In this webinar, the second in a “Meet the Authors” series sponsored by Mission Bio, Jan Cools of the VIB Center for Cancer Biology in Leuven, Belgium will discuss the application of single-cell analysis to determine the clonal heterogeneity of the leukemia cells of ALL cases at diagnosis.
Dr. Cools’ lab used single-cell targeted DNA sequencing (Tapestri, Mission Bio) and single-cell RNA-sequencing (10x Genomics) to determine the clonal heterogeneity of the leukemia cells of 20 ALL cases at diagnosis and monitored the clonal evolution during chemotherapy treatment. Specifically, the lab designed a custom ALL panel and obtained accurate single-nucleotide variant and small insertion-deletion mutation calling for 305 amplicons covering 110 genes in about 4400 cells per sample and time point. Bone marrow and/or blood samples from 12 B-cell ALL and eight T-cell ALL patients were analyzed.
Dr. Cools will discuss how single-cell DNA amplicon sequencing is a sensitive assay to detect clonal architecture and evolution of the malignant cells in ALL, and present his findings published in the Blood paper, “Single-cell DNA amplicon sequencing reveals clonal heterogeneity and evolution in T-cell acute lymphoblastic leukemia.”
Sponsored by Akoya Biosciences
This multi-stakeholder panel discussion will bring together a diverse set of experts who will highlight innovative solutions that demonstrate the integral role of spatial biomarkers in immuno-oncology. Learn about their advancements from biomarker discovery to translational research, and how they are shaping the future direction of the spatial biology field.
In this talk, attendees will:
- Gain an understanding of the current limitations of predictive biomarkers in immuno-oncology
- Become familiar with the different perspectives on the value and important role of multiplex immunofluorescence (mIF) to improve biomarker strategies in immuno-oncology
- Learn about the future direction of spatial biomarkers in translational research & precision medicine
The presenters on this panel are Gavin Gordon, MBA, PhD, vice president, clinical market developmen at Akoya Biosciences, Alexander D. Borowsky, MD, Director, Center for Genomic Pathology & Professor of Pathology and Laboratory Medicine; Center for Immunology and Infectious Diseases; UC Davis Comprehensive Cancer , Bernard A. Fox, PhD, harder family chair for cancer research, Robert W. Franz Cancer Center, Earle A. Chiles Research Institute at Providence Cancer Institute, Elizabeth L. Engle, MS., a senior Laboratory Manager at John Hopkins Hospital, Maryland, and Kurt Schalper, MD, PhD, translational immuno-oncology laboratory lead at Yale Cancer Center.
Sponsored by Oxford Nanopore Technologies
The completion of the first telomere-to-telomere human genome, T2T-CHM13, enables exploration of the full epigenome, removing limitations previously imposed by the missing reference sequence. Existing epigenetic studies omit unassembled and unmappable genomic regions, such as centromeres, peri-centromeres, acrocentric chromosome arms, sub-telomeres, segmental duplications, and tandem repeats.
In this webinar, Ariel Gershman, a doctoral candidate at the Johns Hopkins School of Medicine, will discuss how she and her team leveraged the new assembly to measure enrichment of epigenetic marks with short reads using k-mer assisted mapping methods. This granted array-level enrichment information to characterize the epigenetic regulation of these satellite repeats. Using nanopore sequencing data, the team generated base-level maps of the most complete human methylome ever produced. They examined methylation patterns in satellite DNA and revealed organized patterns of methylation along individual molecules.
When exploring the centromeric epigenome, Gershman and colleagues discovered a distinctive dip in centromere methylation consistent with active sites of kinetochore assembly. With long-read chromatin accessibility measurements (nanoNOMe) paired to CUT&RUN data, the team found the hypomethylated region was extremely inaccessible and paired to CENP-A/B binding. With long reads, they interrogated allele-specific, long-range, epigenetic patterns in complex macro-satellite arrays, such as those involved in X chromosome inactivation. Using the single-molecule measurements, the team clustered reads based on methylation status alone, distinguishing epigenetically heterogeneous and homogeneous areas. The analysis provides a framework to investigate the most elusive regions of the human genome, applying both long- and short-read technology to grant new insights into epigenetic regulation.
Sponsored by Beckman Coulter Life Sciences
Next-generation sequencing of infectious agents is crucial for large-scale genomic surveillance of infectious diseases. Throughout the SARS-CoV-2 pandemic, several consortia across the globe have coordinated efforts to understand the epidemiology of SARS-CoV-2 through the identification and tracking of novel variants in cases of positive patients. In this webinar, we highlight the collaboration between the European Molecular Biology Laboratory (EMBL), New England Biolabs (NEB), and Beckman Coulter Life Sciences to develop an automated high-throughput NGS library prep workflow for SARS-CoV-2 surveillance using the NEBNext ARTIC SARS-CoV-2 Library Prep Kit (Illumina) and the Biomek i7 Hybrid NGS Workstation.
Sponsored by Qiagen
The Association Between Diabetes and Latent TB Infection: The Role of Diagnostics in Improving Outcomes
Someone with untreated latent tuberculosis infection (LTBI) and diabetes is more likely to develop tuberculosis (TB) disease than someone without diabetes. Without proper treatment, diabetes and TB can increase health complications.
In this webinar, Dr. Sonia Qasba will journey through the epidemiology, risk, and treatment recommendations of diabetic patients with LTBI. She will discuss how diabetes potentiates TB and why TB predisposes one to hyperglycemia. Additionally, she will share real-life examples of screening, prevention, and treatment of individuals with LTBI, TB, and diabetes.
Sponsored by Congenica
The time and cost of genomic analysis create significant bottlenecks in clinical labs and are predicted to account for more than half the cost of the clinical use of next-generation sequencing by 2026. This is often a key concern as reimbursement for data interpretation can prove challenging.
Choosing a professional solution for genomic analysis and interpretation can significantly reduce data analysis time while increasing diagnostic yield. For labs that have invested time and money in developing their own customized genomic data analysis solutions, the decision to move to a professional solution can be a difficult one.
In this webinar, Anna Miller, technical specialist at NOAH Clinical Laboratory, will talk about her experience using both professional and in-house solutions. She will discuss the essential attributes needed in a professional solution to deliver significant benefits and return on investment. These include:
- Clinically standardized workflows - A platform that facilitates and supports recommended clinical practices.
- Flexibility - A platform that also enables on-demand integration of existing knowledge bases and historical reference data, allowing users to customize clinical workflows.
- Deployment flexibility - Offering solutions both on-premise and in the cloud.
- Efficiency - Providing automation of known variants and automatic classification of unknown variants to increase efficiency and yield.
- Scalability - Enabling users to scale operations from panels to exomes to genomes without implementing new tools.
- Clinically proven - Demonstrated ability to maximize diagnostic yield.
- Partnership - A company that has the knowledge and expertise to deliver the best possible service.
Sponsored by Beckman Coulter Life Sciences
This webinar is part two of a two-part series on abstract cell-free expression.
In the last decade, CRISPR technologies have revolutionized molecular biology. In this webinar, we show how prototyping CRISPR components can be accelerated by combining a cell-free transcription and translation (TXTL) system with an Echo Acoustic Liquid Handler (LH) from Beckman Coulter Life Sciences. This presentation covers:
- Overview of TXTL and its applications
- How accelerated prototyping can be used to test sgRNAs, new CRISPR, and anti-CRISPR proteins
- Overview and specifications of Echo LH
- The speed and resource savings enabled by the Echo LH in a TXTL lab
- Echo LH and TXTL to characterize CRISPR enzymes and anti-CRISPR proteins
- Echo LH and TXTL to uncover fundamentals of target recognition
- Application of the Echo LH to accelerate CRISPR based genetic circuits
Sponsored by Beckman Coulter Life Sciences
High-throughput reduced-representation sequencing (RRS)-based genotyping methods, such as genotyping-by-sequencing (GBS), have provided attractive genotyping solutions in numerous species. In this webinar, Davoud Torkamaneh, assistant professor at Université Laval, will discuss NanoGBS, a miniaturized, eco-friendly method for GBS library construction.
Using acoustic droplet ejection technology (Echo 525 Liquid Handler), NanoGBS libraries were constructed in tenfold smaller volumes compared to standard methods (StdGBS) and led to a reduced use of plastics of up to 90 percent. A high-quality DNA library and an SNP catalog were obtained with extensive overlap in SNP loci (96 percent) and 100 percent agreement in genotype calls compared to the StdGBS dataset with a high level of accuracy (98.5 percent). Combining NanoGBS library preparation and increased multiplexing can reduce genotyping cost per sample by 72 percent. This approach may greatly facilitate the adoption of marker applications where extremely high throughputs are required and cost is limiting.
Sponsored by Talis Bio
Rapid and accurate point-of-care (POC) testing systems have the potential to improve patient triage and treatment, mitigate the spread of infectious diseases by rapidly identifying infected individuals, improve diagnostics when access to centralized labs is limited, and lower testing costs. The Talis One is a compact, sample-to-answer, and connection-ready molecular diagnostic instrument built with convenience, efficiency, and ease of use in mind. Each Talis One infectious disease test employs a single-use, self-contained, room temperature-stable test cartridge.
In this webinar, Dr. Glen Hansen, assistant professor in the Division of Infectious Disease at the University of Minnesota will:
- Discuss the benefits of POC testing for infectious diseases, e.g., respiratory infections, sexually transmitted infections, etc.
- Highlight how COVID-19 has changed adoption of and perspectives on POC testing.
- Share his preliminary experience using the Talis One COVID-19 Test System.
Dr. Matthew Faron, assistant professor at the Medical College of Wisconsin will:
- Discuss the design, performance, and infectious disease menu for the Talis One system.
- Review preliminary data and personal experience in using the Talis One COVID-19 Test System.
Sponsored by SeraCare
Laboratory Adoption and Clinical Considerations for Prenatal Cell-Free DNA Screening for Common Aneuploidies
Cell-free (cf)DNA screening of pregnancies (also known as non-invasive prenatal testing or NIPT) is a transformative technology that is becoming routine for all pregnancies. Laboratories are potentially faced with adding a new technological approach in order to add NIPT to their repertoire of assays. Laboratories may choose from whole-genome NGS methods or more targeted methods. Furthermore, there are evolving regulatory requirements, a lack of test standardization around the world, and few validation studies targeting rare disorders. Clinical laboratory directors also need to anticipate the complexities of interpreting results from an inconclusive finding or disentangling biological considerations such as placental mosaicism from analytical performance considerations. However, NIPT is still a screening test, and thus confirmation by amniocentesis or chorionic villus sampling and diagnostic testing is required.
In this webinar, expert panelists, Jillian Buchan, PhD FACMG; Glenn Palomaki PhD; Kaarel Krjutškov PhD; and Russell Garlick, PhD will discuss recent experiences adopting NIPT testing for routine use, designing and executing complex validation studies, and interpreting unexpected results.
Panelist presentations will be followed by a discussion of current topics and audience questions.
Sponsored by Tecan
The use of next-generation sequencing (NGS) technologies in the field of infectious diseases has transformed the way pathogens are detected and characterized. Metagenomic sequencing provides a comprehensive and high-resolution analysis of microbial genetic material including bacteria, fungi, viruses, and parasites that is independent from microbial culture. The main challenge of developing a metagenomic sequencing assay is the efficient and unbiased recovery of microbial nucleic acids from degraded samples.
The Karius Test is a liquid biopsy that can non-invasively and rapidly detect over 1,000 pathogens from a single blood sample. When developing the Karius Test, scientists at Karius not only encountered challenges unique to metagenomics but unique to the biomarker that makes the test non-invasive; microbial cell-free DNA (mcfDNA). These challenges include working with degraded samples, unbiased detection of all mcfDNA in the sample, removing host and contaminant nucleic acid, and a streamlined workflow that accommodates a fast turnaround time. Tecan’s patented NGS library preparation technologies have supported laboratories like Karius to develop transformative genomic assays that uncover insights from even the most challenging samples.
In this webinar, Dr. Tim Blauwkamp, Chief Scientific Officer at Karius will discuss:
- Challenges in developing a cell-free DNA metagenomic sequencing assay.
- Approaches to solving these challenges for a liquid biopsy test for infectious diseases.
- Collaboration with Tecan to recover fragments efficiently and without bias in degraded samples.
Tecan genomics reagents are for Research Use Only. Not for diagnostic procedures.
The Karius Test was developed and its performance characteristics determined by Karius. This test has not been cleared or approved by the FDA, nor is it required to be. The Karius laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA ‘88) and is accredited by the College of American Pathologists (CAP) to perform high-complexity clinical laboratory testing.
Sponsored by PerkinElmer
Liquid biopsy assays that analyze circulating tumor DNA in a cancer patient's blood stream have gained traction in recent years, presenting an attractive alternative to current methods for measuring treatment response, monitoring relapse, and predicting outcomes.
With ctDNA testing becoming more established in therapy selection for advanced cancer, the field is now poised to break into new areas, such as the detection of minimal residual disease (MRD) in early-stage patients. Our panel of pioneers in the field of cell-free cancer DNA testing will discuss the latest developments in ctDNA analysis and provide examples of its evolving use in colorectal, breast, lung, and other cancer types.
Sponsored by Seqera Labs
In this webinar, Phil Ewels, team leader for bioinformatics development at the National Genomics Infrastructure (NGI) at SciLifeLab, Brendan Bouffler, head of developer relations, HPC Engineering at Amazon Web Services, and Evan Floden, CEO of Seqera Labs, will discuss and demonstrate how bioinformaticians and data practitioners can create, manage and optimize their data pipelines with cloud-based systems, increasing productivity, reducing the need to manage IT infrastructure, and ultimately allowing them to do more science.
Nextflow enables users to seamlessly run and scale reproducible genomics workflows locally, on high-performance computing (HPC) clusters, or on major cloud providers’ infrastructure. Developed since 2014 and backed by a fast-growing community, the Nextflow ecosystem is made up of users and developers across academia, government, and industry.
Sponsored by Glen Research
Spherical nucleic acids (SNAs) are typically composed of nanoparticle cores with densely functionalized and radially oriented shells composed of short (~10-30mers), synthetic nucleic acids. This novel three-dimensional architecture imparts conjugate properties that make SNAs extremely useful in biomedicine, due in part to their ability to bind complementary strands orders of magnitude more tightly than linear nucleic acids of the same sequence and their ability to enter cells in high quantities without transfection agents. SNAs are highly modular; they have been prepared with dozens of different cores, including biocompatible liposomes and proteins, and with an almost limitless variety of nucleic acid types and sequences, owing to solid-phase chemical synthesis techniques.
In the case of SNA-based vaccines, immunostimulatory oligonucleotides (adjuvants) compose the shell, with specific and even multiple types of antigens incorporated into the SNA shell or core, allowing access to a range of innate and adaptive immune responses and pathways. The discovery that the chemical structure of an SNA conjugate can transition a vaccine from mildly effective to curative has set the stage for a new field of rational vaccinology. This discovery also poses a pressing question: if a target has failed out of clinical trials previously, was it because the composition was incorrect, or was it simply delivered in the incorrect structure? Speaker Chad A. Mirkin and colleagues are answering this question in the context of devastating diseases such as cancer and COVID-19.
In this webinar, attendees will learn how synthetic oligonucleotides:
- Enable the restructuring of medicines on the nanoscale.
- Permit new and usual interactions that are changing how diseases are studied, tracked, and treated.
- Enable rapid clinical translation for the benefit of patients.