GenomeWebinars: Recent

A unique nationwide pilot implemented across Israel has demonstrated that rapid precision medicine based on genome sequencing can benefit critically ill babies, ensuring advanced and equitable care for neonates. Through this pilot, called “Project Baby Bambi,” rapid trio whole-genome sequencing (rtWGS) yielded fundamental information that influenced clinical decision making and ultimately saved lives. Due to the success of the program, the decision was made to enable rtWGS access for critically ill neonates suspected of having a genetic condition in Israel, and a new pilot was designed for critically ill children in Israeli pediatric ICUs (Bambi4Kids).

Over 15 months, Project Baby Bambi: 

• Completed rapid WGS on 130 trio cases of critically ill neonates of diverse ancestry and clinical conditions with a suspected genetic origin.
• Sequenced and analyzed samples in a single center, the Tel Aviv Sourasky Medical Center (TLVMC) Genomics Center.
• Provided diagnoses for 65 babies, with an additional 14 cases showing a variant of unknown significance (VUS) suspected to be causative.
• Led to a change in the management of 24 babies, among whom immediate precision medicine was offered for six of the diagnosed infants (n=65). An additional two received palliative care and two were transferred to nursing homes.
• Achieved a mean rapid turnaround time of 7 days.
• Diagnosed 22 different rare conditions, including a novel candidate gene.

In this webinar, Daphna Marom, deputy director of The Genetics Institute and Genomic Center, Tel-Aviv Sourasky Medical Center and chief of pediatric and adult genetics service, will present the project’s findings followed by a panel discussion on the project and its impact on the clinical practice with Hagit Baris Feldman, director of the Genetics Institute and Genomic Center at Tel Aviv Sourasky Medical Center, former chair of the Israeli Medical Geneticists Association and associate professor at Tel Aviv University, Amihood Singer, community genetics researcher and the head of the community genetics department at the Israeli Ministry of Health, Smadar Eventov-Friedman, director of the department of neonatology at Hadassah hospital,  Arieh Riskin, head of the neonatology department at the Bnai Zion Medical Center and chairman at The Israel Neonatal Society, and Maria Martinez-Fresno, director of medical affairs, for genetic disease and reproductive health, in Europe at Illumina.

This panel discussion on using methylation-based ctDNA testing for MRD and response monitoring in clinical trials will feature three experts in drug and biomarker development: Minakshi Guha, associate director of liquid biopsy strategy and precision and translational medicine at Takeda Pharmaceuticals; Jonathan Beer, senior director of diagnostic sciences at Bristol Myers Squibb; and Diana Merino Vega, senior director of cancer biomarker development at AstraZeneca.

The panelists will discuss how MRD and response monitoring using liquid biopsy can accelerate drug development by:

• Enhancing patient enrollment by reducing trial sizes and costs, improving cohort quality and statistical power of clinical studies.
• Providing early therapy response monitoring through serial testing that monitors tumor dynamics more effectively than standard imaging, predicting therapy response about eight weeks earlier.
• Expediting study evaluation with ctDNA levels that also serve as surrogate markers for dose optimization and efficacy endpoint determination. 

Kimberly Banks, vice president of global scientific affairs at Guardant Health, will moderate the discussion and will close with a brief presentation on Guardant Infinity, a methylation-based tissue-free approach to ctDNA detection and quantification for sensitive and more precise MRD detection and response monitoring.

Measurable Residual Disease (MRD) is a crucial biomarker for analyzing and tracking tumor evolution, evaluating treatment effectiveness, and predicting relapse in acute myeloid leukemia (AML). Among the various technologies used to detect MRD, next-generation sequencing (NGS) stands out for its exceptional sensitivity and specificity. Guidelines from the European LeukemiaNet provide recommendations for MRD assessment, including the use of NGS, to ensure consistency and reliability in clinical practice. However, NGS faces challenges, particularly related to its limit of detection (LOD). The intrinsic error rate of NGS can interfere with the clear discrimination of target signals from background noise, making it difficult to detect very low levels of MRD. This limitation necessitates careful standardization of bioinformatics pipelines to ensure accurate results.

In this webinar, Silvia Salmoiraghi, biologist at the Ultra-Specialist Laboratory of Clinical Pathology-Hematology, at ASST Papa Giovanni XXIII Hospital in Bergamo, Italy, will discuss the performance of the Sophia DDM Residual Acute Myeloid (RAM) Solution.

Salmoiraghi will cover:

• The process of evaluating and implementing this new capture-based NGS application.
• The accurate detection of MRD while assessing multiple biomarkers.
• The advantages of adopting an NGS-based application compared to other technologies.

The US Food and Drug Administration’s new final rule regulating laboratory-developed tests (LDTs) will be phased in over a five-stage ramp up over the next four years. In this webinar, John Hanson, VP of customer success at Blackhawk Genomics will provide a concise review of the rule and its milestones, then discuss various considerations labs should keep in mind as they navigate compliance, focusing on the first three phases of the new regulations. Hanson will bridge the gap between understanding the rule and taking actionable steps to help meet compliance requirements.

Key Takeaways:

• A clear understanding of the FDA’s final rule and its implications for LDTs.
• Process-based guidance to clarify compliance requirements for the first three phases.
• Practical strategies that can be implemented right away.
• Confidence that tools and support are available for your lab to navigate the new regulation.

As next-generation sequencing keeps making inroads in the field of oncology, there are practical considerations for its implementation in clinical labs.

In this virtual roundtable discussion, leading experts Tracy Stockley from the University of Toronto, Nicole Pfarr from the Technical University of Munich, Yi Ding of Geisinger Health and Ravindra Kolhe, from the Georgia Cancer Center will explore pitfalls and best practices for cancer NGS workflows. From sample preparation to the pros and cons of panels versus whole-exome or whole-genome testing to variant analysis and interpretation, this discussion will delve into challenges and solutions in this ever-evolving field.

Additionally, we will explore how emerging technologies, such as long-reading sequencing, may shape NGS cancer testing moving forward.

Targeted therapies have expanded treatment options for diseases like non-small cell lung cancer. While NGS-based tumor profiling can detect multiple targetable alterations from limited tissue, many settings employ only single-variant and single-gene analysis. Improved detection of amplifications and gene rearrangements can provide more complete tumor characterization to identify all possible therapies.

This white paper from Labcorp presents data showing that comprehensive genomic profiling with PGDx elio tissue complete demonstrates high concordance with conventional diagnostic approaches for ALK gene rearrangements and provides greater insight into the underlying genomic events and genomic co-alterations that may impact clinical outcomes.

BostonGene is a CLIA/CAP certified next-generation sequencing (NGS) lab specializing in whole-exome and RNA sequencing, supporting institutions in interpreting complex NGS data. The lab, founded in 2015, collaborates with cancer centers and foundations to pioneer technologies for developing and validating novel precision medicine approaches.

Automating NGS library preparation and target enrichment is crucial for labs conducting complex NGS testing. In this webinar Jessica Scher, senior research associate in NGS automation at BostonGene, will showcase how BostonGene employs multiple automation solutions to improve accuracy, efficiency, and scalability. The presentation will explore the impact of increased sample throughput on each step of the workflow, including sample preparation, quality control (QC), library prep, and enrichment. Attendees will learn how to scale up with automation while maintaining data quality and consistency.

Attendees will learn how to:

• Streamline NGS library preparation and target enrichment workflows, including sample QC, with automation solutions.
• Achieve reliable sample quality and reproducible results using automated, integrated NGS solutions for library prep and enrichment, and sample quality control.
• Address high-throughput NGS lab challenges with the Agilent Bravo NGS Workstation.
• Complement the Bravo NGS Workstation with the fully walkaway Agilent Magnis NGS Prep System for a streamlined workflow to run complex NGS assays for various sample types.

The US Food and Drug Administration’s recently issued final rule on laboratory-developed tests, or LDTs, marks a major change in the clinical testing landscape as it formally brings these tests under the agency’s oversight. Much discussion of the FDA rule has focused on the challenges and disruptions it could bring to clinical labs, but the rule and its requirements are likely to affect in vitro diagnostic companies as well, potentially altering their relationships with their lab customers and creating new competitive dynamics.

Please join us to hear three experts discuss how the FDA’s LDT rule could impact IVD vendors: Jonathan Genzen, CMO and medical director of automation at ARUP; Donna Hochberg, partner with Health Advances; and Zach Rothstein, executive director at AdvaMedDx.

The panelists will discuss the FDA rule, the challenges it presents to clinical laboratories, and the ways clinical labs may look to their IVD vendors for help in navigating these challenges.

Proteomics represents an unparalleled information source for understanding human health —including the impact of behaviors and pathology — because protein network patterns are downstream of genetic inputs and environmental changes. Deciphering these networks requires generating many measurements in parallel with sufficient statistical power to detect subtle effects. But often, making more measurements raises the chance of false discoveries, which can reduce the impact of findings. Thus, sensitivity to change and target specificity are of paramount importance in proteomic platforms as they expand and scale.

In this webinar, Stephen Williams, chief medical officer at Standard BioTools, will explore how flexibility in oligo design and the quality of oligonucleotides enhance microarrays, transforming them into advanced tools for many applications requiring ease of use, reproducibility, and sensitivity. He will present metrics from the SomaScan Assay as an example and discuss applications in discovery and clinical trials. Valentina Maran, senior product manager in the microarrays diagnostics and genomics group at Agilent, will join Williams to discuss how Agilent’s array platform has enabled the development of the SomaScan Assay, which profiles 11,000 protein measurements in a 55-μL sample.

Advances in biomarker testing, analytical methods, and real-world datasets (RWD) that include biomarker and clinical data are rapidly enhancing precision oncology, enabling both forward and reverse translation and allowing for more effective patient-specific treatments. These innovations play a crucial role in drug development, as well as clinical, payor and regulatory decision making. However, it's crucial to consider the strengths and limitations of different approaches and datasets when designing analyses and interpreting precision oncology data.

In this webinar, Milan Radovich, chief scientific officer at Caris Life Sciences, Professor Charu Aggarwal, from the University of Pennsylvania, and Neal Meropol, vice president of research oncology at Flatiron Health, will explore the evolving state of precision oncology research and the pivotal role that high-quality linked clinical and multiomic RWD plays in accelerating all stages of drug development to maximize the success of novel therapeutics. The webinar will be moderated by Flatiron’s Kristin Zimmerman Savill, director of scientific engagement for precision oncology.

The speakers will discuss:

• The rapidly evolving state of precision oncology research.
• Key considerations for different methodological approaches and datasets when designing or interpreting data from precision oncology research.
• Case studies highlighting how RWD can be used more effectively in precision oncology research to drive the development of novel and effective therapies, guide clinical, payor and regulatory decision-making, and improve patient outcomes.

With over 1,500 clinical trials incorporating liquid biopsy testing, the use of ctDNA monitoring is rapidly expanding. Initially used to identify acquired resistance variants, ctDNA is now crucial for evaluating residual disease and assessing molecular responses to therapies, such as antibody-drug conjugates, or ADCs. This allows for quick decision-making in translational research.

In this webinar, Jonathan Beer, senior director of diagnostic sciences at Bristol Myers Squibb, will share the pharmaceutical sector’s perspective on the multifaceted applications of ctDNA. Learn how ctDNA aids in selecting therapy based on specific biomarkers and offers early insights into molecular response.

Christine Petersen, director of business development at Foundation Medicine, will present new data from the FoundationOne Monitor ctDNA monitoring assay and its potential for enabling researchers and drug developers to gain insights using ctDNA throughout clinical programs.¹ She will also report on how biopharma partners have used FoundationOne Monitor to optimize dose selection for new therapies in early-phase trials and add value beyond standard pharmacodynamic analysis.

The speakers will:

• Explore ctDNA monitoring applications in biopharmaceutical drug development.
• Examine case studies highlighting ctDNA's impact in clinical trials.
• Introduce FoundationOne Monitor, a tissue-naive test for ctDNA monitoring
• Reveal how ctDNA can enhance drug development strategies.  

1. For Investigational Use Only. The performance characteristics of this product have not been established.

US-F1M-2400006

Climate change, zoonotic disease outbreaks, and antibiotic resistance are escalating global crises that demand a rapid, accurate, and scalable diagnostic infrastructure, highlighting the critical role of molecular diagnostics in both detection and prevention within today's public health strategies. While quantitative real-time PCR (qPCR) has become the benchmark technology for detecting pathogens due to its exceptional sensitivity, specificity, and accuracy, time-consuming workflows and high costs pose significant limitations. One factor contributing to these limitations is that both assay designs and the basic protocols used for qPCR testing have remained largely unchanged over the past three decades.

In this webinar, Stephen Bustin, professor of molecular medicine at Anglia Ruskin University, will explain the concept underlying FlashPCR, a combination of novel assay design, reagents, and low ∆T amplification that reduces the time required for PCR amplification. This breakthrough retains the high sensitivity and specificity characteristic of traditional qPCR-based diagnostics while making it ideally suited for point-of-care testing environments.

Additionally, Stephen Bustin will discuss a modification that can help reduce the complexity of the PCR protocol by using a single defined low denaturation temperature, enabling the completion of qPCR assays in as fast as two minutes. These innovations represent a significant leap forward in molecular diagnostics, offering the potential to allow significant changes in support of timely clinical decision making, lower the cost of testing, and improve patient outcomes in diverse healthcare settings in the future.

In this webinar, Rui Chen, director of the Center of Single Cell Omics at Baylor College of Medicine, will report on the generation of a comprehensive atlas of full-length transcript isoforms in the mouse retina at the single-cell level using long-read single-cell RNA Sequencing. Chen’s team profiled approximately 30,000 mouse retina cells using a combination of 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore long reads.

Important findings:

• Results in gene expression and cell annotation between long-read and short-read datasets were comparable. The lab’s results indicate that single-cell long-read RNA sequencing alone would be sufficient to capture the information.

• Leveraging long-read scRNA-seq, the lab detected a total of 44,325 transcript isoforms, among which over 16,000 are novel. Furthermore, the team pinpointed 7,383 isoforms exclusive to specific cell classes, a considerable portion of which were novel.

• Isoform usage patterns varied among different cell classes and subclasses.

• A total of 1,055 intra-chromosomal gene fusions were detected within the mouse retina.

With increasing antimicrobial resistance, providing rapid antibiotic susceptibility testing (AST) results to clinicians treating bacteremia patients is becoming ever more important. Hopefully, such fast, potentially life-saving answers will soon become the standard of care for these seriously ill patients.

In this webinar, speakers from two US clinical microbiology labs will discuss their evaluation of ASTar, a recently FDA-cleared high-throughput fully automated rapid AST system for Gram-negative blood cultures. They will describe their motivation for exploring rapid AST options for positive blood cultures, their labs’ experience with ASTar’s usability, and the timing and accuracy of its results compared to legacy AST methods. They will also discuss retrospective chart reviews of patients to examine the potential clinical impact of faster AST results for patients with bacteremia and sepsis.

In this webinar, Lina Shao, clinical professor of pathology and pediatrics at the University of Michigan, will discuss cytogenomic studies for detecting acquired abnormalities in hematological malignancies and solid tumors, focusing on chromosomal microarray analysis in B-cell acute lymphoblastic leukemia (B-ALL) and central nervous system tumors.

Attendees will learn:

• The important role of cytogenomic studies in hematological malignancies and solid tumors.
• The WHO-defined genetic abnormalities in B-ALL and essential genetic abnormalities in oligodendroglioma.
• How chromosomal microarray analysis (CMA) provides a whole-genome view and identifies intrachromosomal amplification of chromosome 21 (iAMP21)  in B-ALL and 1p/19q co-deletion in oligodendrogliomas more accurately than targeted assays.
• The importance of CMA with an SNP component in distinguishing hyperdiploidy from masked near-haploidy or low-hypodiploidy, which have opposite prognoses in B-ALL.