GenomeWebinars: Recent

The diagnostic process for hematologic malignancies can be complex and time consuming; it includes morphological analysis of bone marrow and peripheral blood, immunohistochemistry, flow cytometry, cytogenetics and, under certain circumstances, additional testing.

Starting with morphology, flow cytometry, and cytogenetics can help reduce unnecessary or duplicative testing that may not be covered by insurance. Additional testing can then be performed if recommended by guidelines or if results are inconclusive. This workflow requires close collaboration between clinicians and laboratory staff but enables more timely and efficient diagnostic and prognostic information to help guide treatment decisions.

In this webinar, Girish Kunapareddy, clinical assistant professor of medicine at Indiana University School of Medicine, and Stephanie McAlhany, medical director at Labcorp Oncology’s Brentwood Laboratory, will review a case and discuss how clinicians and laboratory staff can work together to alleviate complexities in the diagnostic process for hematologic malignancies.

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.

New short-read sequencers, characterized by improved read quality, are reaching the market. Yutaka Suzuki and colleagues in the Department of Computational Biology and Medical Sciences at the University of Tokyo have installed and started operating an AVITI sequencer from Element Biosciences, producing read quality data exceeding Q40 (error rate: 0.01 percent).

In this webinar, Suzuki will discuss how the team compared AVITI sequencing results with their conventional sequencer to confirm its performance in mRNA-seq, single-cell RNA-seq, whole-genome sequencing, and panel sequencing, obtaining strong correlations between results. Panel sequencing confirmed low-frequency mutations in peripheral blood mononuclear cells (PBMCs) from healthy elderly individuals in genes associated with clonal hematopoiesis, requiring high confidence in the sequencing reads. Suzuki will also share results from a new sequencing kit from Element called Cloudbreak UltraQ, which increases read quality from Q40 to Q50 (error rate: 0.001 percent).

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.

The transcriptional expression of tumor genomes is exceptionally complex and often driven by extensive structural variation. Key oncogenic drivers can result from gene fusions of proto-oncogenes with novel fusion partners that can be difficult to detect by DNA sequencing alone, making RNA-seq an essential step in somatic tumor profiling approaches. More recently, expressed nongenic “dark matter” in tumors has also been hypothesized as a rich source of cancer neoantigens that may direct antitumor responses. However, a current challenge in enabling routine tumor RNA-seq is the standard use of formalin-fixed paraffin-embedded (FFPE) tissue preservation that causes damage to RNA molecules and can result in poor sequencing quality.

In this webinar, Brian Piening, technical director of clinical genomics at the Providence Molecular Genomics Lab, will describe approaches for unbiased whole-transcriptome profiling in FFPE tissues and describe some key applications of this technology for answering novel questions in cancer biology.

This webinar will cover:

• Lessons learned from the implementation of an FFPE RNA sequencing pipeline.
• Challenges in RNA sequencing with FFPE samples and methods for overcoming those challenges.
• The value of whole-transcriptome sequencing for characterizing fusions.
• RNA sequencing of tumor dark matter and validation with mass spectrometry-based proteomics.
• Key considerations when implementing clinical RNA sequencing pipelines.

In this webinar, three experts in cancer testing and therapeutics will explore the pivotal role of minimal residual disease (MRD) testing in the development of oncology drugs.

Chih-Yi Hsieh, executive vice president and chief medical officer at Impact Therapeutics, Johannes Nippgen, chief medical officer, Ionova, and Zhihong Zhang, director, CTO, and general manager at Burning Rock Dx will discuss how precise MRD diagnosis can revolutionize personalized treatment strategies for cancer patients.

The speakers will discuss:

• Recent Advancements: The newest MRD detection technologies and methodologies and the latest research advancements in this field.
• Patient Care: How MRD technology enhances cancer diagnosis and guides clinical treatment, offering a non-invasive method for monitoring cancer progression and treatment response.
• Drug Development: The influence of MRD on the direction of oncology drug development and its implications for future therapies.

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.

Memorial Sloan Kettering’s Single-Cell Analytics Innovation Lab (SAIL) is a leading platform for cutting-edge molecular profiling and data analysis serving the broader MSK community. Since its inception in 2017, SAIL has grown to serve more than 100 laboratories spanning basic and translational research. Its mission is to assimilate emerging technologies in the rapidly advancing fields of single-cell sequencing and imaging-based profiling and provide robust analytical solutions.

In addition to an experienced laboratories team, SAIL hosts a dedicated computational team that benchmarks new tools and generates pipelines to support an expanding set of technologies and data modalities. SAIL technologies have been applied to a spectrum of pressing basic and translational research questions at MSK, including the study of developmental processes, metastasis, immunotherapy, and wound healing.

In this webinar, Ronan Chaligne, director of SAIL, will introduce the lab’s most recent efforts in optimizing single-cell and spatial methods and improving clinical sample tissue preparation.

Traumatic brain injury (TBI) remains a significant health concern, demanding a deeper understanding of its complex molecular mechanisms. Single-cell and spatial transcriptomics methods have emerged as valuable tools to analyze the intricate cellular and spatial changes within TBI.

In this webinar, Michelle Theus and Caroline de Jager from Virginia Tech will describe the advantages of utilizing both single-cell and spatial-resolution transcriptomics to elucidate relevant biological pathways altered by traumatic brain injury. They will also share results of single-cell and spatial sequencing of the injured murine cortex, showcasing transcriptome level changes and biological targets in TBI research.

To date, liquid biopsy testing has largely been provided by large centralized CLIA reference laboratories. To help maximize global access to liquid biopsy and associated targeted therapies, biopharmaceutical organizations are interested in establishing diagnostic partnerships to drive liquid biopsy testing at local and regional laboratories, leveraging in-house NGS platforms to provide testing closer to patients, enabling more timely, efficient, and cost-effective care.

In this webinar, John Longshore, head of scientific affairs for global oncology diagnostics at AstraZeneca, and Pantelis Constantoulakis, the scientific director at Genotypos Science Labs, will discuss:

1. The importance of liquid biopsy testing in guiding access to precision therapies and clinical trials.
2. The challenges faced by global pharmaceutical companies regarding patient access to liquid biopsy and new strategies to improve access.
3. A laboratory evaluation of the performance, workflow, and cost of Pillar Biosciences’ suite of kitted liquid biopsy-based assays.

Enabling global access to precision medicine with liquid biopsy CGP testing has been challenging. Obstacles include standardizing a complex liquid biopsy testing workflow globally and varying regional healthcare guidelines and regulatory policies.

In this panel discussion, Jean-Francois Martini, head of biomarker clinical assay and technology at Pfizer, and Lawrence Wang, chief financial officer at Adicon, will take a deep look into challenges, considerations, and breakthroughs in enabling access to the China population for global clinical trials. Vafa Amirkia, Guardant Health’s director of biopharma business development in China, will lead the discussion.

Following the discussion, Simranjit Singh, CEO of the Asia, Middle East, and Africa (AMEA) regions at Guardant, will highlight how the company has successfully enabled in-country access to their robust, validated liquid biopsy technology for patients around the world.

The discussion and presentation will be followed by an audience Q&A.

Respiratory testing decisions can be impacted by patient type (immunocompromised, pediatric, pregnant, elderly), patient risk (inpatient, outpatient, travel history, geography), and time of year (incidence of different respiratory viruses throughout the year). These unique attributes necessitate flexible testing algorithms to best serve varied patient populations and changing respiratory testing needs throughout the year. Additionally, streamlined workflows for respiratory testing can potentially decrease costs, hands-on time, and FTEs needed to process all samples in the laboratory.

In this webinar:

• Rangaraj Selvarangan, director of the microbiology laboratory at Children's Mercy Hospital, will present clinical trial data on a recently FDA-cleared molecular test for respiratory viruses that detects and differentiates SARS-CoV-2, influenza A, influenza B, and RSV.
• Jim Dunn, director of the medical microbiology and virology laboratories at Texas Children's Hospital, will review the respiratory testing algorithm used at the hospital, discussing how test ordering is modified throughout the year to accommodate seasonality, how different platforms are utilized to best serve patients, and how flexible testing platforms allow for optimal management of diagnostic stewardship.
• Matthew Binnicker, medical director of the clinical virology laboratory at Mayo Clinic, will discuss the respiratory testing algorithm employed by a large reference laboratory with a diverse patient population, including a result masking strategy to accommodate different test order combinations. He will also review the 2023-2024 winter respiratory season experienced at Mayo Clinic and provide his perspective on what respiratory viral activity we might see in the year ahead.

Molecular testing for use at home and the point of care has boomed in the wake of the COVID-19 pandemic, and sexually transmitted infections have been a key area of focus for test developers and manufacturers after respiratory testing. Companies large and small have emphasized the importance of molecular point-of-care STI testing, particularly in light of rising rates of sexually transmitted infections in the US.

Now that molecular point-of-care testing technology has continued to advance, what are test users looking for in their tests and platforms, particularly when it comes to turnaround time or multiplexing? Where should test developers focus their efforts? How does molecular testing at both the point-of-care and at home fit in with other options for testing? What changes are on the horizon in the next three years as technology continues to develop?

In this virtual roundtable, our panel of experts on sexually transmitted infections and molecular point-of-care testing will discuss these questions. Our expert panelists include Jeffrey Klausner a clinical professor of medicine in infectious diseases at the University of Southern California; Thomas Schaus, head of R&D and scientific cofounder at molecular diagnostic company 3EO Health; Barbara Van Der Pol, professor of medicine and public health at the University of Alabama at Birmingham and director of the UAB STD Diagnostics Laboratory; and Yukari Manabe, professor of medicine and director of the Center for Innovative Diagnostics for Infectious Diseases at Johns Hopkins University.

This webinar presents an in-depth look at how Memorial Sloan Kettering Cancer Center (MSK) is routinely using its molecular assays — MSK-IMPACT and MSK-ACCESS — together to inform precision oncology approaches.

MSK-IMPACT is a targeted tissue-based sequencing test for comprehensive genomic profiling. MSK-ACCESS is a liquid biopsy test that enables non-invasive profiling and longitudinal disease monitoring. Together, they provide robust insights that help guide treatment decisions for improved outcomes in patients with advanced cancer. Unlike most tests, MSK leverages matched tumor-normal sequencing to remove germline and clonal hematopoietic variants, revealing genomic alterations of true somatic origin.

In this webinar, A. Rose Brannon, director of clinical bioinformatics at MSK, and Anita S. Bowman, associate director of clinical bioinformatics at MSK, will:

• Highlight the benefits of matched tumor-normal sequencing to reduce biological false positives.
• Discuss the clinical utility of combining tissue- and cell-free DNA-based sequencing approaches, with insights from real clinical cases.
• Explore opportunities for clinical, translational, and basic research.