GenomeWebinars: Recent

Precision oncology approaches have made great strides harnessing individual tumor mutation profiles to guide targeted therapy choices. However, deeper molecular insights are needed to improve personalized treatment decisions that are tailored to specific molecular characteristics of a tumor. Integrating gene expression analysis in personalized oncology provides an additional level of insight that cannot be provided by genomic data alone. These analyses include evaluating expressed mutations and drug targets, novel gene fusions, clinically relevant signatures, and the tumor immune microenvironment (TME).

Comprehensive molecular tumor analysis (CMTA) is an NGS-based tumor diagnostic test developed by Alacris Theranostics. The test integrates whole exome and transcriptomic sequencing (WES and RNAseq) and is deployed as an end-to-end accredited diagnostic platform from tumor sample uptake (FFPE or frozen) to personalized clinical interpretation reports. Designed to serve all cancer patients, CMTA is a tumor-agnostic test that displays a unique molecular view of each sample and is particularly well-suited to refractory cancers with complex patterns or tumors of unknown origin.

In this webinar, Alacris Theranostics will discuss the benefits of comprehensive tumor profiling in clinical settings and present the strategy implemented in their bioinformatics pipeline to identify cancer-relevant somatic events. In addition, the diagnostic company will share how they use QIAGEN Clinical Insight (QCI) Interpret to annotate variants and identify potential therapeutic entry points.

Chronic lymphocytic leukemia (CLL) is a slow-developing, incurable leukemia. The availability of multiple diagnostic tools and platforms enables the identification of the disease and disease time course as well as better-informed treatment decisions. With the advent of advanced multiparameter flow cytometric (MFC) assays, CLL-specific molecular biomarkers may provide predictive and prognostic information, permitting population stratification into subsets defined by disease progression, response to therapy, etc.

In this session, Joseph Annunziata of Kindred Healthcare will discuss diagnostic and measurable residual disease (MRD) monitoring approaches to CLL and the benefits of predictive and prognostic assessments using multimodality peripheral blood analyses. Moreover, this talk will include an emphasis on the role of MRD in CLL drug development.

During this webinar, Annunziata will:

1. Compare various diagnostic approaches for CLL.
2. Highlight the predictive and prognostic benefits of molecular testing for CLL.
3. Assess MRD methods for long-term monitoring in CLL patients.
4. Explore the advanced role of MFC-based CLL MRD in drug research and development.

The PAOLA-1/ENGOT-ov25 Phase III trial is a first-line-treatment study for advanced ovarian cancer which showed that the maximum benefit of the PARP inhibitor olaparib plus bevacizumab maintenance is observed in patients with homologous recombination-deficient (HRD) tumors.

In this webinar, Pascal Pujol of the University of Montpellier will describe a retrospective clinical evaluation — using PAOLA-1 data — of an HRD scoring solution based on low-coverage and cost-effective whole-genome sequencing (WGS). The SeqOne HRD solution combines genomic instability and CCNE1 gene amplification features extracted from WGS, as well as pathogenic mutations in BRCA 1/2 genes. Pujol will describe dilution experiments that determine the lower limit for sequencing coverage and tumoral content. The clinical evaluation of 368 patients from the PAOLA-1 trial included progression-free survival (PFS) data and comparisons with the MyChoice CDx test. The evaluation found the SeqOne HRD solution to be cost-effective and efficient with a low tumoral content while being flexible by accommodating different lab configurations.

Pujol will be joined by Michael Blum, director of research and development at SeqOne, who will describe the SeqOne approach to HRD testing.

Multiplex NGS panels are emerging as the standard-of-care solution for genomic profiling in myeloid neoplasms including myelodysplastic syndrome, myeloproliferative neoplasms, and acute myeloid leukemia. Wojciech Swat, the medical director of the cancer genomics and molecular pathology divisions at GenPath, uses rapid-throughput NGS research panels leveraging anchored multiplex PCR (AMP) technology to assist hematopathology colleagues in their morphologic evaluations of myeloid malignancy in bone marrow biopsies. Such panels help in diagnosis, risk stratification, prognosis, and longitudinal tracking of malignant clones. Genomic profiling by NGS can significantly streamline laboratory workflows, provide comprehensive assessments with vastly reduced TATs, and improve analytic sensitivity and specificity in comparison with traditional testing methodologies such as PCR/fragment analysis and Sanger sequencing.

During this presentation, Swat will talk about his experience at GenPath laboratories with the rapid-throughput, multiple-panel Archer VariantPlex Myeloid and FusionPlex Myeloid Research Use Only (RUO) Assays, which are capable of delivering results in two days, can track the MRD of specific clones, and can detect the emergence of subclones with variant allele frequencies as low as 0.1 percent.

Involving a transfer-to-manufacturing team in the IVD device design process early on increases the probability of successfully transferring a medical device design to production. Additionally, concurrent engineering and regulatory activities will drive shorter development times, reduced production costs, and improved product quality.

The transition from low-volume pilot lines to fully automated manufacturing requires the effort of a highly skilled technology transfer team to determine scale-up parameters, establish correct methodologies, and design specialized process equipment. ISO-certified and flexible manufacturing assets able to adapt to production ramps are also strategically important. These integrated capabilities dramatically reduce the risk in technology transfer while simultaneously increasing the success of product commercialization.

In this roundtable discussion, industry experts in IVD operations, transfer to manufacturing, and regulatory will discuss challenges and needs for a well-managed transition to production and considerations for selecting a strategic partner that unites the full suite of regulatory, development, and manufacturing services to avoid undesirable outcomes such as product redesigns, low manufacturing yields, or unexpected increased cost.

The SARS-CoV-2 pandemic required an exponential increase in the sequencing capacities of epidemiological laboratories monitoring the virus.

In this webinar, Quentin Semanas and Richard Chalvignac of Hospices Civils de Lyon will discuss the miniaturization and automation of SARS-CoV-2 sequencing in their lab. Their protocol has made it possible to multiply sample processing capacity by 52 percent, allowing them to sequence up to 5,000 samples per week in the epidemic peak phases.

In the wake of the COVID-19 pandemic, many non-COVID respiratory pathogens are demonstrating a resurgence. Influenza and respiratory syncytial virus (RSV) in particular are both demonstrating increasing positivity.

RSV is the most common single cause of respiratory hospitalization of infants and is the second largest cause of lower respiratory infection mortality worldwide. This year RSV rates are exceeding the usual number of cases, exacerbated by the immunity gap of the SARS-CoV-2 pandemic. As a result, healthcare resources are being stretched, creating new challenges.

This webinar will provide an overview of the current respiratory disease landscape from the perspective of clinicians working in diagnostics and patient care.

Our speakers will:

• Provide an update on COVID-19 testing and treatment trends
• Highlight clinical considerations for influenza and RSV resurgence post-pandemic
• Discuss what increasing positivity of non-COVID respiratory pathogens means for labs and healthcare systems this respiratory season

Clinical expectations for BCR-ABL monitoring have evolved over time both in response to more sensitive tests being developed and new treatments and management approaches emerging. Largely in response to these medical advances, many CML patients have been able to successfully manage their diseases over time, as evidenced by increasing long-term survival rates. Chronic management of an increasing population of CML patients, however, places unique pressure on supporting laboratories, requiring that testing become sensitive enough to support a broad spectrum of clinical decisions while also being scalable to accommodate an ever-increasing number of tests.

This on-demand webinar from Asuragen discusses how the CE-IVD-certified QuantideX qPCR BCR-ABL IS Kit can overcome challenges in CML monitoring, providing a simple, sensitive, and scalable approach to BCR-ABL monitoring that meets today’s clinical expectations for testing.

Hosted by Justin T. Brown, principal scientist of research and development at Asuragen, the webinar covers:

• How molecular monitoring fits within CML practice guidelines and how that continues to evolve and add incremental burden to laboratories.
• Key performance data for the QuantideX qPCR BCR-ABL IS kit and how it exceeds monitoring requirements while maintaining operational efficiency.
• Why CML management during the COVID-19 pandemic requires continued monitoring.

In this on-demand webinar from Asuragen, Dolors Colomer of the hematopathology section at Hospital Clinic Barcelona presents her perspective on the QuantideX qPCR BCR-ABL IS Kit as a simple, sensitive CE-IVD solution for BCR-ABL monitoring.

Chromosomal microarray analysis (CMA) is a well known first-tier molecular cytogenetics test helping to identify potential genetic causes of developmental delay, autistic spectrum disorders, or intellectual disability. In this webinar, Miguel Milan, director of prenatal genetic diagnosis at the Igenomix medical testing lab in Spain, will discuss how his lab is using chromosomal microarrays to detect free circulating DNA in maternal blood for the evaluation of aneuploidies. Milan will discuss why it was important for the lab to have a high-resolution platform that was futureproofed against new regulations.

Additionally, Anna Sadio, EMEA regulatory affairs senior manager at Thermo Fisher Scientific will highlight the key points and timelines in the new European IVDR (EU IVDR  2017/746) regulations. In this webinar, attendees will discover potential routes to compliance and sources of information to ease potential pitfalls.

Attendees will learn:

• How a major testing laboratory specializing in reproductive genetic services uses chromosomal microarrays.
• How important regulations concerning genetic testing were influential in the lab’s choice of platform.
• The impact the IVDR regulations will have in Europe.
• Ways to ease the path to compliance.

The University of Nebraska Medical Center/Nebraska Medicine’s (UNMC/NM) Fred & Pamela Buffett Cancer Center (FPBCC) offers a novel precision oncology program that is dedicated to improving patients’ overall cancer care. Through the use of genomics and diagnostic tools, the UNMC/NM-FPBCC employs precision oncology to customize care for each cancer patient in order to enhance diagnostic opportunities and outcomes.

To strengthen the data enablement, decision support, and analytics processes within their precision oncology program, UNMC/NM has partnered, since 2015, with GenomOncology. GenomOncology’s precision oncology solutions are designed to be flexible and customizable to augment institutional workflows and processes. By integrating GenomOncology’s solutions into their workflows, UNMC/NM-FPBCC has been able to streamline the utilization and interpretation of complex precision oncology information within their precision oncology program.

During this 1-hour webinar, Allison Cushman-Vokoun of UNMC/NM and James Cole of GenomOncology will cover:

• The challenges UNMC/NM-FPBCC faced with streamlining the precision oncology processes within their institution.
• How UNMC/NM-FPBCC implemented GenomOncology’s precision oncology solutions to improve data enablement, decision support, and insights and analytics workflows within their precision oncology program.
• The results and impacts of the implementation of GenomOncology’s solutions within UNMC/NM-FPBCC precision oncology program.

In the decade since it was introduced, pre-exposure prophylaxis, or PrEP, has revolutionized care for people at risk of acquiring HIV infection. However, PrEP medications can prevent the HIV virus from replicating and slow antibody development, potentially delaying diagnosis if a person does become infected. Catching an early HIV infection before initiating PrEP is also critical in order to prevent the possibility of the medication applying a selective pressure that leads to antiretroviral resistance. This panel of experts in HIV patient care and molecular diagnostics will critically review the current molecular screening guidelines for people on PrEP, discuss various types of available HIV testing methods and the role they play in testing prior to and during PrEP, and address ways to increase access to PrEP and associated testing requirements.

Infectious diseases remain one of the most significant overall causes of morbidity and mortality. Proper and accurate diagnosis of a pathogen is critical for patient treatment. A delayed or incorrect diagnosis can lead to a multitude of adverse events, including unnecessary use or misuse of antibiotics, increased healthcare costs, and worsened patient outcomes.

In this webinar, Gang Liu, chief of the Infectious Diseases Department at Beijing’s Children’s Hospital, and Jingwen Ai, attending physician at Huashan Hospital, will discuss advances in point-of-care diagnostics, sequencing diagnostics, and multi-omics studies that are encouraging for precision medicine in infectious diseases.

Dr. Liu will discuss the application of clinical metagenomic sequencing for the diagnosis of severe infectious diseases, while Dr. Ai will speak about the importance of a tertiary diagnostic network and the setup of a step-wise pathogen identification protocol.

Chromosomal microarray analysis (CMA) is a first-tier molecular cytogenetics test helping to research and identify potential genetic causes of developmental delay, autistic spectrum disorders, or intellectual disability.

CytoScan AIR (AIR: automated interpretation & reporting) is an end-to-end data analysis solution that streamlines and automates the interpretation and reporting by combining the features of Chromosome Analysis Suite (ChAS) software and Franklin software by Genoox.

In this webinar, Yuval Yaron, director of the prenatal diagnosis unit at the Tel Aviv Sourasky Medical Center, will discuss his case study work using Franklin and how CytoScan AIR Tokens will allow his team to perform comprehensive CNV detection, analysis, and interpretation and efficiently research and understand complex genetic cases.

Professor Yaron will be joined by Assaf Sheffer, vice president of product at Genoox, who will review the key features of the CytoScan AIR solution including AI-driven clinical research interpretation dedicated for CNV gains, losses, and LOH, as well as updated relevant guidelines, CMA reporting, laboratory database management, and community-driven sharing of curated data.

The ChAS software is for research use only. Not for use in diagnostic procedures.

Postoperative pain control remains a major challenge for patients, providers, and healthcare systems with no tools available to routinely personalize medication selection. Multiple genes have been implicated in explaining some of the variation among postoperative patient response, and initial randomized controlled trials indicate that single-gene pharmacogenetic analysis can improve postop outcomes. However, most professional guidelines to date (e.g. CPIC) only provide recommendations for single gene/drug interactions.

In this webinar, Jeremy Stuart, CSO of Precision Genetics, will discuss the Prospective Outcomes and Molecular Implementation Support Registry (PROMISRx) study that aims to better explain the interpatient variability in response to perioperative medications/treatments in an effort to predict postoperative outcomes.  Stuart will share data on key genetic analysis assays including variable-number tandem repeat (VNTR) detection of serotonin transporter genes and various opioid receptor sites using fragment analysis. 

You will learn about:

• Avenues for improved pharmacogenetic analysis.
• Multivariant analysis using fragment analysis.
• Benefits of cooperative relationships between service providers and health systems.