GenomeWebinars

Early detection can save lives. But have you ever explored linking phenotypic and genomic or other -omic data to assess the full view of the patient journey?

In this webinar, experts from Genetic Technologies and DNAnexus will discuss how combining genetic and clinical data to categorize a person’s risk of developing a disease is changing the field of personalized predictive genetics. The speakers will discuss:

• Overcoming challenges related to integrating disparate data sets and building a lab-agnostic infrastructure so sample data can be funneled anywhere, without the need for a wet lab, enabling unprecedented scale.
• How an integrated risk assessment platform for multiple cancers, cardiovascular, and metabolic diseases delivers clinically actionable results to empower physicians and patients to proactively manage health.
• Provide a forward-looking perspective on the role of validated tests in making personalized, predictive healthcare a reality.

Candida auris is an emerging fungal pathogen recognized as an urgent global threat by the US Centers for Disease Control and Prevention (CDC). C. auris disproportionately affects vulnerable populations in healthcare settings. It can asymptomatically colonize skin and other body sites for extended periods and can persist in healthcare settings for weeks, leading to mass outbreak potential.

Conventional culture-based detection methods, while essential for antifungal susceptibility testing, can lead to misidentification and mistreatment, and hamper outbreak response efforts due to extended time to result. Despite an urgent need for expanded surveillance screening in some healthcare settings, most molecular testing is currently performed as LDTs on low throughput, semi-automated molecular testing platforms.

In this webinar, Alana Sterkel, associate director of communicable disease division at Wisconsin State Laboratory of Hygiene, Filipe Cerqueira, microbiology and public health CPEP fellow at the University of Texas Medical Branch, Phyu Thwe, associate director of infectious disease testing at Montefiore Medical Center, and Inessa Gendlina, director of infectious diseases and infection prevention at Montefiore Medical Center, will present their development and implementation of Candida auris testing using the Panther Fusion system, a high throughput, fully automated platform to help identify and control potential outbreaks in their healthcare systems.

During this webinar, presenters will discuss:

1. Impact of implementing high throughput RT-PCR testing to control the spread of Candida auris in different healthcare settings.
2. Assay development and workflow optimization strategies for expanded Candida auris testing on the Panther Fusion system.
3.  Candida auris screening strategies in different healthcare settings.

Nucleic acid testing is an essential tool for diagnosis and management of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections. Recent regulatory approvals have brought new molecular tools to market, allowing labs to streamline their testing workflows. At the same time, the expansion of molecular capacity during the COVID-19 pandemic has changed the nucleic acid testing landscape.

Please join us on TK to hear four experts discuss the present challenges and opportunities in molecular testing for HIV and HCV: Ping Ren, professor and association director of the clinical microbiology laboratory at the University of Texas Medical Branch; Sarah Buss, HIV, Hepatitis, STD and Tb program manager at the Association of Public Health Laboratories; Nathan Ledeboer, professor and vice chair in the department of pathology and laboratory medicine at Medical College of Wisconsin; and Stan Schofield, managing principal of the Compass Group and former president of NorDx.

The panelists will discuss current trends in molecular testing for HIV and HCV including the impact of expanded molecular testing capacity post-pandemic and the extent to which new assays and instrumentation are allowing laboratories to address industry-wide challenges like staffing shortages and the need for workflow flexibility.

Despite professional medical society recommendations to offer carrier screening for over 100 different germline disorders to all individuals of reproductive age, insurance coverage for large panels continues to remain a barrier to widespread adoption. Moreover, not all laboratories have the operational means to implement such testing at the cost, turnaround time, and throughput typically required in the setting of prenatal care.

In this webinar, Linda Hasadsri, director of the molecular technologies laboratory at Mayo Clinic, will present the pros and cons of utilizing a custom targeted genotyping array for carrier screening of over 200 different genetic disorders, our unique approach to supplemental coverage and confirms, and, finally, our discovery yield in the first 8,000 samples received for testing.  

The development of multiplex real-time PCR screening for suspected gastrointestinal parasitic infections has helped overcome the many challenges and limitations of traditional microscopic diagnostic methods, supporting timely, appropriate patient treatment and improved epidemiological surveillance. While there are several real-time multiplex PCR panels available to detect parasites, many only test for Giardia spp., Cryptosporidium spp., and Entamoeba histolytica.

In this webinar, three experts in medical diagnostics, Susan Madison-Antenucci, Damien Stark, and Marc Couturier, will describe the benefits of employing a broader syndromic panel to include the detection of other leading pathogenic parasites causing gastrointestinal diseases, with a focus on Dientamoeba fragilis and microsporidia.

D. fragilis and microsporidia, despite their frequent association with human gastrointestinal (GI) disorders and disease, are often overlooked in their role as pathogens, and subsequently excluded from routine testing for suspected GI infections. The speakers will discuss the clinical significance of D. fragilis, and microsporidia, and the benefits of including these targets in the broader syndromic molecular detection of GI parasites.

In this webinar, Ann-Kristin Afflerbach of University Medical Center Hamburg-Eppendorf will introduce nanopore sequencing as a potential method for routine molecular diagnostics of cell-free DNA from cerebrospinal fluid (CSF) supernatants, and Carlo Vermeulen of the UMC Utrecht Center for Molecular Medicine and Oncode Institute will discuss nanopore sequencing for intraoperative tumor classification.

After analyses of more than 150 samples from patients with a suspected brain tumor or a history of brain tumors, Afflerbach and colleagues have shown that nanopore sequencing of cell-free DNA (cfDNA) in CSF can identify diagnostic or prognostic copy number changes. It may further determine the molecular brain tumor class based on an algorithm that compares the global DNA methylation pattern of the cell-free DNA in the CSF with a reference cohort of over 2,500 methylation profiles from well-characterized brain tumor tissue samples. This approach is valuable for diagnosing inaccessible brain tumors and for minimal residual disease monitoring.

Vermeulen will discuss how his team can collect a sparse DNA methylation profile with as little as 30 minutes of intraoperative nanopore sequencing; “Sturgeon”, a neural network classifier that can discern 80 different classes of brain tumors from methylation profiles; and how the sample processing, nanopore sequencing, and Sturgeon classification workflow has a turnaround time of 90 minutes, a timeframe that would allow adjustment of future surgical strategies based on the tumor class.

Metastases to the central nervous system from solid primary tumors are a frequent and fatal complication of cancer with limited therapeutic options. Despite the advent of immunotherapy, it remains largely unknown whether and how metastatic cells in the brain and surrounding cerebrospinal fluid (CSF)-filled leptomeninges interact with the immune system.

To approach these interactions in an unbiased manner, Jan Remsik and his colleagues profiled an unexpectedly heterogeneous population of cell types in human and mouse CSF with single-cell analytics. These samples were inherently challenging to process due to a relatively low number of cells from each human subject or mouse collection, extreme cell fragility, and contamination by myelin and other unwanted debris in the case of the mouse samples. Since FACS-sorted samples suffered an unbearable amount of stress that prevented their processing, the team used the LeviCell 1.0 system to deplete the debris and enrich for viable cells in stress-free conditions. Incorporating the LeviCell run into their pipeline resulted in the capture of sufficient numbers of high-quality cells for CITE-seq. Such a proteogenomic approach, combining more than 100 cell surface signals with whole transcriptome sequencing, allowed Remsik and his colleagues to elucidate the response of the CSF immune system to cancer at an unprecedented resolution.

With the development of genomic tools, there has been increasing awareness of germline variants associated with cancer predisposition. Maturing technologies, such as next-generation sequencing (NGS), have made the identification of hereditary cancer (CGx) variants fast and affordable enough for clinical use. Despite these advances, significant challenges remain for high-complexity CLIA laboratories to adopt CGx. These include domain knowledge of NGS, genomic interpretation of germline variants, production-level processes in the laboratory to meet turnaround time demands, and the reimbursement landscape. In this webinar, Jeremy Stuart will outline these and other challenges his laboratory has faced as they developed, validated, and established production-level CGx testing.