In the next five years, the majority of clinical diagnostic labs competing to offer NGS oncology testing will be performing comprehensive genomic profiling (CGP). Yet scaling to CGP introduces unique challenges that clinical diagnostic labs must overcome, such as contending with exponentially more variants, encountering a greater number of incidental germline findings and variants that are less characterized, and accurately interpreting co-occurring variants that interact with each other to impact prognosis, diagnosis and treatment responses.

In this webinar, we present a workflow-agnostic, informatics software solution that enables clinical diagnostic labs to scale to CGP while reducing cost, time, and labor. Already used and trusted to interpret over 3 million patient cases worldwide, this software solution leverages the world’s largest and fastest growing knowledge base to simplify and accelerate variant interpretation and build custom, patient-specific reports with the latest diagnostic and prognostic information, as well as biomarker-directed therapies and clinical trials.

When you attend this webinar, you will:
• Learn how to overcome unique challenges of CGP, including identifying incidental germline findings and interpreting co-occurring variants.
• See why 90,000 users trust QIAGEN Digital Insights for knowledge curation—how we have built the most trusted, fastest growing knowledge base and why our curation process is unrivalled in the industry.
• Receive step-by-step guide of how to perform CGP and go from VCF to final report with greater speed, precision, and confidence (all registrants can receive custom report if VCF files are provided).
• Qualify for a complimentary demonstration and trial of this industry-leading software to see how your lab can scale to CGP while reducing costs, time, and labor.

With the revolution of lateral flow assay use in Point-of-Care and Over-the-Counter testing resulting from Covid-19, saliva has become an attractive sample matrix. To continue to grow lateral flow assay use in these sectors, there is a need for simple and non-invasive testing that saliva as a matrix can provide. It is not without its challenges, however. Saliva is prone to matrix effects, varies greatly from patient to patient, and may have lower analyte concentrations than other sample types. Combine these challenges with the complexities associated with the collection, filtration, and dispensing of sample onto a test, saliva can be a very difficult matrix to work in. In this session, we will discuss how proper planning and the selection of reagents can address these unique challenges to produce a successful saliva-based lateral flow assay.

Learning Objectives:

1. Explain the unique challenges of saliva relative to other sample matrices.

2. Discuss how reporter probe selection can help achieve high sensitivity even in difficult matrices.

3. Describe approaches to successful saliva-based lateral flow assay design that enable scaled manufacturing.

With recent emergences in new infectious diseases and their variants, there is a need to develop faster and more specific analytical tools to detect different respiratory infectious diseases such as SARS-CoV-2 or influenza viruses. Not only are their initial symptoms similar, but they are also both enveloped viruses with several common biological properties, often leading to challenges in disease identification. Although polymerase chain reaction (PCR) is a valuable tool in infectious disease testing, the recent pandemic demonstrated the need to develop analogous testing methods that utilize different consumables.

Infectious disease particles contain proteins that are biomarkers of infection. One approach capable of detecting such proteins is bottom-up mass spectrometry (MS). Proteolytic digestion of proteins generates peptides, which can be separated by liquid chromatography (LC) and detected by MS. Targeting multiple signature peptides of different proteins has been demonstrated to simultaneously detect peptides from five common respiratory infectious disease biomarkers; SARS-CoV-2, influenza virus A and B, respiratory syncytial virus, and human coronavirus (HCoV-229E).

In this talk, multiple workflows for infectious disease detection by LC-MS will be discussed. These workflows contain different sample preparation techniques, such as peptide enrichment via stable isotope-labelled standard and capture by anti-peptide antibodies (SISCAPA), immunoprecipitation of target proteins via antibody-coupled Dynabeads and a minimal sample preparation technique involving protein precipitation.

Learning Objectives:

1. Determine why peptide enrichment provides better sensitivity and selectivity of target peptides.

2. Elaborate how you can simultaneously detect a panel of infectious disease.

3. List the steps in quantifying proteins in biological matrices from sample to reporting.

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a novel virus that causes COVID-19 and has considerable variability in clinical outcomes among infected patients. The GENCOV study links laboratory data (including genetic, immunology, biochemistry, microbiology and hematology) and patient characteristics to provide a comprehensive understanding of factors that contribute to variability in COVID-19 patient outcomes. GENCOV includes 25 co-investigators and collaborators across 6 hospital sites in Ontario to study 1,500 Covid-19 patients over a 12-month period. This lecture will describe the GENCOV study protocol and the clinical characteristics of Covid-19 infected patients that increase odds of hospitalization, including age, ethnicity, BMI, viral variant and presence of hypertension. Surveys results that relate to participants understanding of Covid-19 serological testing will be described. To our knowledge, GENCOV is the first study to assess public knowledge of SARS-CoV-2 antibodies and serological testing. Our findings indicate that age, household income and level of education play a role in understanding information related to Covid-19 serology. Lastly, serial antibody titer levels, antigen target and viral neutralization are longitudinally assessed using an in-house developed immunoassay and the Health Canada approved Roche Elecsys® SARS-CoV-2 immunoassay. Our findings show that unvaccinated inpatients 1-month post-infection have significantly greater IgG antibody levels against all antigen targets (spike, receptor binding domain or nucleocapsid) when compared to unvaccinated outpatients. Patients with breakthrough or hybrid infections show higher antibody levels at 1 and 6 months post infection in comparison to those who are infected without vaccination. Understanding the basis for the variation in immune response and how this correlates to patient outcomes will help to better characterize future vaccine development and roll out plans.

Learning Objectives:

1. Describe how laboratory and clinical characteristics can be linked to provide a comprehensive understanding of factors that contribute to variability in COVID-19 patient outcomes.

2. Describe short and long-term COVID-19 serological findings in vaccinated and unvaccinated individuals.

3. Identify populations at risk of knowledge gaps related to COVID-19 serology.

The next-generation sequencing (NGS) technologies have led to shifting paradigms for hereditary cancers genetic testing. With the increasing sensitivity of new technologies and the reduction of sequencing costs, there was an increase in the number of genes that could be evaluated simultaneously. NGS-based tests encompassing multi-gene panels, whole-exome (WES), and whole-genome sequencing (WGS)  entered the market in a number of laboratories becoming an integral part of the clinical diagnostics in oncology. This approach offers a huge potential to improve the detection rate of hereditary cancer syndromes and to reveal associations between mutations in different genes and clinical phenotypes.

However, by increasing the number of genes that we evaluate, we generate a vast number of genetic variants per individual. Sometimes, our ability to generate massive amounts of genetic data has far outpaced our ability to interpret their clinical significance. Results misinterpretation is also an important issue to consider especially when variants of unknown significance (VUS) are involved.

In this webinar, Dr. Ana Krivokuca presents a real-world use-case of how the Institute for Oncology and Radiology of Serbia (IORS), a National Cancer Research Center that provides routine NGS testing for cancer patients, uses the QCI Interpret in their NGS testing pipeline to annotate, assess, and better understand the clinical significance of detected germline variants in the context of hereditary cancers. 

This webinar will be dedicated to:
• The importance of adequate variant classification for inherited cancer syndromes
• The challenges in variant classification especially with the limited bioinformatics capabilities and end-to-end workflows
• Manual data curation and its downsides
• The advantages of bioinformatics solutions and computational variant classification

Attendees will:
• Learn how IORS uses QCI Interpret to evaluate genomic profiles of hereditary cancers, discriminate between variant classes, re-evaluate VUS, evaluate novel guideline recommendations, accelerate germline data analysis pipeline, confidently identify those variants that have clinical utility, and generate comprehensive clinical reports

Rapid genomic surveillance of pathogens can provide valuable insights, in order to guide public health interventions. Novel workflows using nanopore technology enables for real-time sequencing of clinical samples. However, current library preparation workflows are limited and can take up to 5 hours whereby PCR takes around 3,5 hours. 

By using NextGenPCR technology it is possible to decrease the PCR library preparation to 27 minutes for the SARS-CoV-2 Midnight protocol from Nikkie Freed et al. While optimizing this SARS-CoV-2 PCR tiling, the world faced a monkeypox pandemic. At the beginning of the pandemic, public health institutes were limited to metagenomics approaches. Using this method, the coverage depth becomes the limiting factor that prevents to multiplex multiple samples on a single flowcell, making sequencing very costly.

A collaboration between AmsterdamUMC (Netherlands), Rigshospitalet Copenhagen (Denmark), and Molecular Biology Systems (Netherlands) resulted in a successful optimalisation and validation of an amplicon-based sequencing approach, inspired by SARS-CoV-2 Midnight protocol and the ARTIC network. This allows labs to increase depth of coverage and multiplex up to 20 samples per flowcell. 

Using this fast developed sequencing workflow, we were able to get fast insights of the spread of monkeypox in the region of Amsterdam, which resulted in a publication in Eurosurveillance about the first pediatric case in the Netherlands. 

Learning Objectives:

1. Discuss the benefits of having faster Next Generation sequencing data in outbreak settings.

2. Discuss the use of PCR tiling for Monkeypox sequencing.

3. Explain the potential of PCR tiling methodologies for other applications.

Inflammatory myopathies are a group of rare diseases that are characterized by progressive muscle weakness due to chronic skeletal muscle inflammation. Classification of these rare diseases is based on a combination of clinical presentations, autoantibodies, and muscle histopathology. This presentation will discuss the pathophysiology, clinical classification, and current laboratory methods, including their advantages and disadvantages, used in the detection of autoantibodies associated with inflammatory myopathies.

Learning Objectives:

1. Describe the etiology, clinical presentation, and classifications of idiopathic inflammatory myopathies.

2. Describe the methods used in the detection of autoantibodies associated with IIM.

3. Describe the advantages and disadvantages of each detection method.

In spite of significant progress in disease diagnosis and treatment, racial and ethnic minorities experience lower quality of care and poorer outcomes for certain conditions than non-minorities. Sequencing of the human genome enabled scientists to re-examine the relationship between race, ethnicity and genetics and revealed that race is not an accurate representation of human genetic variation. Nevertheless, the use of race as a biological proxy persists in several areas of science and medicine. The consideration of race in clinical care is nuanced. Some argue that race serves as a proxy for underlying population genetics and is therefore clinically useful; however, in the absence of patient-specific genetic ancestry data the question of whether it is more beneficial or deleterious to use racial or ethnic groupings remains a topic of debate.  This session will review the relationship between race, ethnicity and genetics and discuss the implications of the use of these categories in medicine.  

Learning Objectives:

1. Describe the concepts of race, ethnicity and genetics

2. Discuss the limitations associated with using race-based classifications to describe biological differences  

3. Critically assess the utility of race and ethnicity in science and medicine

Each year, more monoclonal antibodies (mAbs) are approved by regulatory agencies to treat a wide range of diseases with an expected market value of over $200 billion by 2026. The advantage of using therapeutic mAbs lies in their inherent specificities for recognizing and counteracting foreign substances (so-called antigens). Due to their molecular complexity, including post-translational modifications, biopharmaceutical companies have embraced many advanced analytical techniques such as mass spectrometry to better characterize and quantify mAbs during the development stages. In clinical testing, the presence of endogenous immunoglobulins in patients' samples with nearly identical structures to therapeutic mAbs adds an additional challenge to the accurate quantitation of therapeutic mAbs. Accordingly, mass spectrometry has also gained substantial popularity for therapeutic mAb monitoring (i.e., TDM of mAb) in clinical laboratories due to its great versatility to detect both tryptic peptides and intact light and heavy chains quantitatively.

Here we present the intact light chain quantitation approach for measuring concentrations of therapeutic mAbs in human serum using the Orbitrap Exploris 240 MS for clinical research. One of the benefits of intact light chain quantitation is a simplified workflow with faster sample preparation compared to peptide quantitation. Additionally, it can provide a solution for mAbs that contain limited or no signature tryptic peptides and are not possible to differentiate from endogenous IgG. Protein L magnetic beads were used for the selective purification of antibodies containing kappa light chains. This way, endogenous lambda light chains from human serum are not captured, which can improve the purity of isolated antibodies and potentially be applied to other modality antibodies or Fab fragments containing kappa light chains.

Learning Objectives:

1. Discuss how HRAM mass spectrometry is applied for monitoring therapeutic mAbs.

2. Explain the purification process to accurately analyze intact proteins such as mAbs.

3. Define how intact proteins can be measured by mass spectrometry and why isotopic distribution is important.

The World Health Organization (WHO) classified monkeypox as a zoonosis, that is, a disease that is transmitted from animals to humans. Since early May 2022, many instances of monkeypox have been reported in countries where the disease is not endemic and continues to be reported from several endemic countries. 
 
The monkeypox virus is classified as an orthopoxvirus and causes a disease with symptoms similar to smallpox. Transmission between humans is limited. Monkeypox can be transmitted through contact with body fluids, internal mucosal surfaces, skin lesions in the mouth or throat, respiratory droplets, and contaminated objects. Sometimes, it is difficult for clinicians unfamiliar with diseases resembling monkeypox to differentiate it from other viral, bacterial, or other conditions. Nonspecific clinical presentations, lesions, and inflammation of the pharyngeal mucosa have been observed. These symptoms can be seen in many other viral and non-viral infections. For these reasons, accurate laboratory diagnosis of the disease is of particular importance.
 
Under current guidelines, anyone suspected of having monkeypox should be tested in properly equipped laboratories by personnel trained in the relevant safety procedures. The confirmation of monkeypox virus infection is based on the Nucleic Acid Amplification Test (NAAT), using conventional or real-time Polymerase Chain Reaction (qPCR), for the detection of viral DNA. Antigen and antibody detection methods do not distinguish between orthopoxviruses and are therefore not recommended.
 
A Laboratory Information Management System (LIMS) can help streamline and automate operations in a clinical diagnostic laboratory. A clinical diagnostic LIMS enables laboratories to manage patient data, manage the collection and storage of monkeypox samples, report test results following FDA and CDC reporting guidelines, deliver test results securely and digitally, and manage workflows, SOPs, staff training, and inventory.
 
Learning Objectives:

1. Review the monkeypox virus and its characteristics from the current outbreak.

2. Discuss the latest guidelines and recommendations for testing.

3. Identify how a LIMS can help streamline and automate operations in clinical diagnostic laboratories.
 

Cancer is a heterogeneous but related group of diseases wherein cells in certain tissues of the body proliferate uncontrollably and eventually invade adjacent and distant tissues. The oldest known archaeological evidence of human cancer dates back 1.7 million years. Tumor markers are molecules produced by the tumor or by the body in response to the tumor and may reveal the presence of the tumor. A variety of substances act as tumor markers including catecholamines, certain hormones, enzymes, and even antibody components. In 1847, Bence-Jones protein, the first tumor marker put into clinical use, was isolated from acidified boiled urine. Tumor markers can be employed for screening, diagnosis, prognostication, guiding therapy, as well as post-therapy surveillance. However, laboratorians need to consider sensitivity, specificity, clinical impact, and availability of convenient assays when it comes to putting a tumor marker into clinical practice. This presentation will discuss important pre-analytical, analytical, and post-analytical factors that clinical labs should consider when offering tumor marker testing. Limitations of tumor markers and CA125 as an example tumor marker in the context of ovarian cancer will also be discussed.

Learning Objectives:

1. Describe the types and characteristics of tumor markers.

2. Discuss considerations for clinical laboratories offering tumor marker testing.

3. Explain the utility of CA125 in ovarian cancer management.