GenomeWebinars

In this webinar, Claudio Plaisant of the University Hospital of Bordeaux will discuss implementing an automated whole-exome sequencing (WES) workflow In a rare disease genetics laboratory using the MagnisDx NGS prep system and SureSelect Human All Exon V8, in parallel with the Agilent CGH array workflow, to offer biologists an all-in-one solution from sample to analysis reporting on the Alissa platform. The combination of Magnis Dx NGS prep system and SureSelect Human All Exon V8 (WES V8) allows the lab to obtain excellent reproducibility and uniformity in their data, raising confidence in the SNV and CNV analysis. In this webinar you will learn how:

• WES V8 fastq files can be aligned to a reference genome using Alissa Reporter, which enables QC metrics evaluation, variant calling of single-nucleotide variants (SNV), and copy number variants (CNV).
• VCF files can be transferred to Alissa Interpret enabling annotation and reporting of pathogenic SNV and CNV from WES V8, as well as CNV obtained by CGH-array with the Agilent CytoGenomics software.

In this webinar, Jeffrey Klausner, clinical professor of population and public health sciences at the University of Southern California Keck School of Medicine, will discuss recent developments in the current epidemiology, diagnosis, treatment, case management, and prevention of syphilis. Klausner will cover emerging trends, novel FDA-approved point-of-care diagnostics, new clinical research findings and technology, changes in treatment, vaccines, and innovative prevention strategies.

Klausner will discuss:

• Testing and prevention of congenital syphilis.
• Rapid syphilis testing and same-day treatment.
• Populations at increased risk for syphilis.
• New concepts in syphilis clinical management.
• Syphilis vaccine development.

In this webinar, Mo Serrano will discuss how implementing an array-based workflow enabled his CLIA-certified laboratory to streamline operations and deliver results quickly and accurately. In addition, Serrano will discuss previously utilized solutions, their shortcomings, and how a newly developed microarray supports more comprehensive cytogenetic analysis. Serrano will also present concordance results from proof-of-concept studies. 

Daniel Saul of Bionano Genomics, a biotechnology company that offers a suite of tools enabling genomic analysis, will discuss the design of the Infinium Global Diversity Array with Cytogenetics-8 BeadChip (GDA-Cyto) with the use of NxClinical software for data analysis.

In this webinar, we will cover:

• Technological limitations of existing cytogenetic methods.
• Benefits of using a modern SNP array for cytogenetic testing.
• Key considerations when determining what solution to use.
• Concordance results from proof-of-concept experiments.
• Genomic data analysis as part of a modern SNP-array based workflow.

CVR Genomics, the sequencing facility at the University of Glasgow Centre for Virus Research (CVR), has a remit to provide the CVR community and its collaborators with expertise in high-throughput sequencing to contribute to the understanding of viruses. The team has developed extensive knowledge in viral genomics and expertise in a range of specialist techniques and technologies, including metagenomics, bulk transcriptomics, and targeted enrichment with sequencing on Illumina and Oxford Nanopore instruments. This broad knowledge forms a crucial foundation for tailoring protocols to the individual needs of each project.

In early 2020, CVR received the first Scottish case of COVID-19 for full-genome sequencing. The pandemic highlighted the importance of large-scale surveillance sequencing and the challenges of higher throughputs. CVR initially opted for the low-throughput ARTIC amplicon protocol, which the lab adapted for high-throughput sequencing using the SPT Labtech Mosquito nano-dispensing robots and Illumina sequencing. Amplicon enrichment of viral genomes is well suited to large-scale sequencing workflows but carries a high risk of contamination. One way to reduce this is to streamline the workflows, which CVR accomplished first with high-throughput Oxford Nanopore libraries and finally with Nimagen amplicon and Illumina sequencing. This enabled not just an increase in the number of samples (to ~400 per batch) but also in reliability, with a reduction in the time taken, the number of people required, and, importantly, the cost per sample.

In this webinar, Katherine Smollett, research associate at CVR Genomics, will discuss:

• The challenges of viral genomics.
• Adapting sequencing workflows to academic questions.
• Comparing probe and amplicon-based targeted enrichment methods.
• Surveillance sequencing considerations.
• Switching to automated protocols.
• Managing contamination.

Aberrant DNA methylation patterns found in cancer tissue are seen as the first and most persistent phenotypic expression biomarkers. Consequently, there is a major translational research effort to advance cell-free assay technologies for early cancer screening and for clinical diagnostics to support patient monitoring and treatment. However, accurate and precise measurement of methylated DNA markers across the genome or for specific genes that are found in plasma is technically complex and not yet standardized.

This webinar brings together a panel of academic, clinical, and industry experts in the field of methylated DNA testing who will discuss the promises and challenges of early cancer screening. The panel will discuss tissue plasma concordance, preanalytical variables, accurate measurement of methylated and unmethylated DNA, and the use of reference materials to help standardization. 

Our panelists on this session will be Dennis Lo, MD, PhD, Director at the Li Ka Shing Institute of Health Sciences and Li Ka Shing Professor of Medicine at The Chinese University of Hong Kong, Jimmy Lin, MD, PhD, MHS, Chief Scientific Officer at Freenome Company and Yves Konigshofer, PhD, Director of Technology Development at LGC Clinical Diagnostics.

With the increasing number, complexity, and diversity of biomarkers to be tested in support of precision medicine therapy matching, limited tissue availability and patient health status can be barriers to genomic testing. Liquid biopsy provides oncologists with an alternative to invasive tissue sample collections to match patients with appropriate therapies based on their genomic profile.

In this workshop, Chris Karlovich, associate director of the Molecular Characterization Laboratory at the Frederick National Laboratory for Cancer Research, will share key takeaways from the validation of an NGS-based comprehensive genomic profiling (CGP) liquid biopsy assay to meet the specified criteria for clinical needs. Karlovich will also discuss a retrospective analysis of clinical cohorts with the CGP ctDNA assay, which identified clinically relevant somatic alternations with high sensitivity.

Learn:

• The value of a CGP assay from liquid biopsy samples.
• Considerations for bringing a CGP ctDNA assay in house.
• How to identify clinically relevant somatic alterations with high sensitivity using the CGP ctDNA assay in clinical cohorts.
• Lessons from entering the ctDNA and liquid biopsy field.