GenomeWebinars

This webinar will present the utility of a personalized in silico analytical approach for the routine clinical diagnosis of channelopathies and cardiomyopathies.

The advent of next-generation sequencing (NGS) has greatly improved the ability to rapidly assess many genes at the same time, but the analysis and interpretation of complex genomic variants still remains a challenge. In order for NGS to find use in routine diagnostics, clinical laboratories must be able to overcome this complexity and enable better outcomes for patients.

Dr. Alexandre Janin, member of the molecular cardiogenetic lab at Hospices Civils de Lyon in France, has solved this complexity and successfully characterized difficult variants by adopting the Sophia Platform.

Dr. Janin will discuss how the platform:

• Enables fast and comprehensive analysis;
• Detects copy number variations quickly and efficiently;
• Facilitates variant interpretation by sharing knowledge among members of the national network for Hereditary Cardiac Diseases (Cardiogen)

Dr. Janin will be joined by Dr. Audrey Coiffic, Clinical Application Product Manager at Sophia Genetics, who will discuss the most recent developments in targeted solutions for the advanced detection of inherited cardiac diseases.

Sequencing workflows require library quantification and normalization to ensure data quality and reduce cost. Traditionally, prior to sequencing, next-generation sequencing library technicians and automation strategies have had to undertake numerous steps to quantify and normalize NGS libraries.

In this webinar, Tony Brooks, Senior NGS Specialist at University College London Genomics, discusses how his core facility implemented the Swift Normalase Kit, a novel enzymatic library normalization product that streamlines the cumbersome steps following NGS library preparation. 

Compared to conventional normalization, Swift Normalase saves sequencing costs by reducing read depth variation within a pool from a typical CV of 10-25% to a CV <10%. With a simple bead-free, quantification-free, two-step workflow, Normalase enables bulk processing of samples and expedites library pooling and loading to save time and cost.

Tony shares how his lab used the Swift Normalase kit for RNAseq library normalization to improve his facility's sequencing workflow and to reduce cost.

This webinar provides a comparison of next-generation sequencing (NGS) approaches for human transcriptome sequencing, including short-read Illumina sequencing and synthetic long-read sequencing technology.
 
NGS is a powerful method for characterizing eukaryotic gene expression. While short-read transcriptome sequencing data is inexpensive, it has major shortcomings, including difficulty detecting isoforms and gene fusions, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long-read sequencing such as PacBio Iso-Seq, meanwhile, offers long reads but at increased cost, higher error rates, and reduced quantification abilities.
 
Another approach, LoopSeq synthetic long-read sequencing technology from Loop Genomics, uses unique molecular identifiers to generate synthetic long reads on short-read Illumina sequencing instruments and no additional hardware. This method offers a promising option for human transcriptome sequencing by providing full-length mRNA sequencing coupled with UMI-based transcript counting for gene expression quantification.
 
In this webinar, Ana Conesa, Professor of Bioinformatics at the University of Florida, discusses a comparison study of short-read Illumina transcriptome sequencing and LoopSeq Transcriptome sequencing data for human transcriptome studies.

This is the second Loop Genomics GenomeWebinar on the topic of long-read versus short-read sequencing approaches. The first, which compared these methods in the context of microbiome sequencing, is available on demand here.

Outbreaks of influenza infections are seasonal and can range from regional outbreaks to nationwide epidemics or even global pandemics. Mortality can range from 4 percent to 60 percent for at-risk patient populations, depending on the strain circulating in the environment. Rapid diagnostics can significantly improve patient care and control outbreaks by treating with antivirals and informing patients of proper precautions to reduce spread.

Over the past decade, there has been a large shift in diagnostic options, moving from cell culture to rapid point-of-care testing. Today, multiple CLIA-waved assays are approved and laboratory managers must decide which methods and assays are appropriate for their healthcare environment.

In this webinar, Dr. Faron will discuss current trends in influenza epidemiology, evaluate current FDA-cleared assays, and present the MCW team's findings on a recent time-of-motion study comparing three rapid influenza assays. Overall, these data should aid healthcare providers to improve and implement rapid influenza testing.

This webinar demonstrates how a research team at the Firestone Institute for Respiratory Health at McMaster University developed a cellular and molecular phenotyping pipeline using archived samples of lung tissue derived from patients diagnosed with fibrotic interstitial lung disease. 

Dr. Kjetil Ask discusses how the clinically relevant tissues were obtained, clinically categorized and deidentified. He provides his perspective on the requirement of cross-disciplinary expertise and the associated technological platform required for the identification and quantification of cellular and molecular targets in fibrotic lung disease. Dr. Ask also discusses the potential application of this platform to pre-clinical models of lung disease. 

Megan Vierhout presents her research on the role of alternatively activated macrophages and endoplasmic reticulum stress in fibrotic lung disease. She shows specific examples of automated immunohistochemistry and associated in situ hybridization technology using ACD RNAScope and BaseScope assays to demonstrate molecular phenotyping and target identification. 

This webinar describes a project that applied Oxford Nanopore long-read RNA-seq to explore the transcriptional landscape of a damaging agricultural pest.

Anthony Bayega of McGill University discusses the study, which looked at the transcriptional dynamics that occur during early embryo development of the olive fruit fly (Bactrocera oleae), a key pest of cultivated olive trees that costs the olive fruits industry an estimated $200 million annually.

Anthony and colleagues combined absolute gene quantification using internal RNA spikes, full-length cDNA sequencing using Oxford Nanopore long-read RNA-seq, and high-resolution timescale experimentation for the study. They generated a de novo transcriptome assembly and identified 3,553 novel genes and a total of 79,810 transcripts.

Dr. Bayega discusses how he and his team also refined gene models for key sex-determining genes, which might provide insights into biological control of this fly.