GenomeWebinars

This webinar discusses an effort underway at the University of North Carolina Medical Center's to overcome limitations in the hematological genomic testing workflow with artificial intelligence (AI) from Sophia Genetics.

In the first part of this webinar, Dr. Nathan Montgomery of the UNC Medical Center discusses the rigorous evaluation his lab performed to evaluate Sophia Genetics Myeloid Solution against the overall performance of other vendors' solutions.

The Myeloid Solution is a molecular application that bundles Sophia AI with a capture-based target enrichment kit and full access to Sophia DDM platform. The application is designed to accurately characterize the complex mutational landscape of relevant hematological disorders associated with leukemia, myelodysplastic syndromes, and myeloproliferative neoplasms.

Dr. Montgomery first explains the limitations and challenges of the current myeloid test workflow, and the rationale for the group's decision to evaluate other solutions, including the need to perform orthogonal testing of genes with high GC content such as CEBPα. Then, he will lay out the strategy he and his group applied to objectively assess the overall strengths and weaknesses of each technology. Finally, Dr. Montgomery presents his team's conclusions and the reasons they decided to work with Sophia Genetics.

In the second part of this webinar, Dr. Montgomery gives an update on UNC Medical Center's progress with in-house validation and the lab's next steps.

In the last part of the webinar, Dr. Alexander Kurze of Sophia Genetics briefly introduces a solution that will be soon available to test for gene fusions in hematological diseases.

In this webinar, the third in the “New Frontiers in Liquid Biopsy Research” series, Dr. Liya Xu of the University of Southern California Michelson Center for Convergent Biosciences discusses her team’s work using liquid biopsy technology for breast cancer research.

In particular, Dr. Xu presents her team’s experience establishing the Ion Torrent Oncomine Breast cfDNA Assay v2 at USC, including installation of the sequencing instruments. This new workflow for quantitative evaluation of cell-free DNA is an expansion of the team’s existing HD-SCA (high-definition single cell analysis) workflow and an update of the previous qualitative Ion AmpliSeq Cancer Hotspot Panel pipeline.

Dr. Xu presents data from liquid biopsy research samples from metastatic breast cancer, demonstrating integration of analytical variables of cfDNA samples obtained from the Oncomine Breast cfDNA assay v2 and genomic analysis and protein marker data from single circulating tumor cells. An overarching application of this work is to provide a more comprehensive understanding of the disease.

For information on all webinars in this series, click here.

This webinar will highlight the use of high-throughput sequencing of post-mortem human brain tissue to identify neurodegenerative markers and identify potential drug targets.

Dr. Steve Sheardown, Head of Molecular Biology and Cell Engineering at pharmaceutical company Cerevance, will discuss a technology platform  called NETSseq (Nuclear Enriched Transcript Sort sequencing). Cerevance uses NETSseq to interrogate the molecular diversity of individual neuronal cell types in human tissue to understand their genetic complexity, the contribution that each of these make to circuit function, and, in the context of brain disorders, their potential for therapeutic intervention.

Cerevance is building an extensive collection of transcriptomes from cell types selected for relevance to human disease covering both sexes and spanning different ages from donor samples obtained from diseased populations. Since commencing clinical data collection in October 2017, Cerevance have already accumulated over 1,300 high quality individual transcriptomes. Using this unique resource, the company aims to identify and pursue novel drug targets to address areas of high unmet medical need within the field of central nervous system disorders.

Dr. Sheardown will discuss how his team has transformed NETSseq from a low-throughput proof of concept to a robust high-throughput process for generating deep sequencing libraries from limited quantities of fixed post-mortem tissue. To achieve this, Cerevance has rigorously tested a range of products at every stage of the process, focusing on yield, quality, reproducibility, and automatability.

Drawing on examples from the company's transcriptome dataset, Dr. Sheardown will illustrate the depth of information that his team can generate using its NETSseq platform.

This webinar provides an in-depth case study demonstrating how reference standards can be used to develop and validate circulating tumor DNA (ctDNA)-based assays.

Our speaker, Samuel Woodhouse, Head of Technology and Assay Development at Inivata, shares his experiences testing and benchmarking technologies capable of detecting a range of cancer alterations at near single-molecule resolution.

Given the minimally invasive nature of ctDNA analysis and the availability of therapies that are targeted against cancers with specific alterations, this approach is quickly transforming cancer care. As patients have been shown to respond to targeted therapies even when the actionable mutations detected in their circulating DNA were present at low variant allele fractions (VAFs) (< 0.5%), highly sensitive methods are required for optimal clinical use. Along with creating technologies able to look for genetic alterations in ctDNA, it is critical to have suitable reference material with known mutational signatures and fragmentation patterns to ensure consistent and accurate assay validation and performance benchmarking.

Inivata’s InVisionFirst Lung is a qualitative laboratory-developed test that uses targeted sequencing to detect single nucleotide variants (SNVs), copy number variants (CNVs), insertions and deletions (INDELs), and structural variants in selected genes from DNA isolated from plasma samples from patients with non-small cell lung cancer (NSCLC). Dr. Woodhouse discusses how, using Horizon Discovery’s control material as a known reference, InVisionFirst Lung demonstrated outstanding sensitivity for mutation calling and a specificity of 99.9997% per base. He will also share how his team used a custom gene fusion reference standard from Horizon Discovery to show that InVisionFirst Lung is the first amplicon-based ctDNA assay to detect ALK and ROS1 gene fusions. Comparison of VAFs between the InVisionFirst assay and the Horizon Reference Standard showed excellent concordance (R² = 0.965).

Proximity ligation technology generates multi-dimensional next-generation sequencing data that is proving to solve unmet needs in genomic research. Learn about some of the applications for this datatype and specifically how it helps create high-quality assemblies to overcome challenges of working with non-model organism genomes.

This webinar highlights three projects where proximity ligation technology and scaffolding software were used to create high-quality and highly contiguous genome assemblies for different organisms. Our speakers will also discuss the scientific discoveries enabled by these high-quality genome assemblies.

View this webinar to:

• Learn how proximity ligation technology works and the applications for this multi-dimensional NGS datatype from cancer research to genome assembly
• Hear how proximity ligation overcomes one of the main challenges of studying non-model organisms: being able to easily generate high-quality and contiguous genome assemblies