GenomeWebinars

Thu
Apr
26
11:00 am2018
Sponsored by
Thermo Fisher Scientific

Evaluation of a Pan-Cancer Cell-Free Assay to Meet Unmet Research Needs

Genome Webinar

Senior Director, R&D Unit, Senior ConsultantMolecular Pathology Unit, University Hospital Basel | Institute for Medical Genetics and Pathology 

In this webinar, the second in the “New Frontiers in Liquid Biopsy Research” series, Luca Quagliata, Senior Consultant in the Molecular Pathology Unit at University Hospital Basel, will share two specific unmet needs within his lab’s liquid biopsy research that led to the eventual evaluation, adoption, and implementation of the latest liquid biopsy Oncomine NGS solutions from Thermo Fisher.

Dr. Quagliata’s lab at University Hospital Basel’s Molecular Pathology Unit has established methodologies for the genomic analysis of circulating cell-free tumor DNA (cfDNA) for lung and colon cancer research. The team’s validated workflow includes cfDNA extraction from plasma followed by next-generation sequencing with commercially available or specific custom-made gene panels and clinical interpretation of results to support their study.

Dr. Quagliata will discuss two challenges that his lab faced with early liquid biopsy assays: 1) they could not detect fusions, and 2) they could not detect mutations from multiple cancer types with one NGS assay. He will share details of how the Ion Torrent Oncomine Lung Cell-Free Total Nucleic Acid Assay addresses the first of these challenges and how the Ion Torrent Oncomine Pan-Cancer Cell-Free Assay addresses the second.

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

Sponsored by

Head of Technology and Assay Development, Inivata

This webinar will provide 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, will share 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 will discuss 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).

Instructor, Department of Pathology & Biomedical Data Science,
Stanford Medical School

Director of Product Management, Dovetail Genomics

This webinar will discuss a proximity ligation-based method for studying structural variation in formalin-fixed paraffin-embedded (FFPE) tissue.

FFPE tissue produces highly fragmented, low-molecular weight nucleic acids, presenting a principal challenge to identifying relevant genetic variants with tumor sequencing. This sub-optimal input specimen was previously not thought to contain long-range (Mbp+) information needed to accurately and robustly identify balanced and unbalanced large-scale structural variation and phasing from these specimens.

This webinar will highlight a proof-of-concept study for using Hi-C chromosome conformation capture methodology for FFPE tissue, called Fix-C, which yields phased read pairs spanning distances up to full chromosomes and enables unambiguous structural variation detection and variant phasing in archival specimens.

Join this webinar to:

  • Learn how proximity ligation technology works and proven applications for this multi-dimensional NGS datatype from structural variation detection to genome assembly
  • See how proximity ligation overcomes the main challenge of highly fragmented DNA for studying structural variation from FFPE samples with data from a proof of concept study
Tue
May
22
11:00 am2018
Sponsored by
Thermo Fisher Scientific

From Qualitative to Quantitative: Experiences with a cfDNA Assay in Metastatic Breast Cancer Research

Genome Webinar

Postdoctoral Scholar, Kuhn/Hicks Laboratory, USC Michelson Center for Convergent Biosciences 

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 will discuss her team’s work using liquid biopsy technology for breast cancer research.

In particular, Dr. Xu will present 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 will present 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.

Sponsored by
Recent GenomeWebinars

PhD Student,
Petrov and Hadly Labs, Department of Biology, Stanford

Director of Product Management,
Dovetail Genomics

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
Tue
Mar
27
10:00 am2018
Sponsored by
Thermo Fisher Scientific

Adding CNVs and Fusions to a Lung cfDNA Assay: Impact on Oncology Clinical Research

Genome Webinar

Head of Pathology, Hospital Del Mar, Spain 

Director, R&D, Clinical Next Generation Sequencing Division, Thermo Fisher Scientific

In this webinar, the first in the “New Frontiers in Liquid Biopsy Research” series, Bea Bellosillo, head of pathology at the Hospital del Mar, discusses her experience evaluating an early-access lung cancer panel that detects copy number variants and fusions.

Dr. Bellosillo’s research lab was previously using the Ion Torrent Oncomine Lung cfDNA Assay from Thermo Fisher when it enrolled as a test site for an early-access program for the new lung panel that detects CNVs and fusions. Preliminary testing with the Oncomine Lung cfTNA (circulating free total nucleic acid) Assay indicated the presence of a RET fusion, which had not been detected previously. The finding led to a retrospective study of that sample where the RET fusion on the primary tumor was confirmed by FISH.

Following Dr. Bellosillo’s talk, Kelli Bramlett, senior director of R&D at the Clinical Next- Generation Sequencing Division at Thermo Fisher Scientific, presents a new white paper that showcases the performance of the new variant types introduced in the Oncomine Lung cfTNA Assay that Dr. Bellosillo was evaluating.

 

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

Sponsored by

Laboratory Specialist, Clinical Genetics, University Medical Center Utrecht (UMCU)

 

This webinar shares how clinical genetics labs can integrate cytogenetics and molecular data to assess abnormalities using a single sample on a single workflow platform.

The current standard of care in genomics diagnostics laboratories is advancing toward array testing and whole exome sequencing on a single sample. Additionally, labs are shifting to the analysis of all molecular events for a patient sample – whether structural (CNVs, deletions, duplications, LOH regions, translocations) or molecular (SNPs, insertions, deletions). Labs do this because they are confident the diagnostic yield of combined CNV / NGS analysis exceeds that of each individual assay type, making 1+1=3.

Moreover, historically, the cytogenetics lab and the molecular lab were separate domains, within different groups at the lab or hospital. Cartagenia Bench Lab software, which was acquired by Agilent in 2015, catered to these different customer types with separate applications. While labs that did both arrays and sequencing could make the modules talk together and collaborate, they were not tightly integrated.

Today, with Alissa Interpret, the next evolution of Cartagenia Bench Lab recently released by Agilent, array data and WES data can now be integrated for a single patient sample, allowing for combined CNV/SNV analysis on a single workflow platform.

In this webinar, Ellen van Binsbergen, a laboratory specialist in clinical genetics at the University Medical Center Utrecht (UMCU) in The Netherlands, shares how Alissa Interpret was used in a case of multiple skeletal abnormalities to assess data from CNV analysis via SNP array and from WES analysis. By jointly triaging, classifying, and curating molecular and structural variants, she shows how UMCU was able to pinpoint variants inherited from the father AND deletions in the maternal allele – all yielded from a single sample, on one platform.

Assistant Professor, Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University

This webinar discusses an optimized protocol for methyl-CpG binding domain sequencing (MBD-seq), which enables comprehensive, adequately powered, and cost-effective large-scale methylome-wide association studies (MWAS) of almost all 28 million CpG sites in the genome.

Studies of DNA methylation provide a promising route to gain further insight into many complex phenotypes, but detailed biological knowledge linking specific methylation sites to phenotypes is lacking, making MWAS critical. Whole genome bisulfite sequencing (WGB-seq) provides comprehensive coverage of the methylome, but is not yet practically feasible with the sample sizes required for MWAS. This limitation may explain why MWAS is commonly performed using microarray-based technologies, which assay only a very small fraction of the methylome.

Comparisons show that optimized MBD-seq approximates the coverage obtained with WGB-seq, but this performance is achieved at a fraction (~5%) of the reagent costs for WGB-seq, bringing it within the approximate price point of array-based methods. The MBD-seq protocol also allows for as little as 5-50 ng of high-quality genomic DNA as input, which allows for many sample types of limited availability to be assayed.

In this webinar, Karolina Åberg of Virginia Commonwealth University presents findings from MWASs of major depressive disorder and childhood trauma using DNA from brain, whole blood, and blood spots to provide a proof of concept that MBD-seq based MWAS can shed light on disease etiology and identify potential clinical biomarkers.

Sponsored by

Emery-Dreifuss Muscular Dystrophy Patient Advocate

Head of Lab; Clinical Genomics and Personalized Medicine Specialist,
Congenica

Deputy Head of Clinical Services,
Congenica

In this webinar, Jill Viles, an Iowa mother with no clinical training, shares her story of how she self-diagnosed her rare condition, a muscle-wasting disease caused by a mutation in the LMNA gene. She also discusses how she discovered that a mutation in the same gene is the underlying cause for the excess muscle phenotype exhibited by Canadian Olympic hurdler Priscilla Lopes-Schliep. 

Members of Congenica's clinical team also discuss their identification of a potential modifying gene, SMAD7, which may contribute to Jill’s alternative phenotype, and how these are being used to further research the cause of her disease.

This webinar will cover:

  • Jill's steps to discovery and how she first started working with Congenica
  • How Congenica found the potentially modifying variant
  • The SMAD7 gene mutation, and how Sapientia can be used to make similar diagnoses
  • How Jill is acting on this information and looking to the future
Thu
Feb
22
11:00 am2018
Sponsored by
SeraCare

A Practical Guide to Clinical Genomics Assay Validation

Genome Webinar

Founder,
Gnosity Consults

CSO,
SeraCare Life Sciences

This webinar walks through key considerations and helpful guidelines to accelerate next-generation sequencing (NGS)-based clinical genomics assay validation for less money and greater confidence in results.

NGS has revolutionized how assay developers, laboratories, and clinicians are diagnosing, treating, and managing disease. But before a clinical genomics assay can help guide patient care, it must be thoroughly validated. While validation principles are universal, the complexities of NGS can make the process a daunting task. In this webinar, clinical genomics expert Dr. Bob Daber uses real-world examples to highlight how highly multiplexed, patient-like biosynthetic reference materials offer substantial time and cost advantages over traditional materials and methods.


View this webinar to learn:

  • Specific ways you can save time and money while thoroughly validating an NGS-based clinical genomics assay
  • Validation best practices from leading clinical genomics laboratories
  • How to navigate the many guidelines and requirements of the various authoritative bodies for clinical genomics testing
Sponsored by

University of Vermont Health Network

College of Medicine, University of Vermont

Q2 Solutions, a Quintiles Quest Joint Venture

Genomenon

In this webinar, an expert panel discusses how they used a genomic search engine to mine the genomic literature for two key applications: variant interpretation and the development of evidence-based diagnostic gene panels.

Nikoletta Sidiropoulos and David Seward from the University of Vermont College of Medicine first discuss their approach and the tools used to quickly and thoroughly mine the scientific literature to interpret variants in somatic cancer cases.

Next, Victor Weigman from Q2 Solutions presents an evidence-based method that his team used to select the content for gene panels by mining millions of full-text genomic articles to identify disease-gene-variant relationships. Dr. Weigman discusses how he created an evidence-based gene panel in under a week with prioritized literature citations for each biomarker.

Finally, Mark Kiel, founder and chief scientific officer of Genomenon, discusses a comprehensive, evidence-based cancer panel that was produced using automated machine learning techniques. The pan-hematopoetic cancer panel is a comprehensive cancer panel of more than 300 genes supported by specific literature citations from among millions of research publications. Dr. Kiel discusses how his team used the Mastermind Genomic Search Engine software to objectively correlate genes and genetic variants with the quality and frequency of scientific literature citations.