GenomeWebinars

Tue
Jun
26
12:00 pm2018
Sponsored by
Lexogen

The Landscape of Alternative Polyadenylation in the Lung Cancer Transcriptome

Genome Webinar

National Cancer Institute, Center for Cancer Research

This webinar outlines a study that sought to characterize the landscape of alternative polyadenylation (APA) in the lung cancer transcriptome in order to gain insight into the role of APA in cancer progression.

APA involves the selection of an alternate poly(A) site on the pre-mRNA that leads to generation of isoforms of various length. In cancer, APA is emerging as an alternative mechanism for proto-oncogene activation in the absence of somatic mutations. Recent studies show a correlation of APA profiles with cancer prognosis, suggesting that APA is an important mechanism of cancer progression. In addition, environmental exposures such as temperature and exogenous hormones can also induce APA as a stress-response mechanism.

In this webinar, Dr. Adriana Zingone of the National Cancer Institute, Center for Cancer Research will discuss her team's work to characterize APA in the lung cancer transcriptome and to test a hypothesis that smoking modulates differential usage of polyadenylation sites within mRNA transcripts.

Sponsored by
Thu
Jun
28
1:00 pm2018
Sponsored by
PerkinElmer

An Optimized NGS Workflow for Human Metagenomic Analysis

Genome Webinar

Senior Scientist, Genomic Applications Department, Illumina

This webinar will review a standardized, high-throughput, and fully automated library prep protocol for human metagenomic analysis. 

The human gastrointestinal tract hosts up to 100 trillion microbes with the greatest numbers residing in the distal gut. Given the vast presence of microbial genetic information, the ability to characterize communities from fecal material via next generation sequencing (NGS) has revolutionized the understanding of the human microbiome, and its influence on health. In order to gain further insight on these influences, the need for a standardized and scalable NGS metagenomics protocol is needed to minimize inconsistencies among existing methods (sample collection, sample storage conditions, experimental design, and scalability), which typically lead to data disparities and misrepresentation of the true state of the human microbiome.

In this webinar, Dr. Agata Czyz of Illumina's Genomic Applications Department will discuss a comparative metagenomics study that relied on a high-throughput and automated library prep protocol for stool. Dr. Czyz will discuss several parameters and methodologies that her team tested as well as the key findings of the study.

Sponsored by

Founder, AdvaGenix

This webinar offers a look at how an advanced genetics laboratory implemented and validated a commercial bioinformatics system to help scale its operations. 

William Kearns, founder of genetics testing lab AdvaGenix, will share his team's experience as it sought to increase its testing throughput while maintaining high quality standards. After studying the time and cost associated with building and validating a bioinformatics platform from scratch, as well as the cost of maintaining such a system, the AdvaGenix team decided to look for commercial solutions. 

AdvaGenix needed a solution that adhered to society guidelines and also included domain expertise in genetic testing. The team ultimately opted for a system from Qiagen and has since been able to scale up its operations by at least 25-fold.  Dr. Kearns will discuss his team's experience and learnings from this implementation and the results they have seen so far.

Sponsored by
Thu
Jul
19
11:00 am2018
Sponsored by
Thermo Fisher Scientific

Advances in NGS for Ultra-High Sensitivity Applications in Translational and Clinical Research

Genome Webinar

Co-founder & Chief Technology Officer, Amplexa Genetics

 

This webinar will discuss how ultra-highly sensitive and customizable targeted next-generation sequencing panels are applied in inherited disease research. In particular, the seminar will highlight a study that sought to test the hypothesis that causative genetic variants for inherited diseases that often fall into the category of “de novo mutations” are sometimes the result of undetected mosaicism in the parents.

In this webinar, Hans Atli Dahl, co-founder and chief technology officer at Amplexa Genetics, will share how this study led to the evaluation of the coming soon Ion AmpliSeq HD* targeted NGS solutions from Thermo Fisher Scientific. He will share details of how the Ion AmpliSeq HD* panels address the need for ultra-high sensitive detection and its potential to deliver new insights about the causes of these types of genetic diseases.

Amplexa Genetics, based in Denmark, specializes in clinical genetic testing and clinical variant interpretation associated with a variety of disorders. The company has a long history of NGS analysis in epilepsy and other encephalopathies and recently moved into molecular genetics of endocrine disorders and direct-to-consumer testing for recessive inheritance risk-assessment.

 

For Research Use Only. Not for use in diagnostic procedures.

*The content provided herein may relate to products that have not been officially released and are subject to change without notice.

Sponsored by
Wed
Jul
25
1:00 pm2018
Sponsored by
Streck

Antibiotic Gene Surveillance: What You Don’t See Can Hurt You!

Genome Webinar

Professor & Director, Center for Research in Anti-Infectives and Biotechnology. Department of Medical Microbiology and Immunology, Creighton University

This online seminar will discuss the advantages of incorporating molecular testing into the microbiology laboratory to aid in the identification of relevant antibiotic resistance mechanisms. 

Surveillance of resistance mechanisms, hospital infection control, and epidemiology require accurate detection of extended-spectrum beta-lactamases (ESBLs), AmpC beta-lactamases, and carbapenemases. For example, an important aspect of infection control is to determine how resistance is spread. Is the spread of resistance due to a clonal outbreak or the movement of mobile genetic elements?

The majority of ESBLs and relevant carbapenemases are encoded on mobile genetic elements; however, AmpC production can be either chromosomal- or plasmid-mediated. Several phenotypic methodologies have been developed to address the detection of beta-lactamase genes, but few can detect the production of AmpC, and none can discern the difference between a chromosomal and plasmid-mediated AmpC producer. Furthermore, a major concern for infectious disease personnel is the inability to detect ESBLs in the presence of AmpC production.

Molecular techniques are required to determine the presence of multiple beta-lactamases within a single isolate or to discriminate between different types of beta-lactamases leading to similar beta-lactam susceptibility patterns. In addition, resistance mechanisms are emerging to other antibiotic classes. The challenge for the infectious disease community is to determine when and if to use molecular testing to aid in the identification of relevant resistance mechanisms, especially when encountering complex susceptibility patterns.

This seminar will highlight the most relevant beta-lactamases and the challenges facing the incorporation of molecular testing into the laboratory. Targets in addition to beta-lactamase genes will also be discussed.

Sponsored by
Recent GenomeWebinars
Tue
Jun
19
1:00 pm2018
Sponsored by
Advanced Cell Diagnostics

RNA in situ Hybridization: The Next Generation of Immunohistochemistry?

Genome Webinar

Director of Anatomic Pathology, Department of Laboratory Medicine,
Geisinger Health System

Chief Medical Officer,
Advanced Cell Diagnostics

This webinar provides evidence for the use of RNA in situ hybridization (RNA ISH) as a replacement for immunohistochemistry (IHC) in cancer research and diagnostic applications.

IHC is the gold standard for many diagnostics, but the approach has some shortcomings, including low diagnostic sensitivity, background staining, unstable antibodies, no available antibodies and a multitude of staining protocols.

RNA ISH has the ability to overcome these problems with IHC and has the potential to address issues with other technologies, including molecular “grind and bind” methods such as PCR, next-generation sequencing and gene expression profiling. The RNAscope RNA ISH method from Advanced Cell Diagnostics uses a brightfield in situ hybridization-based assay to visualize cellular RNA in formalin-fixed, paraffin-embedded tissue sections. The highly sensitive assay shows promise for detecting biomarkers that are missed by other methods.

In this webinar, IHC expert Fan Lin of Geisinger Health System reviews the common applications of RNA ISH in anatomic pathology, discusses how to interpret RNA ISH results and touches on the potential pitfalls of RNA ISH.

Sponsored by
Thu
Jun
14
11:00 am2018
Sponsored by
Sophia Genetics

Overcoming Challenges in Hematological Genomic Testing with Advanced AI

Genome Webinar

Assistant Professor, UNC School of Medicine

Clinical Application Product Manager, Sophia Genetics

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.

Sponsored by
Tue
Jun
5
11:00 am2018
Sponsored by
Linguamatics

Text Mining at Sanofi for Genotype-Phenotype Associations in Multiple Sclerosis

Genome Webinar

Associate Director, Translational Sciences,
Sanofi

Head of Life Science,
Linguamatics

This webinar discusses how Sanofi used literature mining to annotate the association of human leukocyte antigen (HLA) alleles with diseases and drug hypersensitivity as part of a multiple sclerosis (MS) biomarker discovery project.

For any drug development project, it is important to have a comprehensive understanding of the genetic associations for the disease of interest. While public databases of genomic variants provide valuable information, there can be many gaps in the biological knowledge. For Sanofi’s internal MS biomarker project, they needed a comprehensive catalogue of annotations to HLA alleles and turned to Linguamatics I2E to text-mine the scientific literature.

The HLA region is the most polymorphic region of the human genome. HLA alleles have been associated with more than 40 different autoimmune diseases, various types of cancer, infectious disease, and drug adverse events. However, there are no known resources that systematically annotate the association of HLA alleles and diseases.

For the Sanofi MS project, a workflow was established for whole-exome sequencing-based HLA typing and analysis. This identified more than 400 HLA alleles. The Linguamatics I2E platform was used to search the literature to annotate the association of the HLA alleles with diseases and drug hypersensitivity. This project resulted in more than double the previous disease associations and the curated annotations were fed into a knowledge base for broad use within the Sanofi team.


What will you learn?

  • How natural language processing (NLP) text mining can extract structured data from unstructured text in scientific papers
  • How text mining is used at Sanofi to extract the most up-to-date published knowledge for a gene or group of genes, including information on diseases and specific allele variations
Sponsored by
Tue
May
22
11:00 am2018
Sponsored by
Thermo Fisher Scientific

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

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 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.

Sponsored by
Tue
May
15
11:00 am2018
Sponsored by
Tecan

Reaping the Benefits of Algorithm-Driven Research in Synthetic Biology

Genome Webinar

Co-Founder & CEO, LifeFoundry

This webinar discusses how an algorithm-driven synthetic biology system can enable engineering of biological systems for a range of applications.

Synthetic biology applies engineering principles to study biological systems through design-build-test cycles and offers great promise for applications in healthcare, the biochemical industry, as well as fundamental discovery. However, the workflows are still mainly driven by human scientists, making it slow, expensive, and prone to human error and biases.

Our speaker, Ran Chao of the University of Illinois, shares details of a fully automated and highly versatile biological foundry that allows algorithms to directly design biosystems, orchestrate workflows, and analyze data. Dr. Chao discusses the latest applications of algorithm-driven synthetic biology at the University of Illinois as well as at LifeFoundry, a synthetic biology startup. He also shares applications of Tecan liquid handling systems in high-throughput TALEN (transcription activator-like effector nucleases) synthesis as well as rapid strain development processes.

Sponsored by

Head of Molecular Biology and Cell Engineering, Cerevance

Product Manager, NuGEN

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.

Sponsored by
Tue
May
8
1:00 pm2018
Sponsored by
Dovetail Genomics

Structural Variation Detection by Proximity Ligation from FFPE Tumor Tissue

Genome Webinar

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

Director of Product Management, Dovetail Genomics

This webinar discusses 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 highlights 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
Sponsored by
Tue
May
1
1:00 pm2018
Sponsored by
Horizon Discovery

Analytical Validation of a Liquid Biopsy Assay for High-Sensitivity Molecular Profiling

Genome Webinar

Head of Technology and Assay Development, Inivata

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).

Sponsored by
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, shares 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 discusses 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 shares 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
Tue
Apr
3
1:00 pm2018
Sponsored by
Dovetail Genomics

Enabling Non-Model Organism Genomics with Multi-Dimensional NGS Datatype

Genome Webinar

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
Sponsored by
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