GenomeWebinars

Anna and Zbigniew Scheller Professor of Medicine; Chair, Division of Experimental Pathology and Laboratory Medicine; Department of Laboratory Medicine and Pathology, Mayo Clinic

 

In this webinar, Dr. Fergus Couch from the Mayo Clinic will present data from a large study that used a targeted sequencing panel to determine pancreatic cancer risk associated with inherited mutations in several cancer predisposition genes.

Inherited germline mutations have been suggested to put individuals with prior family history at risk of developing pancreatic cancer. However, the risk of developing pancreatic cancer due to these mutations without a family history of the disease remains largely unknown. To address this, Dr. Couch and colleagues sequenced the coding regions and consensus splice sites of 21 cancer predisposition genes using an optimized custom DNA panel in more than 3,000 pancreatic cancer patients. Inherited mutations in six cancer predisposition genes were identified to be significantly associated with pancreatic cancer.

Dr. Couch will outline challenges of current targeted sequencing approaches for such large studies, detail the methodologies used to analyze this cohort, and present results of this study.

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

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

GenomeWebinar

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

Institute for Clinical Genetics at TU Dresden

This webinar will present the results of an evaluation of a web-based variant interpretation software system for clinical next-generation sequencing. 

NGS presents clinical laboratories with an ever-increasing amount of novel sequence variants that need to be interpreted in terms of their clinical relevance as transparently, accurately, and as fast as possible. In order to minimize inconsistencies between different labs, various guidelines for variant interpretation have been developed. Although these guidelines are very useful, they require a large set of criteria (like the 28 criteria of the American College of Medical Genetics and Genomics) that need to be assessed and checked for each variant. Doing this manually is very time-consuming.

In this webinar, Andreas Rump of the Institute for Clinical Genetics at Technical University Dresden will share his lab’s experience testing the web-based variant analysis software Qiagen Clinical Insight – Interpretation (QCI-I).

Dr. Rump’s team compared its manual interpretation of 278 missense variants in various genes with the automated interpretation from QCI-I. The concordance of interpretation results was very high.

Dr. Rump will share the results of the assessment, which found that QCI-I is fast, reliable, and standard-compliant, making it a useful asset for labs that use large NGS panels for the diagnostics of multigenic diseases. 

Sponsored by
Thu
Aug
9
1:00 pm2018
Sponsored by
Agena Bioscience

Analytical Utility of Mass-Spec Liquid Biopsy for NSCLC and Melanoma Samples

GenomeWebinar

Postdoctoral Fellow and Senior Researcher,
School of Medical and Health Sciences,
Edith Cowan University

Director, Clinical Genomic Testing Center
Kingmed Diagnostic

Senior Director, Scientific Affairs,
Agena Bioscience

In this two-part webinar, Dr. Elin Gray, from Edith Cowan University, and Ms. Weiwei Zhao, from Kingmed diagnostic, will compare the highly sensitive, multiplexed UltraSEEK technology, on the MassARRAY system, to digital droplet PCR (ddPCR) results on melanoma and non-small cell lung carcinoma samples.

Dr. Elin Gray will first demonstrate how the UltraSEEK Melanoma panel, probing for 61 mutations over 13 genes, provided equivalent analytical sensitivity and accuracy to ddPCR. This study included a blinded analysis of 68 mutations detected in 48 plasma samples from stage IV melanoma patients. Ms. Weiwei Zhao will also discuss her study between UltraSEEK EGFR to ddPCR for the detection of T790M, and other EGFR activating mutations in NSCLC. In this study, 94 cfDNA samples from advanced lung cancer patients, who were progressing on EGFR TKI, were run on UltraSEEK and ddPCR. Both UltraSEEK EGFR and ddPCR were able to achieve 0.1% minor allele fractions.

The two studies summarized in this webinar further demonstrate the benefits of using a highly sensitive and multiplexed technology when testing plasma-derived ctDNA for somatic mutations in cancer.

Due to our speakers being located in different time zones, this webinar will be pre-recorded. All webinar registrants have the opportunity to submit questions on the registration page and/or you can email them in after the webinar is released on August 9th.

Sponsored by

President & CTO, Genosity

This webinar will explore advances in next-generation sequencing (NGS) library prep technologies and their relationship to the evolution of targeted gene panels.

Our speaker will review different aspects of genomic sequencing across both germline and somatic applications and will explore the role that a robust exome can play in replacing smaller panels.

Specifically, this webinar will address:

  1. The process of developing new capture panels and optimizing assay performance;
  2. The technical performance of the Twist Human Core Exome probe design as it relates to covering the human exome; and
  3. The value in establishing a robust exome workflow for research and discovery.
Sponsored by
Wed
Aug
15
1:00 pm2018
Sponsored by
Swift Biosciences

The Cancer Avatar Project: Analyzing ctDNA to Monitor Treatment Response

GenomeWebinar

Senior Scientist,
California Pacific Medical Center Research Institute

Product Manager,
Swift Biosciences

This webinar will discuss the Cancer Avatar Project at the California Pacific Medical Center Research Institute (CPMCRI) and the efforts to overcome complexity of tumor profiling using the Accel-Amplicon sequencing workflow from Swift Biosciences.

In the first part of this webinar, CPMCRI's Dr. Pierre-Yves Desprez will discuss the Cancer Avatar Project, a multimodal approach that includes living biology, genomics, high-throughput pharmacologic screening, and informatics to design highly individualized treatment options for fast-growing solid tumors (8 different types of cancer) in patients who have exhausted standard-of-care options.

His team has optimized a method for sequencing circulating tumor DNA (ctDNA) obtained from patients' blood. Mutations identified in ctDNA can reflect alterations found in the primary tumor. Using Swift’s Accel-Amplicon 56G Oncology Panel v2 kit for target amplification (and the Genialis platform for analysis), ctDNA samples were sequenced with the Illumina MiSeq machine. Dr. Desprez will share DNA sequencing results from more than 100 matched tissue and ctDNA samples to reveal driver mutations. Additionally, he will outline the lab’s strategy to analyze mutational profiles of longitudinal blood biopsies to monitor each patient’s response to treatment and/or evolution toward resistance in real time and in a non-invasive manner. This information will be instrumental in designing treatment strategies in patients with recurrent or progressive disease.

In the second part of this webinar, Dr. Drew McUsic of Swift Biosciences will give a brief overview of Swift’s Accel-Amplicon NGS workflow and the new customizable cancer panels for targeted sequencing studies

Sponsored by
Thu
Aug
16
11:00 am2018
Sponsored by
Dovetail Genomics

De Novo Assembly of a Model Species to Study Asexual Reproduction in Plants

GenomeWebinar

National Scientific and Technical Research Council, Argentina

This webinar will discuss a project to sequence and assemble the genome of Eragrostis curvula (weeping lovegrass), a perennial grass native to Southern Africa, as a model species to study asexual reproduction in plants.

Apomixis is defined as asexual reproduction by seeds, avoiding meiotic reduction and fertilization, being generally present in polyploid plant species. Weeping lovegrass can be considered as a model for the discovery of genes that govern pseudogamous diplosporic apomixis since its polyploid cytotypes (4x to 8x) may undergo sexual reproduction, facultative apomixis, or obligate apomixis whereas diploids are always sexual.

Our speaker, Viviana Echenique of Argentina's National Scientific and Technical Research Council, will discuss the first sequence of the E. curvula genome. The cultivar selected was a sexual diploid (~1,200 Mb) that originated from in vitro culture of inflorescences of the apomictic cv. Tanganyika (2n=4x=40). Sequencing was performed on the Pacific Biosciences platform and after the assembly one Dovetail Chicago and one Dovetail Hi-C library was added, obtaining chromosomes size contigs covering 95 percent of the diploid genome.

The high proportion of annotated genes is expected to enable the identification of genes related to reproduction. This genome is the starting point to obtain more complex tetraploid genomes that harbour the regions involved in apomixis.

Sponsored by

Graduate Student, University of California, Santa Cruz

Graduate Student, University of Washington

Research Technician, Stowers Institute for Medical Research

This webinar will provide an overview of recent advances in single-cell RNA sequencing from the perspectives of three research organizations.

Our first speaker, Ashley Byrne of the University of California, Santa Cruz, will discuss a long-read cDNA sequencing approach based on Oxford Nanopore sequencing technology to evaluate RNA isoform diversity in single B cells.

Using this approach, Byrne and colleagues have been able to reconstruct isoform-level transcriptomes using their analysis pipeline Mandalorion. They also discovered that much of the RNA isoform diversity observed is found across B cell-specific receptors, which could have implications for immunotherapy design — specifically for targeting B cell lymphomas.

Next, Junyue Cao of the University of Washington will share a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei.

Cao's team used the method, called sci-RNA-seq (single cell combinatorial indexing RNA sequencing) to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 stage, which is over 50-fold “shotgun cellular coverage” of its somatic cell composition. Cao will discuss how the data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.

Our third speaker, Kate Hall of the Stowers Institute for Medical Research, will share two different workflows her team has developed to streamline single-cell RNA-seq services.

The first workflow uses the Single Cell Chromium Controller from 10X Genomics and allows thousands of cells to be pooled together and processed as a single reaction. The high-throughput nature of this method can help identify unique cell populations in a given pool. The second workflow uses the Mantis small-volume pipetting robot from Formulatrix to set up quarter-sized reactions for cDNA synthesis on individual cells. This workflow is more suitable for a smaller sample set as it can help give a more detailed view of specific cell types via full-length transcript sequencing.

For more information on other webinar in this series, click here.

Sponsored by

Chief Operations Officer,
Institute for Protein Innovation 

This webinar will discuss an automated, high-throughput method of generating high-quality antigens and antibodies.

James D. Love, Chief Operations Officer of the Institute for Protein Innovation, will discuss the method, which was developed in line with the institute's mission to generate open-source antibodies against every human extracellular and secreted protein.

Dr. Love and colleagues have developed expression platforms capable of generating high-quality antigens and antibodies. These platforms are based on prior research for high-throughput production of integral membrane and other challenging proteins. Optimized transient transfection is performed via automated processes at 1 mL and 30 mL scales, and semi-automated for larger scales in HEK and CHO cells. 

Dr. Love will also discuss how the challenges associated with high throughput at larger scales are being addressed with new liquid handling platforms. 

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
Wed
Aug
29
1:00 pm2018
Sponsored by
Canon BioMedical

Implementing Novel Technologies in the Core Lab: Spatial Transcriptomics and Sci-MET

GenomeWebinar

Chief Operating Officer, Spatial Transcriptomics

Next Generation Sequencing and Single Cell Genomics Platform Head, Functional Genomics Center Zurich

PhD Candidate, Oregon Health & Sciences University

This webinar will discuss two potentially disruptive technologies — spatial transcriptomics and single-cell methylome combinatorial indexing (sci-MET) — along with considerations for implementing them in a core facility setting.

Spatial transcriptomics combines traditional histological information with genome-wide transcriptome data by using high-resolution tissue imaging and RNA capture. This is made possible by placing thin tissue sections on microscopic glass slides, which are covered with spatially barcoded cDNA primers. Researchers using this technology have produced high-quality data from a variety of tissue types (for example brain, breast cancer, prostate cancer and heart) and organisms (human, mouse, and plants) and spatially barcoded arrays have also been applied to study single cells in solution.

Single-cell combinatorial indexing (sci-) is a robust and generalizable protocol family developed for the interrogation of single-cell omics. Sci- protocols follow a shared strategy of forming a unique barcode per nuclei through multiple iterations of indexing, pooling, and random sampling. With this method, protocols for single-cell library generation assaying the transcriptome, chromatin accessibility, genome-wide copy-number variation, chromatin conformation, and most recently, the methylome have been described. The methylome protocol (sci-MET) was used to generate 3,282 high-quality single-cell whole-genome methylation libraries. With low coverage, sparse methylation information was shown to be sufficient in discriminating cell types, both in a synthetic mixture of cell lines and in a neuronal subtype from mouse cortical samples. Sci-MET, as well as the other sci- protocols, provide an avenue for high-throughput single-cell omics necessary to interrogate the nuance and complexity of complex and developing tissue. 

In this webinar, our panelists will discuss specifics of these technologies and their applications, within a particular focus on their implementation in core facilities.

For more information on other webinar in this series, click here.

Sponsored by

Associate Director, Global Clinical Operations, Illumina

Lab Operations Director, Navican

Lab Director,
University of Illinois Chicago

Today’s challenging clinical next-generation sequencing applications require a rigorous, comprehensive quality control management program to ensure confidence in results.

In this roundtable discussion, three industry experts will share practical learnings on implementing a best-in-class clinical NGS lab QC management program on time and budget.

Learn how QC has been implemented by your peers as the panel expands on the results of the most comprehensive survey to date on NGS QC practices.

 

 

Registrants for this webinar are encouraged to take the survey here. Data from the survey will be shared during the webinar, and the survey provides the opportunity for registrants to share questions for the panel.

Sponsored by
Tue
Sep
18
11:00 am2018
Sponsored by
Horizon Discovery

Validation and Internal QC of Clinical NGS to Support an Accredited Diagnostic Workflow

GenomeWebinar

Head of Bioinfomatics, Sarah Cannon Molecular Diagnostics

In this webinar, Kevin Balbi, head of bioinformatics at Sarah Cannon Molecular Diagnostics, will discuss the validation of targeted sequencing panels on the Ion Torrent platform using Horizon Discovery’s Tru-Q controls. He will also discuss how those controls are being used for ongoing internal quality control (IQC) and how this has supported a recent laboratory inspection by the United Kingdom Accreditation Service under ISO15189.

Sarah Cannon Molecular Diagnostics, part of HCA Laboratories in London, offers a range of molecular assays, from single-gene variant analyses through to a 50-gene panel somatic variant analysis, MLH1 promoter hypermethylation, T & B cell clonality assessment, and microsatellite instability status.

Validation of targeted sequencing panels for clinical diagnostic use requires reference material with a range of known variants and confirmed variant frequencies. Additionally, the continual assessment of assay performance is key to ensuring robust and reliable results.

Dr. Balbi will demonstrate how his team has validated three targeted DNA sequencing panels for clinical diagnostic use and assessed their limit of detection using the Horizon Discovery Tru-Q controls. He will explain the lab's approach to IQC, also showing the reliability of the assays over time. These data contributed to the accreditation of the bioinformatics workflow under ISO15189.

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

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

GenomeWebinar

Co-founder & Chief Technology Officer, Amplexa Genetics

 

This webinar discusses how ultra-highly sensitive and customizable targeted next-generation sequencing panels are applied in inherited disease research. In particular, the seminar highlights 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, shares how this study led to the evaluation of the coming soon Ion AmpliSeq HD* targeted NGS solutions from Thermo Fisher Scientific. He shares 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.


Sponsored by

Principal Investigator of the Laboratory of Functional Neurogenomics, University of Miami, Miller School of Medicine

This webinar discusses a project that is analyzing the “Human Brainome” – genome, transcriptome, proteome, and phenome interaction data -- to gain insights into Alzheimer’s disease pathogenesis.

Amanda Myers of the University of Miami Miller School of Medicine describes the study, which used two separate sets of human brain tissue for analysis. Genome, transcriptome and proteome data was collected and analyzed to determine key drivers for Alzheimer’s pathology. Both an analysis of single effects (DNA driving downstream expression of one target) as well as multi-target analysis (transcript and peptide networks) was performed. 

From a set of ~ 5.2 million SNPs, ~15,000 transcripts and ~2000 peptides a small subset of targets was discovered that are computationally predicted to be crucial to disease processes and replicated between our two sets of tissues. Targets were validated in the wet lab to insure that these targets on their own had effects on the specific Alzheimer’s disease brain pathology. Several targets on their own effected disease processes, demonstrating that our pipelines are robust and nominating these targets as new Alzheimer’s disease candidate genes.

 

For more information on other webinar in this series, click here.

Sponsored by

VP of Clinical Affairs, Veritas Genetics

Founder, Genomenon

This webinar discusses an approach for automating variant classification based on the American College of Medical Genetics and Genomics guidelines.

Variant interpretation presents a bottleneck for many labs, posing a challenge to the broader adoption of precision medicine. The ACMG/AMP variant classification framework has provided a foundation for this process, but several key obstacles remain. In particular, the identification and prioritization of key publications presents a time- and resource-intensive challenge for many labs.

View this webinar for a discussion on how Veritas Genetics collaborated with Genomenon to develop a new Literature Classification Tool within the Mastermind Genomic Search Engine to address these challenges.

The speakers demonstrate:

  • How to more efficiently identify and prioritize publications by ACMG variant classification guidelines
  • How increased specificity and immediate access to annotated search results accelerates variant interpretation workflow
  • How increased sensitivity in literature search results in fewer false negatives

The speakers discuss promising Veritas trial results that point to a better and faster variant interpretation workflow using the new Literature Curation tool in the Mastermind Genomic Search Engine.

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

An Optimized NGS Workflow for Human Metagenomic Analysis

GenomeWebinar

Senior Scientist, Genomic Applications Department, Illumina

This webinar reviews 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 discusses a comparative metagenomics study that relied on a high-throughput and automated library prep protocol for stool. Dr. Czyz discusses several parameters and methodologies that her team tested as well as the key findings of the study.

Sponsored by
Wed
Jun
27
1:00 pm2018
Sponsored by
Roche

Clinical Utility of Liquid Biopsy for Targeted TKI Therapy in NSCLC

GenomeWebinar

Chair, Solid Tumor Oncology and Investigational Therapeutics, Donald S. Kim Distinguished Chair for Cancer Research, Levine Cancer Institute, Atrium Health

Director of Molecular Pathology, Carolinas Pathology Group

This webinar presents data from the Flaura trial and shows the clinical utility of liquid biopsy in identifying non-small-cell lung cancer (NSCLC) patients who may benefit from targeted TKI therapies. .

Recently, the US Food and Drug Administration approved AstraZeneca's Tagrisso (osimertinib) for first-line treatment of patients diagnosed with advanced NSCLC whose tumors have epidermal growth factor receptor (EGFR) exon 19 deletions or exon 21 L858R mutations. This approval expanded the options for clinicians to use tyrosine kinase inhibitors to treat their patients with newly diagnosed EGFR-mutated NSCLC.

In parallel to this approval, the FDA also approved expanded indications for the use of the cobas EFGR Mutation Test v2 as a companion diagnostic to Tagrisso with either tumor tissue or plasma.

This webinar reviews the key findings from the Phase III FLAURA trial that supported these approvals. Additionally, as lung cancer has been at the forefront for liquid biopsies, this webinar will present data supporting the clinical utility of liquid biopsy in providing patients with a) a non-invasive alternative to a traditional tumor biopsy when no tissue is available, and b) faster time to results about their tumor mutation status, thus allowing physicians to initiate targeted therapy expeditiously when warranted.

Sponsored by

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 discusses 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
21
1:00 pm2018
Sponsored by
Roche

Evaluation & Implementation of NGS Liquid Biopsy Assays

GenomeWebinar

Berlin Institute of Health Genomics Core Platform

This webinar provides a detailed look at how a genomics lab implemented next-generation sequencing (NGS) liquid biopsy assays into its in-house clinical research program.

Interest in liquid biopsy has escalated in recent years due to the minimally invasive sampling method, potential to overcome the challenges of tumor heterogeneity, and the potential for longitudinal monitoring of tumor burden through serial sampling.  Furthermore, the growing adoption of NGS allows more labs to perform NGS liquid biopsy tests in house.

In this webinar, Dr. Tomasz Zemojtel of the Berlin Institute of Health discusses how his lab implemented Roche's Avenio ctDNA Analysis Kits for in-house clinical research testing. He will discuss:

  • Utility and flexibility of liquid biopsy assays for various research applications
  • Specific parts of the liquid biopsy workflow that are critical for achieving high technical performance and accurate results, such as molecular barcoding and hybrid capture technology
  • Implementation strategy for liquid biopsy assays using artificial plasma samples
  • Data analysis and interpretation

Lastly, Dr. Zemojtel discusses the data obtained with the Avenio assay workflow from clinical research subjects with ovarian cancer.

Sponsored by
Wed
Jun
20
11:00 am2018
Sponsored by
PerkinElmer

Expert Tips on Sequencing and Library Prep from the Wellcome Sanger Institute

GenomeWebinar

Senior Staff Scientist - R&D Sequencing, Wellcome Trust Sanger Institute

In this webinar, Michael Quail of the R&D Sequencing team at the Wellcome Trust Sanger Institute will provide an expert perspective on library prep for next-generation sequencing. 

The Sanger Institute is a large-scale biomedical research and genome center funded by the Wellcome Trust. The institute was an early adopter of Illumina sequencing technology and was one of the first labs in the world to automate library prep. 

Dr. Quail discusses problems and biases that can occur during NGS library prep and ways to avoid them. He reviews the various steps in sequencing library construction and discuss how biases in genomic content and sample representation can arise in sequencing libraries. 

Dr. Quail's presentation includes recommendations on how to avoid such biases, resulting in more even sequence coverage and fewer samples with insufficient coverage for meaningful analysis.

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

RNA in situ Hybridization: The Next Generation of Immunohistochemistry?

GenomeWebinar

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

GenomeWebinar

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
12
1:00 pm2018
Sponsored by
Philips Genomics

Bridging the Gap Between Testing and Treatment in Precision Oncology

GenomeWebinar

Chief Technology Officer, Navican

Chief Technology Officer, Philips Genomics

This webinar highlights a comprehensive end-to-end solution for precision care in oncology, comprising sample acquisition through to sequencing and analysis, treatment recommendations, and follow-through.

Scott Skellenger, chief technology officer of Intermountain Healthcare spinout Navican, discusses the infrastructure Navican has put in place to match patients with prioritized treatment options in order to deliver better outcomes while reducing the overall cost burden on the healthcare system.

Navican's services assist oncologists and their patients throughout the process of acquiring and profiling a tumor sample, reviewing the case and making a prioritized treatment recommendation with the molecular tumor board, facilitating therapy access and appeals, and ongoing patient follow-up.

Navican has partnered with Philips to leverage IntelliSpace Genomics as the hub of its clinical and informatics infrastructure. Scott discusses how Navican is using IntelliSpace Genomics to capture and transform genomic and clinical data in support of providing treatment decisions.

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

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

GenomeWebinar

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

GenomeWebinar

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.

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Professor, Dept of Clinical Genetics, Uppsala University Hospital, Sweden

This webinar discusses how streamlined selection of library preparation, data analysis, and variant assessment workflows can make next-generation sequencing readily accessible for labs studying inherited disorders, particularly in cases where data analysis is currently a bottleneck.

Our speaker, Professor Marie Louise Bondeson of Uppsala University, from the department of Clinical Genetics, shares her lab’s experience building an NGS research workflow comprising gene panel testing, exome sequencing, and data analysis.  

Dr. Bondeson’s team has evaluated the SureSelect Custom Constitutional Panel 17Mb (CPP17) for implementation of gene panel testing. The CPP focuses only on genes with known disease associations. For whole-exome sequencing, her lab has evaluated SureSelect Human All Exon v7, which is a comprehensive exome that focuses on the interpretable part of the genome.

Dr. Bondeson describes how her team analyzed the NGS data with an in-house bioinformatics pipeline and then compared that with Alissa Align & Call. Filtration and variant interpretation was performed using Alissa Interpret according to the lab’s workflow.

 

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Senior Research Scientist, New York Genome Center’s Technology Innovation Lab

Resident Physician, Department of Anatomic Pathology, division of Neuropathology, University of California San Francisco

This webinar introduces new technologies that enable multidimensional measurements from single cells to obtain a more complete picture of a cell’s phenotype and gene expression.

The first part of the webinar describes two recently developed applications that use antibody conjugated oligos to enhance existing single-cell RNA-seq platforms: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing), which allows measurement of a potentially unlimited number of protein markers in parallel to transcriptomes; and Cell Hashing, which enables sample multiplexing, robust multiple detection, and super-loading of scRNA-seq platforms, allowing confident recovery of four times as many single cells per experiment.

The second part of the webinar covers the recently developed Patch-seq technique, which combines whole-cell patch clamp recording, immunohistochemistry, and single-cell RNA-sequencing to obtain high-quality morphology, electrophysiology and scRNA-seq data in parallel from single cells.

Our expert panelists present an overview of the key protocol steps and quality control measures, as well as a discussion of potential applications and ongoing efforts to increase throughput.

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