GenomeWebinars

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

Assistant Professor, Department of Molecular and Human Genetics; Human Genome Sequencing Center, Baylor College of Medicine

Luke Stewart, BS, Senior Manager, Field Applications, Fluidigm Corporation

This webinar will share details of how the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine implemented a sample identity assay as part of its next-generation sequencing (NGS) workflow.

The importance of ensuring sample integrity and quality from sample acquisition to final data analysis and delivery is a shared concern among researchers involved in clinical and translational research — particularly with complex, multiphase studies.

The HGSC generates data to support numerous research programs that require rapid delivery of high-quality sequencing data. To ensure end-to-end sample and data integrity, the HGSC has implemented the Fluidigm SNP Trace assay to confirm sample identity in its workflow. 

In this webinar, Jianhong Hu will describe the HGSC’s high-throughput sequencing and reporting pipeline and discuss how the center has integrated sample identification into its overarching workflow. Luke Stewart, Senior Manager of Field Applications at Fluidigm, will conclude the discussion with information on new advancements in sample identification offered by Fluidigm.

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
Wed
Sep
12
11:00 am2018
Sponsored by
Qiagen

T-Cell Receptor Sequencing for Melanoma Immunotherapy Monitoring

GenomeWebinar

Inserm Research Director, Tumor Immune Responses and Immunotherapy
Inserm Cancer Research Center

Researcher, Tumor Immune Responses and Immunotherapy
Inserm Cancer Research Center

This webinar will discuss ongoing work to apply T-cell receptor sequencing (TCRseq) approaches to immunotherapy monitoring for melanoma patients.

Despite its undisputed superior clinical efficacy compared to chemo- or radiotherapy, anti-PD-1 monotherapy remains inefficient on more than 60 percent of cancer patients. Acute toxicities are less common than those reported for anti-CTLA-4 therapy but remain an appreciable risk for patients. For these reasons, defining early and robust predictive markers of clinical response is crucial both to improve patient management and to reduce treatment costs. Furthermore, the comprehensive analysis of PD-1 regulation and signaling will also have a considerable impact on the optimization of other immunotherapies such as T-cell-based immunotherapies.

In this webinar, researchers from the Inserm Cancer Research Center in Nantes, France, will share findings from studies seeking to understand the molecular mechanisms regulating PD-1 expression in melanoma-specific T lymphocytes. Their work points toward methods for monitoring the immune responses of cancer patients treated with anti-PD-1 antibodies as well as for the selection of optimal effector T cells for adoptive cell transfer treatments.

The presentations will offer new prospects for patient monitoring based on TCRseq approaches.

Sponsored by

Senior Lab Manager,
LifeLabs Genetics

Senior Scientific Director,
Research Animal Diagnostic Services,
Charles River Laboratories

Global Product Support Manager,
Agena Bioscience

This webinar will share details of how two large reference and service laboratories have rapidly deployed highly multiplexed genotyping assays to meet their clients' testing needs.

Our first speaker, Connie Lisle from LifeLabs Genetics, the largest clinical laboratory in Canada, will discuss various pharmacogenetics panels her lab has developed on the MassArray system.

Our second speaker, Dr. William Shek from Charles River Laboratories, a pre-clinical and clinical laboratory service provider, will share his laboratory’s experience with developing preclinical assays on animal models to support drug discovery and development with the MassArray MassARRAY system.

Sponsored by

Associate Director, Global Clinical Operations, Illumina

Lab Operations Director, Navican

Lab Director,
University of Illinois Chicago

Gregory J. Tsongalis, PhD, HCLD, CC,
Professor of Pathology;
Director, Laboratory for CGAT;
Department of Pathology and Laboratory Medicine,
Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine at Dartmouth

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
Thu
Sep
20
1:00 pm2018
Sponsored by
St. Jude Children's Research Hospital

Cloud-based Data and Analysis Tools Yield Novel Insights for Cancer Research

GenomeWebinar

Professor and Associate Director of Computational Biology,
Jackson Laboratory of Genomic Medicine

Manager of Bio Info Software Development,
St. Jude Children's Research Hospital

Group Lead, Bioinformatics Analysis,
St. Jude Children's Research Hospital

This webinar will provide an overview of how St. Jude Cloud, a public repository of pediatric cancer genomics data and analysis tools, is impacting cancer research.

Developed in partnership with Microsoft and DNAnexus, the St. Jude Cloud offers next-generation sequencing data and analysis tools in a secure cloud-based environment. Access to data is simple, fast and does not require downloading prior to exploration. Researchers can also upload their own data in a private, password-protected environment to use the St. Jude Cloud visualization and analysis tools.

In this webinar, Scott Newman, biological lead, and Clay McLeod, lead developer of St. Jude Cloud, will provide an overview of this platform, which includes more than 5,000 whole-genome, 5,000 whole-exome, and 1,200 RNA-seq datasets from more than 5,000 pediatric cancer patients and survivors. They will also demonstrate the collection of bioinformatics tools and visualizations to help both experts and non-specialists gain novel insights from genomics data.

In addition, Roel Verhaak of the Jackson Laboratory for Genomic Medicine, will discuss how his lab is using the whole genome sequencing datasets available on the Cloud to study the processes that underlie treatment resistance and progression in brain tumors.

Sponsored by

Molecular Pathology Department;
University Hospital Dijon

This webinar describes the implementation of a digital PCR system in an academic hospital setting to manage the treatment of cancer patients.

Benjamin Tournier, from the molecular pathology department of University Hospital Dijon, will share details of his lab's liquid biopsy setup, which is using the Naica 3-color Crystal Digital PCR system from Still Technologies to manage melanoma and lung cancer patients under targeted therapy.

Attendees of this webinar will:

  • Gain a better understanding of the liquid biopsy process for metastatic melanoma and lung cancer patients
  • Understand the Naica System workflow and its advantages
  • Learn the benefits of digital PCR for the detection of circulating tumor DNA, circulating tumor cells, and circulating tumor exosomes in liquid biopsy
  • Understand the advantages of digital PCR for monitoring patients and their treatment
Sponsored by
Wed
Sep
26
11:00 am2018
Sponsored by
PerkinElmer

Implementation and Validation of a High-Precision, Non-NGS NIPT Platform

GenomeWebinar

Professor of Pathology and Laboratory Science
Women & Infants Hospital
Alpert Medical School at Brown University

Project Manager,
Cerba Xpert

Chief Technology Officer, Co-Founder,
Vanadis Diagnostics, a PerkinElmer company

This webinar will provide a comprehensive overview of an automated, high-precision non-invasive prenatal testing (NIPT) platform that does not rely on next-generation sequencing or PCR amplification, enabling precise measurement of chromosomal aneuploidies for high performance screening minimizing both false positives, false negatives and no-calls.

In this webinar, three speakers will provide different perspectives on the Vanadis NIPT platform and its implementation in the lab setting.

First, Fredrik Dahl, chief technology officer of Vanadis, will provide a brief outline on the system and will discuss supporting clinical data on both high- and low-risk cohorts. Dr. Dahl will provide details of how Vanadis differs from NGS-based NIPT systems as well as clinical proof-of-principle data.

Glenn Palomaki of the Alpert Medical School at Brown University will then provide an update on an external research study of the Vanadis system in the US. The study, called VALUE (Validation of a Lower Cost Aneuploidy Screen), aims to enroll 2,400 women from the general pregnancy population and 250 high-risk pregnancies. Along with screening performance characteristics (detection rate, false positive rate, and test failure rate), the study is collecting information on turn-around-time, costs of equipment and supplies, and needed training.

Finally, Jérémie Gautier of Cerba Xpert will discuss a validation study using the Vanadis NIPT system. Dr. Gautier will outline his laboratory’s experience of the installation process, training, and the day-to-day activities involved in operating the system.

Sponsored by

Assistant Director, Genomics Shared Resource,
Roswell Park Comprehensive Cancer Center

This webinar will discuss a comparison of several different library preparation methods for whole-exome sequencing of formalin-fixed paraffin embedded (FFPE) tissue.

FFPE procurement is the standard for tumor banking and remains part of the clinical standard of care. These samples provide an excellent opportunity to advance cancer research with well characterized histological and pathological annotation combined with extensive clinical data.

The ability to use archival FFPE samples to screen entire exomes for both known and novel mutations will have a strong impact on clinical and basic research initiatives, but the use of DNA extracted from FFPE for whole-exome sequencing (WES) is presently limited. The pre-capture PCR step within the WES protocol is the most critical when working with degraded samples, which can therefore significantly affect the quality of sequencing data.

In this webinar, Prashant Singh of the Roswell Park Comprehensive Cancer Center will discuss his team's project to test several different methods for adding adaptors (pre-capture PCR) within the WES protocol. Dr. Singh will share the results of the comparison and the impact of this work on downstream analysis.

Sponsored by
Recent GenomeWebinars
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
Wed
Aug
15
1:00 pm2018
Sponsored by
Swift Biosciences

The Cancer Avatar Project: Using Targeted NGS to Analyze Circulating Tumor DNA

GenomeWebinar

Senior Scientist,
California Pacific Medical Center Research Institute

Product Manager,
Swift Biosciences


This webinar will cover the Cancer Avatar Project at the California Pacific Medical Center Research Institute (CPMCRI), and Swift Biosciences’ technology that helps to overcome the complexity of tumor profiling, namely the company’s Accel-Amplicon NGS sequencing workflow.

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. Dr. Desprez will share DNA sequencing results from more than 100 matched tissue and ctDNA samples to reveal driver mutations. Additionally, he will outline his 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 is anticipated to 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 sequencing workflow and the new customizable cancer panels for targeted sequencing studies, including Swift’s Accel-Amplicon 56G Oncology Panel v2 kit for target amplification.

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
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

Vice President,
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

Institute for Clinical Genetics at TU Dresden

This webinar 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 shares 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 shares 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
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 discusses 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 highlights 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

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 presents 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 outlines 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
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.

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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.

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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.

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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
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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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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