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GenomeWebinars

Tue
Apr
7
12:00 pm2020
Sponsored by
Agilent

Application of Target Enrichment to Pathogen Genomics and Transcriptomics

GenomeWebinar

Professor of Virology, Division of Infection and Immunity, University College London & Great Ormond Street Hospital for Children

 

Target enrichment has been shown to be more sensitive than metagenomic methods and PCR amplicon sequencing for pathogen genomes, and faster than traditional methods for analysis of hard to culture pathogens, for example viruses and some bacteria.

In this webinar, Judith Breuer of University College London & Great Ormond Street Hospital for Children will show how Agilent’s SureSelect targeted enrichment technology:

  • Allows her team to generate high quality consensus sequences and preserves the population structure of minority variant sequences compared to sequencing directly from clinical samples.  
  • Enables them to interrogate clinical samples for better understanding of the evolution of drug resistance and pathogen transmission. 
  • Offers a useful tool study the impact of drugs on pathogens and the recovery of pathogen transcriptomes as part of understanding pathogenesis.

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

Sponsored by
Thu
Apr
9
1:00 pm2020
Sponsored by
GenomeWeb/ABRF

Affordable Quantitative Single-Cell Proteomics with SCoPE2

GenomeWebinar

Graduate Research Assistant, Slavov Lab, Northeastern University

This webinar will discuss SCoPE2 (Single Cell Proteomics by Mass Spectrometry, Version 2), an approach for quantitatively analyzing proteins in single cells using only commercially available equipment and reagents.

Harrison Specht of Northeastern University will share details of the methodology, which lowers cost and hands-on time by introducing automated and miniaturized sample preparation while substantially increasing quantitative accuracy.

Using SCoPE2, Specht and colleagues quantified more than 2,700 proteins in 1,018 single monocytes and macrophages in 10 days of instrument time, and the quantified proteins allowed them to discern single cells by cell type. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that SCoPE2 samples 20-fold more copies per gene, thus supporting quantification with improved count statistics. Joint analysis of the data indicated that most genes had similar responses at the protein and RNA levels, though the responses of hundreds of genes differed.

In his presentation, Specht will share details on how researchers can adopt SCoPE2 in their labs. He will discuss equipment that can be used to successfully execute SCoPE2 sample preparation, as well as reagent selection and study design, including the types of cells that are likely to perform well with SCoPE2. Additionally, he will discuss approaches to optimizing liquid chromatography and mass spectrometry instrumentation for SCoPE2 samples.

Sponsored by
Thu
Apr
16
1:00 pm2020
Sponsored by
GenomeWeb/ABRF

Metaproteomics Approaches for Characterizing Human Gut Microbiome Development

GenomeWebinar

Distinguished Research Staff Member, Oak Ridge National Laboratory

This webinar will discuss a mass spectrometry-based metaproteomic approach to examine microbiome temporal functional shifts during microbial colonization of the preterm human infant gut.

Robert L. Hettich of Oak Ridge National Laboratory will discuss his recent work developing advanced “shotgun” mass spectrometry techniques for the comprehensive characterization of microbial metaproteomes. His lab's recent work has focused on improved methods for cellular lysis and proteome extraction, coupled with automated multi-dimensional LC-MS/MS on QExactive mass spectrometric systems. This has been coupled with an improved data analysis/data mining pipeline for enhancing peptide/protein identification and quantification.

Dr. Hettich will discuss a study in which fecal metaproteomes of 94 preterm infant samples, each collected at discrete time points over several months, were measured by LC-MS/MS and yielded identification of tens of thousands of proteins, many of which corresponded to enzymes that mapped onto a large and deeply interconnected network of metabolic reactions.

Tracking metabolic function rather than discrete proteins has the potential of revealing how microbial metabolic function progresses across development of the preterm human infant gut microbiome, and how the overall metabolic potential of the system expands or contracts temporally.

The time-course metaproteomics measurements revealed core metabolic pathways in both human and microbial proteins, indicating the establishment of the mutualistic relationship between the microbiome and human host early in infancy. In total, these results reveal functional stability and inter-individual signatures of the preterm infant gut microbiome.

This webinar is part of the 2020 GenomeWeb/Association of Biomolecular Resource Facilities webinar series, which highlights methods, techniques, and instrumentation that support life science research.

Sponsored by
Thu
Apr
30
11:00 am2020
Sponsored by
10x Genomics

Whole-Transcriptome Spatial Mapping of the Healthy and Infarcted Human Heart

GenomeWebinar

Physician Scientist, University Clinic of the RWTH Aachen, Department of Nephrology

Postdoctoral Researcher, Institute for Computational Biomedicine, Heidelberg University Hospital; Department of Knowledge Technologies, Jožef Stefan Institute

Professor of Medicine and Chair of Nephro-Cardiology, RWTH Aachen University

Professor of Medical Bioinformatics and Data Analysis, Faculty of Medicine, Heidelberg University

Sudden cardiac death following myocardial infarction (MI) is one of the leading causes of mortality in the world, resulting in an estimated 4 million to 5 million deaths each year. Recent advances have drastically improved the acute survival of MI, yet long-term survival rates have only marginally improved over the last few years. Researchers at University Hospital Aachen in Germany aimed to address this unmet medical need for novel, long-term MI therapeutic options using the Visium Spatial Gene Expression Solution from 10x Genomics.
 
In this webinar, Christoph Kuppe, Jovan Tanevski, Rafael Kramann, and Julio Saez-Rodriguez, winners of the 10x Genomics Visium Spatial Scientific Challenge, will describe:

  • How they generated a map of human MI at unprecedented resolution using the Visium Spatial Gene Expression Solution in both healthy human cardiac tissue and old human MI diseased tissue.
  • How they performed state-of-the-art single nuclear RNA sequencing and single cell ATAC (Assay for Transposase-Accessible Chromatin) sequencing in healthy and infarcted cardiac tissue.
  • The significance of combining single-cell, single-nucleus, and spatial gene expression analyses for gleaning novel insights into mechanisms and potential therapeutic targets.
Sponsored by

Project Scientist, Department of Microbiology, Immunology and Molecular Genetics, University of California

Technology Co-Inventor , IsoPlexis

This webinar will discuss the application of single-cell proteomics and immune-imaging in adoptive cell therapy (ACT) for cancer.

Interleukin-2 (IL-2) is a component of most protocols of ACT, but it is limited by short exposure and high toxicities. NKTR-214 is a kinetically engineered IL-2 receptor βγ-biased agonist designed to preferentially activate and expand effector T and natural killer cells over regulatory T cells in the tumor.

In this webinar, Giulia Parisi of the University of California, Los Angeles, will discuss the use of in vivo immuno-imaging to track the biodistribution of the adoptively transferred T cells in relation to anti-tumor efficacy. She will also discuss how this study used single-cell proteomics and functional biomarkers to characterize the functional phenotype of the cell subsets modulated by ACT+NKTR-214.

The objectives of this seminar are to:

  • Provide an overview of the use of an engineered IL-2 receptor agonist in adoptive cell transfer protocols
  • Present methods to track T cell anti-tumor activity and in vivo biodistribution
  • Describe the application of single-cell functional proteomics in identifying biomarkers in next-generation therapies
Sponsored by
Wed
May
20
1:00 pm2020
Sponsored by
Agilent

Identification of Small Segmental Aneuploidies in Preimplantation Embryos

GenomeWebinar

Director of the Pittsburgh Cytogenetics Laboratory,
Associate Professor, Department of Obstetrics, Gynecology & Reproductive Sciences, Pathology and Human Genetics

Preimplantation genetic testing for aneuploidy (PGT-A) of all 24 chromosomes has become a common practice to improve implantation and clinical pregnancy rates in patients undergoing in vitro fertilization. Array comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) enable identification of whole-chromosome aneuploidy and large chromosomal abnormalities. For prenatal and postnatal diagnosis, aCGH and NGS are also used to detect submicroscopic chromosomal imbalances – microdeletions and microduplications. 

In contrast to the 30 percent to 80 percent risk of sporadic whole-chromosome aneuploidy that depends on maternal age, large segmental aneuploidies are independent of maternal age but observed in 10 percent to 15 percent of embryos subjected to PGT-A. These segmental aneuploidies include de novo segmental gains and losses seen in around 10 percent of blastocysts, and genomic imbalances resulting from a known or yet undiagnosed chromosome abnormality in the parents. 

Preimplantation genetic testing for structural rearrangement (PGT-SR) is recommended to such couples, however, around 40 percent of couples with recurrent miscarriages and infertility have normal karyotype analysis despite the presence of a structural rearrangement. Moreover, de novo disease-causing submicroscopic chromosome imbalances affect around 0.3 percent of newborns and are likely more prevalent among preimplantation embryos. Current technologies are limited to identification of chromosomal imbalances larger than 5-10 Mb in size. Embryos affected by cryptic pathogenic aberration that are below the current limits of detection are routinely implanted. 

In this webinar, Svetlana Yatsenko of the Department of Pathology at the University of Pittsburgh will share how her team has used the 60K CGH GenetiSure microarray platform from Agilent to detect large aberrations (greater than 10 Mb in size), as well as aCGH with the “Single Cell Small Aberration Method” to detect copy number variants less than 10 Mb in size. 

 

Segmental imbalances in embryos have a significantly lower potential for implantation, leading to a diagnosis of idiopathic infertility or discovered by karyotype or microarray analysis after a miscarriage. Detection of microdeletions and duplications associated with human pathologies may improve the success rate of in vitrofertilization procedures and reduce the incidence of microdeletion syndromes.

Sponsored by
Recent GenomeWebinars
Mon
Mar
30
1:00 pm2020
Sponsored by
GenomeWeb/ABRF

Computational Approaches for Optimized Nanopore Sequencing Workflows

GenomeWebinar

Postdoctoral Associate in Computational Biomedicine, Institute for Computational Biomedicine at Weill Cornell Medicine

Research Scientist, University of California, Santa Cruz

This webinar features two speakers who will discuss novel computational approaches to optimize sequencing workflows on Oxford Nanopore sequencing platforms.

Our first speaker, Jonathan Foox of the Institute for Computational Biomedicine at Weill Cornell Medicine, will review the rapidly evolving landscape of software to interpret raw Nanopore current data and report modified bases. He will review commonly used and newly available algorithms, and describe the advantages, challenges, and limitations of each. He will also compare base modification call sets generated from Nanopore data against call sets from short-read bisulfite data, as part of the Epigenomics Quality Control study, which aims to describe the reproducibility of genome-wide methylation calling and provide a benchmark of base modification detection across sequencing platforms and library types.

Our second speaker, Miten Jain of the University of California, Santa Cruz, will demonstrate an optimized PromethION nanopore sequencing method that sequenced eleven human genomes on one machine in nine days, using just three flow cells per sample. He will describe computational tools that his team used for this project: Shasta, a de novo long read assembler; and MarginPolish & HELEN, a suite of nanopore assembly polishing algorithms. Dr. Jain will also discuss an evaluation of assembly performance for diploid, haploid, and trio-binned human samples in terms of accuracy, cost, and time and demonstrate improvements relative to current state-of-the-art methods in all areas. He will also discuss how the addition of proximity ligation (Hi-C) sequencing yielded near chromosome-level scaffolds for all eleven genomes.

This webinar is part of the 2020 GenomeWeb/Association of Biomolecular Resource Facilities webinar series, which highlights methods, techniques, and instrumentation that support life science research.

Sponsored by
Thu
Mar
26
11:00 am2020
Sponsored by
Horizon Discovery

Using CRISPR/Cas9-based Gene Targeting to Study Cell Biological Processes

GenomeWebinar

Professor of Biology,
Whitehead Institute for Biomedical Research,
Department of Biology, MIT

A key goal for cell biological analyses is to assess the phenotypes that result from eliminating a target gene. For the past 25 years, the predominant strategy utilized in human tissue culture cells has been RNAi-mediated protein depletion. However, RNAi suffers well-documented off-target effects as well as incomplete and reversible protein depletion. The implementation of CRISPR/Cas9-based DNA cleavage has revolutionized the capacity to conduct functional studies in human cells.

In this webinar, Dr. Iain Cheeseman of the Whitehead Institute for Biomedical Research will describe the strategies that his lab utilizes to analyze the cell biological phenotypes resulting from gene inactivation in human cells using Cas9-mediated gene knockouts.

First, he will discuss an inducible knockout strategy using modified cell lines with a doxycycline-inducible version of Cas9 and a stably expressed single guide RNA (sgRNA) introduced using a lentiviral vector. The inducible and conditional nature of the Cas9 induction allows a researcher to elucidate the consequences of both acute and chronic elimination for a target gene, which is particularly critical when analyzing genes required for cellular fitness, including essential genes. Using this strategy, the Cheeseman lab has generated and characterized a broad collection of inducible CRISPR/Cas9 knockout human cell lines targeting diverse cell cycle and cell division processes.

Second, Dr. Cheeseman will discuss alternate strategies for the effective introduction of the Cas9 guide RNA into target cells using synthetic guide RNA transfection. He will compare the efficiency of synthetic sgRNA and crRNA guides with that of cell lines stably expressing lentiviral-delivered RNA guides and will discuss technical considerations for effective use of synthetic guides for cell biological phenotypes.

Finally, Dr. Cheeseman will discuss strategies to conduct Cas9-based targeting for cell biological phenotypes at a larger scale, towards enabling genome-wide phenotypic screens. Together, these strategies provide a robust, flexible, and scalable approach for conducting functional studies in human cells.

Sponsored by

Head of Business Development, Co-Diagnostics

Chief Scientific Officer, Co-Diagnostics


LGC, Biosearch Technologies, Market Segment Manager MDx, LGC


In this webinar, Joseph Featherstone and Dr. Brent Satterfield from Co-Diagnostics (CoDx) will present insights into the development of the CoPrimer COVID-19 test. They will discuss how innovative design algorithms and a close partnership with a critical component supplier, LGC, Biosearch Technologies, enabled assay design and verification in seven days, making the COVID-19 test available for market. Brent will provide details of the CoPrimer technology and how the new algorithm enabled rapid assay design, while Joseph will share the latest developments toward clinical validation of the assay as well as discuss the CoDx Portable qPCR Lab and its impact in the field.

Dr. Geert Koene from Biosearch Technologies will share the perspective of a component supplier and will discuss details of the company's proprietary BHQ technology, experience in reacting to outbreaks, and the importance of a collaborative partnership.

Sponsored by

Senior Medical Consultant, University Hospital Brugmann, Université Libre de Bruxelles

This webinar discusses data from a recent real-world comparison study evaluating performance of two cell-free DNA methodologies as first-line prenatal screens.

Rapid global adoption of noninvasive prenatal testing (NIPT) by cell-free DNA analysis into clinical care has led to a growing number of technical approaches and menu options. With increasing frequency, the commercial availability of a test greatly precedes the presentation of peer-reviewed data evaluating performance and clinical utility, making it difficult for clinicians to differentiate how the test may impact clinical care. In order to provide high-quality patient care, laboratories and clinicians must have access to evidence that allows critical evaluation of testing options.

In this webinar, Dr. Elisa Bevilacqua of Brugmann University Hospital presents data from a recent study evaluating two cell-free DNA tests as first-line prenatal screens in Belgium: a genome-wide massively parallel sequencing test and a targeted Harmony Prenatal test performed in a local clinical laboratory.

Dr. Bevilacqua describes results comparing sensitivities, false positive rates, failure rates, and turn-around-times, and discuss the clinical utility of additional findings beyond the common trisomies revealed by genome-wide cell-free DNA analysis.

Sponsored by

Professor of Surgery and Emergency Medicine
Washington University School of Medicine

Instructor in the Department of Pathology & Immunology
Washington University, St. Louis

Sepsis is a growing healthcare crisis, causing over 11 million deaths worldwide. Early recognition and timely, comprehensive therapeutic interventions improve patient outcomes and have been codified in current clinical guidelines and government reporting requirements. However, non-specific presenting symptoms that mimic other diagnoses combined with multiple clinical definitions lead to diagnostic uncertainty. Identifying the undiagnosed septic patient within the sea of undifferentiated patients simultaneously presenting to the Emergency Department is challenging and can lead to potential treatment delays with associated increases in morbidity and mortality.

This webinar is presented by Dr. Tiffany Osborn, Professor of Surgery and Emergency Medicine for the Surgical/Trauma Intensive Care Unit and Emergency Department at Washington University School of Medicine and Dr. Christopher Farnsworth, instructor in the Department of Pathology & Immunology at Washington University and medical director of Clinical Chemistry, Point of Care testing, and the Special Pathogens Laboratory at Barnes Jewish Hospital.

During the session, Dr. Osborn and Dr. Farnsworth will discuss how teamwork between the laboratory and clinical medicine can improve patient care through earlier identification and treatment of septic patients. They will discuss the challenges associated with current screening biomarkers, as well as the opportunities presented by a novel sepsis biomarker, monocyte distribution width.

After this webinar, you will be able to:

  • Explain the relationship between early sepsis treatment and improved patient mortality
  • Differentiate among Sepsis-2 and Sepsis-3 definitions and common sepsis screening criteria such as qSOFA and SIRS
  • Review published evidence supporting the effectiveness of monocyte distribution width in early sepsis detection
Sponsored by

Science Leader,
National Measurement Laboratory at LGC 

Since the publication of the “The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments” (dMIQE) in 2013, there has been a large expansion of the applications of dPCR such as single nucleotide variations (SNVs) and copy number variations (CNVs) measurements associated with disease diagnostics. At the same time, international measurement organisations, such as the National Measurement Laboratory (NML) at LGC, have been working towards the development of molecular methods that are SI traceable to support the translation of these applications into the clinic. Digital PCR has the potential to be a traceable method as the concentration of a target is calculated based on the proportion of target-positive partitions and the application of Poisson statistics.

This webinar will focus on the use of dPCR for quantifying gene CNVs frequently used in diagnosis and selection of targeted therapy. Using models, like the HER2 gene in breast cancer, we will investigate the ability of dPCR to measure small changes in the gene copy number with further work to develop methods to counteract the measurement bias that can be caused by linked target copies in the sample. The talk will also highlight key dPCR performance parameters considered in the updated version of the dMIQE guidelines thereby fostering dPCR best practice and the use of dPCR as a gold standard approach.

Sponsored by

Lab Director, Clinic for Special Children

 

Senior Vice President, AutoGen

This webinar will explain how the Clinic for Special Children in Strasburg, Pennsylvania, has transformed its DNA workflows to improve the diagnosis and treatment of genetic illnesses that are prevalent in the pediatric population of its community.

Dr. Erik Puffenberger, lab director at the clinic, will discuss how the organization improved its genetic workflows in order to give patients the best care possible and provide better outcomes for families. Dr. Puffenberger will share details of how the clinic, as a small, specialized organization, balances the desire to adopt new technologies with the realities of working with a limited budget.

One of the many diseases the clinic diagnoses and treats is spinal muscular atrophy (SMA). The occurrence of SMA is much higher within the community the clinic serves, comprising Amish and Mennonite populations, than in the general population. This webinar will highlight how the clinic has evolved its DNA workflows to improve clinical outcomes for SMA and other diseases.

Dr. Puffenberger will detail the DNA extraction technologies that have allowed the clinic to improve its workflows and will also discuss the promise of cell-free DNA for non-invasive prenatal diagnosis and treatment.

Webinar participants will learn about the following areas:

  • How to optimize the workflow in a clinical environment to diagnose and treat genetic illnesses
  • Which sample types provide the best chances for a positive clinical outcome
  • New ways automation enables non-invasive prenatal diagnosis and treatment
Sponsored by

Professor of Pathology,
University of Pittsburgh

This webinar will discuss a study that used long-read, single-cell and probe capture based transcriptome sequencing to explore the distribution of isoforms in colon cancer samples and their metastasis counterparts.  

The complexity of mammalian gene expression involves the combinatorial use of exons during RNA splicing. The selective splicing process generates a plethora of isoforms per gene and accounts for what is arguably the largest source of variation in transcriptome diversity and adaptability. However, the quantification of the diversity of mammalian transcriptome is impeded by the lack of accurate, quantitative, and affordable long-read isoform sequencing.

Accurate analyses of the distribution of isoforms, fusion gene isoforms, and point mutation isoforms remains a huge challenge for human malignancies. In this webinar, Jianhua Luo of the University of Pittsburgh will discuss a study that used the ability to capture transcripts from user-defined sets of genes together with synthetic long-read sequencing of full-length mRNA to characterize the long-read transcriptomes from three pairs of colon cancers and their metastasis counterparts.

Dr. Luo will share how the study demonstrated a unique pattern of RNA isoform redistribution and enrichment for specific mutated isoforms and fusions in metastatic cancer cells in comparison with their primary cancer counterparts. The isoform switching and mutation-enriched isoforms are predicted to have subtle effects on protein structure, which may differentially impact protein signal transduction and response to drug treatment.

The results demonstrate that the use of probe capture and long-read sequencing provides focus and granularity that was previously inaccessible in transcriptome analysis of both bulk and single cell samples. Full-length transcriptome analysis may be essential for our understanding of gene expression regulation in human cancers.

Sponsored by
Thu
Feb
20
11:00 am2020
Sponsored by
Thermo Fisher Scientific

Advances in NGS Gene Expression Studies to Reduce The Cost of Sequencing

GenomeWebinar

Assistant Professor, Division of Microbiology, Tulane University

Senior Global Marketing Manager, Thermo Fisher Scientific

This webinar discusses the use of 3’ mRNA sequencing to reduce the cost of gene expression studies on Illumina NGS systems.

Focusing on a study that used peripheral blood mononuclear cells from pregnant macaques acutely infected with Zika virus, Dr. Nicholas Maness of Tulane University discusses the pros and cons of 3’ mRNA sequencing compared to whole-transcriptome sequencing for gene expression studies. He details the differences in the data collected and the costs of each approach and offers suggestions on when to use each method.

This webinar is a must-see for anyone seeking to reduce the cost of sequencing from gene expression studies or who wish to perform pilot studies inexpensively.

Cris Kinross of Thermo Fisher Scientific provides an overview of the differences between 3’ mRNA-seq, mRNA-seq, and whole-transcriptome sequencing.

 In this webinar, you learn how to:

  • Reduce the cost of NGS gene expression studies
  • Consider if 3’ mRNA sequencing or whole-transcriptome sequencing meets the needs of your project
  • Obtain answers more quickly using smaller data sets
Sponsored by
Wed
Feb
19
1:00 pm2020
Sponsored by
Horizon Discovery

CRISPR-directed Gene Editing in Human Cells: What You Get Is More Than What You Want

GenomeWebinar

Founder and Director of the Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute at ChristianaCare

Product Manager – Gene Editing Reagents, Horizon Discovery

The breakthrough technology CRISPR/Cas has revolutionized molecular approaches to the treatment of disease and provided opportunities for the development of clinically relevant gene therapies. While a wealth of information surrounding gene knockout in human cells is now in hand, we are only beginning to appreciate the intricacies and genetic outcomes resulting from reactions where the aim is to correct a mutation or precisely tag a specific sequence in the genome.

The most well-known method for gene repair is homology-directed repair (HDR), a heterogeneous series of pathways whose activity lead to precise and imprecise genetic alterations. Some pathway activity can lead to unwanted changes.

In this webinar, Eric Kmiec, founder of the Gene Editing Institute at ChristianaCare, will discuss the global distribution of genetic outcomes as a function of CRISPR-directed gene editing, highlighting in vitro and in vivo systems that enable such visualization.

An appreciation for the heterogeneity of HDR products in a whole cell population is becoming essential as therapeutic applications of gene repair advance toward the clinic.

Sponsored by

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