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GenomeWebinars

Tue
Feb
25
1:00 pm2020
Sponsored by
Loop Genomics

Long-Read Sequencing of Human Transcription Provides Insights into Metastatic Cancer

GenomeWebinar

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

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

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

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

This webinar will discuss 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 will present 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 will describe 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
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

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
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

The New York City Police Department will be removing DNA profiles from a local database if they are from people who were never convicted of a crime, the New York Times reports.

Science reports that accusations of sexual assault against a microbiome researcher has also led to questions about his academic certifications.

Wired reports that researchers are analyzing the DNA fish leave behind in water to study their populations.

In Science this week: comprehensive cellular map of the human thymus, evidence of admixture between the ancestors of Neanderthals and Denisovan and a 'superarchaic' population.