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GenomeWebinars: Recent

Jun
09
2021

Sponsored by Lexogen

The Impact and Regulation of the Ribosomal RNA in Arabidopsis Meiosis

This webinar will discuss how homologous recombination at the highly conserved rDNA locus in Arabidopsis thaliana is tightly regulated during meiosis, a fundamental process and key to plant breeding and food security.  

The rDNA locus encodes the ribosomal RNA (rRNA) genes, which constitute the catalytic core of the ribosomes –complex and abundant molecular machines responsible for translating the genetic information from mRNAs into proteins in all living cells. By combining cytological and next generation sequencing approaches, Jason Sims and colleagues at the Max Perutz Labs found that the rDNA locus is embedded within a unique meiotic-refractory environment that is tightly controlled throughout meiotic progression.

Dr. Sims will outline how he and his colleagues revealed the presence of tissue-specific ribosomal variants in Arabidopsis and how the variants are differentially transcribed at different meiotic stages. These findings support the concept of specialized ribosome subpopulations with distinct rRNA composition that are assembled in a tissue-specific manner and may exert regulatory functions based on their rRNA composition.

Sponsored by

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Jun
08
2021

Sponsored by Qiagen

Advancing Personalized Oncology with Transcriptomic Profiling and Mechanistic Modeling

Cancer is a complex and heterogeneous disease requiring patient-specific molecular analysis to support treatment decisions. While molecular profiling using DNA-based methods is routine in precision oncology, the incorporation of transcriptomics is not yet well established in the clinic.

In this webinar, Moritz Schütte, head of next-generation sequencing data analysis at Alacris, will explore the advantages of RNA sequencing alone or in combination with whole-exome sequencing as part of a precision oncology workflow.

In addition to discussing how RNA-seq identifies molecular alterations and illuminates the tumor microenvironment, Dr. Schütte will explain how mathematical modeling of molecular data can predict drug sensitivity. Applications will be shown for metastatic melanoma and acute lymphoblastic leukemia.

In this webinar, you will learn:

  • How comprehensive analysis is able to detect actionable targets not accessible by panel analysis;
  • How deep transcriptome profiling gives insights into the tumor microenvironment and immune composition;
  • How transcriptome sequencing can be applied for molecular profiling of acute lymphoblastic leukemias in relapse;
  • How mechanistic modeling offers a highly complementary information layer and enables in silico testing of drug response.

Sponsored by

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May
26
2021

Sponsored by Lexogen

CaTCH it if you can! CRISPRa-based Exploration of Therapy Resistant Cell Clones

The emergence of cell clones that are resistant to targeted therapies poses a significant issue in the treatment of metastatic melanoma. While founding clones are often extremely rare in a starting population, their isolation and characterization hold unique potential for understanding disease processes, uncovering novel biomarkers, and developing therapeutic concepts. 

In this webinar, Christian Umkehrer of Vienna’s Research Institute of Molecular Pathology describes the development and application of CaTCH (CRISPRa Tracing of Clones in Heterogeneous Cell Populations), which combines precise mapping of the lineage history of millions of cells with the ability to isolate any given clone alive from a complex population based on genetic barcodes. 

CaTCH enables the retrospective isolation and analysis of founding clones from heterogeneous cell populations prior to evolutionary selection. The approach uses QuantSeq 3’ mRNA-Seq to characterize the isolated clones by efficiently profiling gene expression.

In his presentation Christian Umkehrer will explain how CaTCH can:

  • be used to trace and isolate therapy-resistant clones from complex cancer cell populations in vitro.
  • be applied to in vivo studies by investigating the origins of resistance to clinically relevant RAF/MEK inhibition in an immunocompetent melanoma mouse model.
  • address further fundamental questions in basic and translational research (e.g., how cell identity states and trajectories are determined in therapy resistance, metastasis formation, or somatic cell re-programming).

Sponsored by

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May
19
2021

Sponsored by Qiagen

Uncovering Genomic Evidence of SARS-CoV-2 Infection and Reinfection

Is it possible to become reinfected with SARS-CoV-2? If so, how can we identify and confirm reinfection?  What tools can we use to better identify prevalent and emerging strains of SARS-CoV-2?

Joel Sevinsky, Principal at Theiagen Consulting, is an expert in bioinformatics in the public health space and coauthor of a recent paper exploring the genomics evidence for reinfection with SARS-CoV-2 that was published in The Lancet Infectious Diseases. In this webinar, Dr. Sevinsky will discuss:

  • How next-generation sequencing (NGS) and off-the-shelf software confirmed the first documented SARS-CoV-2 reinfection case in the United States;
  • How bioinformatics analysis strongly supports the hypothesis that the patient was infected on two separate occasions by genetically distinct viruses;
  • The rationale for the continued use of NGS-based approaches for analysis and surveillance of SARS-CoV-2 samples.

Leif Schauser, Global Product Manager at Qiagen Digital Insights, will discuss recent product developments at Qiagen that support the detection, NGS analysis, and interpretation SARS-CoV-2-positive samples, including stain typing.  He will discuss solutions that range from Qiagen cloud-based services to scalable applications for on-premises analyses.

Sponsored by

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May
18
2021

Sponsored by Bio-Rad

Put Your Money Where Your Mouth Is: Tracking and Attacking COVID-19 through State-Wide Saliva Surveillance

This webinar will present the details of a COVID-19 saliva screening program that has been implemented at more than 90 different colleges, universities, private schools, and nursing homes across New York state.  

Dr. Frank Middleton of SUNY (State University of New York) Upstate Medical University has helped direct weekly saliva screening for this program since August 202. This has translated into performing more than a million tests to date, often exceeding 20,000 tests per day. Dr. Middleton has also been actively engaged in monitoring for the emergence of mutations in the testing network using whole-genome viral sequencing. 

In this webinar, Dr. Middleton will provide an overview of the process involved in taking an idea for a better qPCR assay from the bench to the bedside and beyond, in the effort to help reduce the spread of SARS-CoV-2. 

Dr. Middleton will also review lessons learned from the US Food and Drug Administration Emergency Use Authorization process, as well as best practices for resource and logistical management of a state-wide surveillance operation. 

Sponsored by

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May
13
2021

Sponsored by LGC SeraCare Life Sciences

Limits of Detection Matter: New Challenges for SARS-CoV-2 Diagnostics and COVID-19 Patient Management

As we pass the one-year anniversary of both the COVID-19 pandemic and the first Emergency Use Authorized SARS-CoV-2 PCR detection assays, there remains significant opportunity for clinical laboratories to advance testing and support improved patient management.

In this webinar, James Kirby, Director of the Clinical Microbiology Laboratory at Beth Israel Deaconess Medical Center, will discuss his lab’s experience establishing quantitative SARS-CoV-2 viral load testing, the clinical relevance of limits of detection and viral load, and the need to benchmark against a universal standard to allow cross-comparison of SARS-CoV-2 detection methods. He will also discuss the importance of validating the clinical sensitivity of SARS-CoV-2 testing platforms.  

Russell Garlick, Chief Scientific Officer LGC SeraCare, will present the technologies used to advance reference materials for assay standardization.

The webinar will include a 15-minute Q&A session. 

Sponsored by

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May
12
2021

Sponsored by Combinati

SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19

This webinar will discuss a recent study that characterized the relationships between SARS-CoV-2 RNAemia and disease severity, clinical deterioration, and extrapulmonary complications (EPCs).

While the determinants of COVID-19 disease severity and EPCs are poorly understood, the varied clinical manifestations of COVID-19 have directed attention to the distribution of SARS-CoV-2 in the body. Although SARS-CoV-2 RNA is most concentrated in the nasopharynx, it has also been found in numerous other tissues, raising questions about dissemination of viral RNA throughout the body as well as the role of this process in disease severity and extrapulmonary complications.  Recent studies have detected low levels of SARS-CoV-2 RNA in blood and have associated RNAemia with disease severity and biomarkers of dysregulated immune response. 

In this webinar, Dr. Nikhil Ram Mohan, a postdoctoral scholar in the Department of Emergency Medicine at Stanford University, will discuss a study that used an array-based dPCR platform to detect and quantify SARS-CoV-2 RNA in specimens collected from the nasopharynx and from plasma of patients diagnosed with COVID-19.

He will discuss how variation in SARS-CoV-2 RNAemia may help explain disparities in disease severity and EPCs from COVID-19 as well as how using digital PCR to test for RNAemia early in the course of illness may help guide patient triage and management.

Sponsored by

May
11
2021

Sponsored by Akoya Biosciences

Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data: Panel Discussion: Analysis Strategies for Enriching Single-Cell Spatial Phenotyping Data

This webinar, which caps off our 4 part Spatial Multiomics Webinar Series, gathers speakers from prior events in the series to discuss the challenges and benefits of integrating imaging-based single-cell spatial phenotyping data with complementary transcriptomic and genomic datasets.

Our expert panelists will review their own strategies for addressing the challenges of integrative multiomic analysis and will share best practices for this rapidly evolving field.

The discussion will be moderated by Dr. Oliver Braubach of Akoya Biosciences and will conclude with a live Q&A in which attendees can post questions to our panelists.

About the Series: Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data

In this multi-part webinar series, our expert speakers will review analytical frameworks and algorithms to integrate imaging-based single-cell spatial phenotyping data with complementary transcriptomic and genomic datasets.

High-plex cell phenotyping methods like single-cell RNA-seq capture the deep cellular heterogeneity of samples, but cell behavior is a function of all that surrounds it. Imaging-based spatial phenotyping platforms enable researchers to visualize and analyze cell diversity, interactive networks, and cellular behavior across whole tissue sections. Both types of data have complementary features, which give researchers the ability to merge information about a cell’s proteome and transcriptome with its single-cell, spatial context.

This webinar series will highlight the latest advances driving integrative multiomics analysis.

Sponsored by

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May
10
2021

Sponsored by MeMed

Predicting COVID-19 Severity: Leveraging the Host Immune Response to Identify High-Risk Patients and Improve Outcomes

Amid the COVID-19 pandemic, hospitals and intensive care units around the world have been overwhelmed by unprecedented levels of demand. Clinicians face the difficult challenge of patient prioritization, identifying which patients to admit and how to effectively triage them within emergency room and hospital settings, and which patients can safely get the care they need at home, in isolation. 

Accurately predicting which COVID-19 patients are at risk of severe disease and deterioration, as well as personalized management of critically ill patients, remains challenging due to the heterogeneous nature of the virus and the limitations of available diagnostic tools. Today, however, novel host immune response technologies are yielding clues on how to best triage COVID-19 patients, showing promise in changing the paradigm in acute care patient management. 

Please join 360Dx and MeMed for a discussion with a panel of international experts on recent advances in the technologies used to probe the host immune response to infections, including COVID-19. Panelists will share new research and insights from their experiences on how predictive biomarkers – and the actionable information they provide – can potentially be used in clinical practice to enable more accurate, rapid diagnoses and timely interventions that can help reduce ICU admissions, the need for ventilation and, ultimately, mortality.

This discussion will cover: 

●      Recent prospective data on the potential utility of a host immune signature, which combines three biomarkers (TRAIL, IP-10, CRP), as a valuable resource for predicting disease severity and progression; 

●      How utilizing IP-10 as a biomarker in real-world settings can aid in monitoring inflammatory status and personalizing treatment strategies for patients with severe COVID-19; 

●      The applications of host immune response technologies in easing the burdens on healthcare systems presented by COVID-19 as well as future pandemics.

Sponsored by

May
06
2021

Sponsored by Akoya Biosciences

Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data: Enriching Spatial Proteomic Data with Parallel CITE-seq Analysis Elucidates Multiomic Changes with Aging

This webinar is part 3 of a 4 part webinar series.

Integrating complementary data sets provides a powerful tool to study complex biological processes. This webinar will focus on the use of CODEX (Co-Detection by Indexing) spatial proteomic data in parallel with CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) data to study tissue regeneration and aging.

The integration of CITE-seq data, where antibodies used in the CODEX system are also captured by droplet-based single-cell sequencing, allows for the multiomic projection of transcriptomic information onto the spatial information of the CODEX System. This multi-omic approach enables the study of cell-cell signaling by assessing relationships between cell types across the tissue and provides a deeper understanding of the biology at play in tissue regeneration and aging.

In this talk attendees will:

  • Learn about the use of multiplex imaging to study spatial dynamics of skeletal muscle regeneration and molecular determinants of aging

  • Understand how to design and align CITE-seq experiments to enrich CODEX data

See how to use single-cell resolution spatial transcriptomes to assess cell-cell signaling

About the Series: Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data

 

In this multi-part webinar series, our expert speakers will review analytical frameworks and algorithms to integrate imaging-based single-cell spatial phenotyping data with complementary transcriptomic and genomic datasets.

High-plex cell phenotyping methods like single-cell RNA-seq capture the deep cellular heterogeneity of samples, but cell behavior is a function of all that surrounds it. Imaging-based spatial phenotyping platforms enable researchers to visualize and analyze cell diversity, interactive networks, and cellular behavior across whole tissue sections. Both types of data have complementary features, which give researchers the ability to merge information about a cell’s proteome and transcriptome with its single-cell, spatial context.

This webinar series will highlight the latest advances driving integrative multiomics analysis. 

Sponsored by

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May
05
2021

Sponsored by Illumina

Establishing a Pharmacogenomic Service for Routine Clinical Care

Adverse drug reactions (ADRs) are responsible for around 5 percent of hospital admissions and occur in 6 percent to 15 percent of hospital stays. Approximately 30 percent of ADRs are caused by drugs with a known major clinically significant pharmacogenomic variant, meaning that nearly one-third of adverse drug-related admissions may be predictable – and thus preventable - by pharmacogenomic (PGx) testing.

This webinar will review the introduction of pharmacogenomic testing into settings where it is likely to be particularly clinically relevant. Paul Leo of Queensland University of Technology will discuss a project that aimed to provide pre-emptive rather than reactive testing in the clinical setting by using rapid genomic technologies and information management integrated into the hospital electronic medical record. This vision required development of a PGx knowledge center and a clinical support database as well as the validation of new technologies to improve cost-effective PGx measurements.

The presentation will focus on the implementation of these goals as well as the challenges of introducing new genomic testing into routine clinical care.

Sponsored by

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May
04
2021

Sponsored by Akoya Biosciences

Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data: Transcriptome-Guided Analysis of Highly Multiplexed Immunohistochemistry Images

This webinar is part 2 of a 4 part webinar series.

Recently developed technologies for digital imaging and highly multiplexed immunohistochemistry (mIHC) advancing the field of histology into a quantitative era, allowing for more complex descriptions of tissue architecture.

Imaging cytometry by time of flight (CyTOF), multiplexed ion beam imaging, and co-detection by indexing (CODEX) can be used to simultaneously profile the expression of dozens of proteins in a tissue section with single-cell resolution. However, annotating cell populations or states that differ little in the profiled antigens or for which the antibody panel does not include specific markers is challenging.

This webinar will present a computational approach that was developed to overcome this obstacle. Spatially resolved Transcriptomics via Epitope Anchoring (STvEA) enriches mIHC images with single-cell RNA-seq data, building upon recent experimental procedures for augmenting single-cell transcriptomes with concurrent antigen measurements such as CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing).

Pablo G. Camara of the Perelman School of Medicine at the University of Pennsylvania will share details of STvEA, which performs transcriptome-guided annotation of highly multiplexed cytometry datasets.

Dr. Camara will demonstrate the utility of STvEA by uncovering the architecture of poorly characterized cell types in the murine spleen using published CODEX and CyTOF datasets, and a CITE-seq atlas of the murine spleen that his team has generated. 

In this talk attendees will: 

  • Learn about current challenges in the analysis of mIHC images 
  • Understand the concept of STvEA and the algorithmic steps involved 
  • Get familiarized with the computational analyses enabled by STvEA 
  • See several examples of the application of STvEA

About the Series: Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data

In this multi-part webinar series, our expert speakers will review analytical frameworks and algorithms to integrate imaging-based single-cell spatial phenotyping data with complementary transcriptomic and genomic datasets.

High-plex cell phenotyping methods like single-cell RNA-seq capture the deep cellular heterogeneity of samples, but cell behavior is a function of all that surrounds it. Imaging-based spatial phenotyping platforms enable researchers to visualize and analyze cell diversity, interactive networks, and cellular behavior within the spatial context of whole tissue sections. Both types of data have complementary features, which give researchers the ability to merge information about a cell’s proteome and transcriptome with its single-cell, spatial context.

This webinar series will highlight the latest advances driving integrative multiomics analysis.

Sponsored by

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Apr
29
2021

Sponsored by Co-Diagnostics

A New Generation of PCR: At-home Testing and Preparing for Emerging Strains of COVID-19

Join Dr. Heather Fehling, Chief Scientific Officer at Clinical Reference Labs (CRL), as she provides some insights regarding the future applications of PCR testing.

CRL recently announced a partnership with Walgreens, offering consumers the convenience of self-collecting COVID-19 saliva tests in their own homes without supervision. Dr. Fehling will detail some of the ways she has been able to adapt her labs to usher in a new era of accessible PCR testing.

Accompanying Dr. Fehling will be Masen Christensen, Senior Design Engineer at Co-Diagnostics, who is responsible for ongoing in silico inclusivity and exclusivity analyses used by the CRL/Walgreens partnership and for monitoring all strains and mutations of SARS-CoV-2.

Christensen will summarize the results of these analyses and outline how to achieve high levels of specificity in saliva PCR by virtually eliminating primer-dimers and the necessity for a fluorescent probe by using the CoPrimer structure developed by Co-Diagnostics.

Attendees of this webinar will learn:

  • How Clinical Reference Labs is able to provide non-invasive and highly accurate saliva PCR tests for at-home collection
  • The results of ongoing in silico inclusivity and exclusivity analyses on COVID-19 mutations and emerging strains
  • How new PCR science and technology is enabling and expanding the applications and accessibility of PCR tests

Sponsored by

Apr
28
2021

Sponsored by Akoya Biosciences

Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data: Integrative Analysis of Single-Cell Omics and Imaging Data

Single-cell omics assays have become essential tools for identifying and characterizing cell types and states of complex tissues. While each single-modality assay reveals distinctive features about the sequenced cells, true multiomics assays are still in the early stage of development.  

This underscores the importance of computationally integrating single-cell omics data from studies conducted on various samples across various modalities. In addition, the advent of multiplexed molecular imaging assays has given rise to a need for computational methods for integrative analysis of single-cell imaging and omics data. 

In this webinar, Kai Tan of the Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania will discuss GLUER (Integrative Analysis of Multiomics at Single-Cell Resolution), a flexible tool for integration of single-cell multi-omics data and imaging data. 

In this talk attendees will: 

  • Learn about a general computational framework (GLUER) for integrating single-cell omics and imaging data
  • Hear strategies to evaluate performance of data integration methods
  • See the utility of integration methods for understanding cell-cell communication

About the Series: Spatial Multiomics: Analysis Strategies for Enriching Single-Cell Phenotyping Data

In this multi-part webinar series, our expert speakers will review analytical frameworks and algorithms to integrate imaging-based single-cell spatial phenotyping data with complementary transcriptomic and genomic datasets.

High-plex cell phenotyping methods like single-cell RNA-seq capture the deep cellular heterogeneity of samples, but cell behavior is a function of all that surrounds it. Imaging-based spatial phenotyping platforms enable researchers to visualize and analyze cell diversity, interactive networks, and cellular behavior within the spatial context of whole tissue sections. Both types of data have complementary features, which give researchers the ability to merge information about a cell’s proteome and transcriptome with its single-cell, spatial context.

This webinar series will highlight the latest advances driving integrative multiomics analysis.


Sponsored by

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Apr
27
2021

Sponsored by Biognosys

Oncology in the Time of COVID-19: Quantitative Proteomic Analysis of Anti-IL6 Treated Patients

This webinar, the first in our Next-Generation Proteomics for Precision Oncology series, will discuss how proteomics can help overcome the challenges of treating COVID-19 patients with oncologic comorbidities.

Recent advances in mass spectrometry-based proteomics have fostered a more precise, deep, and more functional look into clinical phenotypes. Going beyond traditional genomics, proteomics enables more relevant, quantitative, and informative understanding of diseases and treatments.

Jean-Marie Michot, a medical oncologist at Gustave Roussy Institute and Vito Dozio, Scientific Project Manager at Biognosys, will share a study that illustrates the promise of proteomics in understanding responses to new therapies such as anti-IL-6-based treatment and the impact of comorbidities on clinical outcomes.

They will discuss the results of a joint project in which serum from a cohort of patients infected with COVID-19 was submitted for analysis using the Biognosys HRM discovery proteomics platform. They will share details of proteomic profiles associated with clinical outcome, comorbidities, and the response to anti-IL6 treatment, which provide a comprehensive picture of the potential of using next-generation proteomics to enhance personalized medicine. 

About The Series: Next-Generation Proteomics for Precision Oncology

This webinar series will highlight recent advancements in the proteomics field and the impact of proteomics on clinical research in oncology.

Sponsored by

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