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Director of the Bioscience Technology Facility, and Head of Imaging and Cytometry, Department of Biology, University of York

Core facilities support a broad range of scientific studies and must constantly integrate new technologies and analysis to underpin their users’ research. Areas for development include higher multiplex capabilities, greater quantification, correlation to other tools, as well as multi-omics. 

In this webinar, Peter O’Toole, Director of the University of York’s Bioscience Technology Facility, will share his experience integrating digital spatial profiling into the core. He will describe how this technology fits into the wider set of complementary platforms and techniques at the core, with the GeoMx DSP delivering high-plex, quantitative imaging for both protein and RNA studies.

Using the example of leshmaniasis, he will also talk about early successes using the DSP for developing a new understanding of host-pathogen interaction in specific tissue microenvironments. Future applications will support neuroscience, oncology, immunology, and infectious disease.   

Sponsored by
June 01, 2020
Sponsored by
LGC SeraCare Life Sciences

Germline Insights from NGS Somatic Testing: Clinical Challenges and Controversies


President and CEO, My Gene Counsel

Associate Professor of Medical Oncology, Cancer Biology, and Urology;
Sidney Kimmel Cancer Center, Thomas Jefferson University

Assistant Professor of Pathology,
Bigham and Womens Hospital

Licensed and Certified Genetic Counselor, IMPACT Program Navigator;
Corporate Wellbeing Champion Leader, Thermo Fisher Scientific

Associate Professor, Medical Oncology and Cancer Biology;
Thomas Jefferson University

GenomeWeb is hosting a virtual expert panel to discuss challenges, opportunities, and controversies related to informing clinicians, cancer patients, and their families of potential germline insights after receiving somatic testing.

This case-based discussion will provide an overview of best practices and lost opportunities, along with examples of the impact of current reporting practices on clinicians, patients, and their families.

Our panelists will bring their expert perspectives to this issue, representing stakeholders in oncology, molecular pathology, and genetic counseling.

They will discuss the pros and cons of reporting potential germline insights as part of the standard of care, and will address questions related to best practices, cost considerations, informed consent, liability, confirmatory testing, and the impact on patient care.

Sponsored by

Amsterdam University Medical Center

Director, Tumor Genome Analysis Core,
Amsterdam University Medical Center

Accurate detection of translocations is important for diagnosis, prognosis, and therapy decisions in aggressive B-cell lymphomas. 

Currently, lymphoma diagnostics is predominantly performed with fluorescence in situ hybridization (FISH), which is labor-intensive, can be difficult to interpret, and does not always reveal the fusion partner. Alternatives based on next generation sequencing (NGS) are being tested, but the robust detection of structural variants remains a challenge.

The Targeted Locus Amplification (TLA) technology selectively enriches and sequences entire genes based on proximity ligation and enables the comprehensive detection of structural variants in genes of interest. Because TLA is based on the crosslinking and fragmenting of DNA, it has particular advantages in the analysis of crosslinked formalin-fixed, paraffin-embedded (FFPE) samples.

In this webinar, our first speaker, Daphne de Jong of Amsterdam University Medical Center, will explain the important role of genetic information in lymphoma diagnostics, as well as the limitations of current technologies. 

The second speaker, Bauke Ylstra of Amsterdam UMC, will then present the results of a study performed on more than 100 lymphoma FFPE samples from several clinical sites with a TLA-based panel assay.

The study shows that:

  • TLA is more sensitive than FISH and detects small distance fusions not detected by FISH.
  • TLA detects structural variants in areas that are difficult to target or to sequence with standard targeted NGS methods.
  • TLA is easy to execute and enables a single, DNA-based test for detection of all clinically relevant single nucleotide variants and translocations.

As will be presented, TLA-based NGS promises to be a robust alternative for translocation analysis in lymphoma diagnostics and in other cancers.

Sponsored by

Vice President of Bioinformatics and Biostatistics, M2Gen

Chief Scientific Officer, Discovery Life Sciences

M2Gen’s Oncology Research Information Exchange Network (ORIEN) Avatar Research Program collects and studies consented cancer patients’ biospecimens and companion clinical information for the development of improved oncology treatments. Through construction of comprehensive genotypic, transcriptomic, and phenotypic cohorts of consented cancer patients, M2Gen generates in silico avatars. M2Gen uses this information to accelerate cancer research, clinical trial matching, and development of real-world data comparator cohorts. The breadth and scope of the ORIEN Avatar clinical and molecular data enables the discovery of a wide array of DNA and RNA biomarkers, including those biomarkers associated with response to immuno-oncology agents.

As a partner in the ORIEN Avatar program, Discovery Life Sciences’ sequencing and bioinformatics laboratory, HudsonAlpha Discovery, has conducted high-yield, high-quality dual RNA/DNA isolation from formalin-fixed, paraffin-embedded (FFPE) specimens as well as whole-exome sequencing and RNA sequencing services on more than 30,000 tumor and non-tumor samples. These genetic results, sharpened by ORIEN’s clinical data and the significant size of the sample set, accurately elucidate known drivers of cancer, identify new genetic alterations, and reveal novel potential therapeutic targets.

Attend this webinar to learn about:

  • The utility of data from this large, high-quality sample set to guide immunotherapeutic development programs
  • Large-scale sequencing of critical oncology biomarkers, including tumor mutational burden, microsatellite instability, small variants, splice variants, and fusions 
  • Optimized dual extraction methods from a single FFPE block that achieve highly accurate sequencing results across diverse tumor types and normal samples
  • The cancer centers and partners driving M2Gen's ORIEN Avatar program and how you can participate
  • How you can access the ORIEN database to accelerate your oncology drug development studies


Sponsored by
May 27, 2020
Sponsored by

Analyzing Complex Genomic Variants in Somatic Cancer

Partner Webinar

Next generation sequencing (NGS) technologies facilitate the accurate detection of genetic variants. Yet, the process of analyzing and classifying more complex alterations remains challenging.  In this educational webinar, we focus on gene fusions, co-occurring variants, copy number variants, and tumor mutational burden (TMB), and we provide practical strategies for analyzing and classifying these complex variants in the context of somatic cancer.

Sponsored by

Director, Diagnostic Molecular Pathology Laboratory,
Memorial Sloan Kettering Cancer Center

EGFR mutations are among the most common alterations in lung cancer. In advanced disease, the rapid identification of these mutations in liquid biopsies and small tumor tissue samples would allow expedited stratification, and aid in the identification of samples that would benefit from more comprehensive assessment.   

In this educational webinar, Dr. Maria Arcila of Memorial Sloan Kettering Cancer Center will discuss the following:

  • The growing importance of liquid biopsy assays as part of a lung cancer testing algorithm 
  • Updated lung cancer testing recommendations
  • Selection of an EGFR testing methodology compatible with flexible sample types including small biopsies, cytological samples, and cell-free DNA
  • Implementation of rapid, single-gene testing for lung cancer specimens to complement broad next-generation sequencing panels
Sponsored by

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
Partner Webinar

The emergence of COVID-19 has resulted in the need for NGS strategies for characterizing the SARS-CoV-2 viral genome. Sequencing of the full-length genome is critical for identifying mutational variants and contributing to research in the fields of virology, immunology, epidemiology, and molecular evolution, among others. However, maximizing viral RNA sequencing reads from clinical samples can be challenging, particularly due to the amount of human background that may be present.

In this on-demand webinar, we present a targeted NGS strategy which combines the Swift RNA Library Prep with the Arbor Biosciences myBaits Expert Virus SARS-CoV-2 panel. Combining RNA library prep with hybridization capture results in full-length genome coverage from a limited number of viral genome copies in a mixed sample, maximizing data output and offering an advantageous workflow for virus characterization.

Sponsored by

Professor and Associate Director for Basic Science at Sylvester Comprehensive Cancer Center of the University of Miami

Harbour Ocular Oncology Laboratory, MSTP MD/PhD Program, University of Miami Miller School of Medicine


Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy. Despite a well characterized genomic landscape and prognostically distinct molecular subtypes, a complete understanding of UM progression, metastasis and therapeutic resistance remains elusive.

Join Dr. J. William Harbour, Professor and Associate Director for Basic Science at Sylvester Comprehensive Cancer Center of the University of Miami, for a webinar to learn more about his recently published research studying the evolution of UM tumors and their microenvironments.  Using single-cell approaches from 10x Genomics for gene expression, genomic copy number variation (CNV), and T- and B-cell receptor typing, Dr. Harbour and team comprehensively characterized eight primary tumors and three metastatic tumors revealing new insights into UM biology and identifying a new putative checkpoint inhibitor target, LAG3.

During this webinar you will learn about how Dr. Harbour and team:

  • Explored the tumor microenvironment by analyzing gene expression profiles from 59,915 single cells from eight primary and three metastatic tumors to identify key gene expression differences across the tumor classes
  • Used transcriptional trajectory analysis to elucidate the transcriptional states of cells, confirming defined states for class 1 and 2 primary tumors and suggesting phenotypic plasticity within tumors
  • Combined single-cell T-cell receptor typing and gene expression data to reveal clonally expanded exhausted T-cell populations and identify LAG3 as a putative checkpoint inhibitor target
Sponsored by
Partner Webinar

In this webinar, discover how Paragon’s novel CleanPlex® SARS-CoV-2 Research & Surveillance panel uses their multiplex-PCR based targeted sequencing to detect and interrogate the SARS-CoV-2 genome. Turn your lab into a COVID-19 testing powerhouse via sensitive and comprehensive sequencing of the viral genome.

Sponsored by

This webinar discusses 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, discusses 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

Professor of Medicine,
Robert Lurie Cancer Center, Northwestern University 


Breast cancer clinical and molecular heterogeneity is a critical challenge for the implementation of effective therapies in advanced and metastatic disease.  Several clinical factors (patient and tumor-related) are routinely used to predict disease behavior, therefore directing clinical management and interventions.  

In this webinar, Dr. Massimo Cristofanilli of the Robert H Lurie Comprehensive Cancer Center and Feinberg School of Medicine will discuss the use of liquid biopsy diagnostics as an objective and measurable tools to evaluate the dynamic changes of metastatic breast cancer (MBC) at various time points, serving as sensitive, real-time evaluations of intrinsic resistance and molecular drivers of resistance.  

In the first part of the webinar, Dr. Cristofanilli will discuss recent results demonstrating that circulating tumor cell (CTC) enumeration stratifies MBC patients into two distinct prognostic groups, Stage IV aggressive and Stage IV indolent, thus providing an important diagnostic tool for patient stratification with the ability to improve the drug development process. Moreover, it may help physicians assess patients’ prognosis in clinical practice.   

In the second part of the webinar the role of circulating tumor DNA (ctDNA) diagnostics, using NGS panels to improve the capacity of molecular analysis of solid tumors, will be explored. The complementary role of ctDNA and CTCs to monitor MBC patients will be discussed.  

What You Will Learn: 

  • How both CTCs and ctDNA offer real-time complementary predictive information 
  • Ways in which CTC and ctDNA data can be used to tailor therapy and monitor treatment efficacy in individual patients 
  • Why the combination of sensitive blood-based diagnostics with novel target therapies is advancing personalized treatment in breast cancer 
Sponsored by

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

Understanding how gene expression in single cells progresses over time is vital for revealing the mechanisms governing cell fate transitions. RNA velocity, which infers immediate changes in gene expression by comparing levels of new (unspliced) versus mature (spliced) transcripts, represents an important advance to these efforts. A key question remaining is whether it is possible to predict the most probable cell state backward or forward over arbitrary time scales. 

In this webinar, our speaker, Xiaojie Qiu of the University of California, San Francisco, will share an inclusive model, termed Dynamo, capable of predicting cell states over extended time periods. The model incorporates promoter state switching, transcription, splicing, translation, and RNA/protein degradation by taking advantage of single-cell RNA-seq data and transcriptome/proteome co-assay measurements. 

Dr. Qiu will demonstrate how the Dyamo model can be used to infer the entire kinetic behavior of a cell and will show that it is possible to analytically reconstruct the transcriptomic vector field from sparse and noisy vector samples generated by single-cell experiments, especially those produced from metabolic labeling based scRNA-seq (i.e scSLAM-seq, NASC-seq, sci-fate or scNT-seq).

In this webinar you will learn:

  • How to use Dynamo to perform RNA velocity analysis and vector field reconstruction
  • Details of an inclusive model capable of predicting cell states over extended time periods
  • How to analytically reconstruct the transcriptomic vector field from sparse and noisy vector samples generated by single-cell experiments
Sponsored by

This webinar will discuss how to leverage an integrated platform for discovery and research in order to accelerate the translation of insights into clinical understanding, highlighting this process in the context of the fight against the COVID-19 pandemic.

Professor James Batchelor, Director of the Clinical Informatics Research Unit at the University of Southampton, will describe the ways his team adapted an existing framework, in collaboration with BC Platforms, to understand multiple aspects and parameters relating to COVID-19 patient treatment in the NHS.

In the context of COVID-19, which has already proven to be a significant burden on healthcare systems worldwide, hospitals are looking to apply and integrate more technology-based solutions to share data and insights in order to help solve this global challenge. The University Hospital of Southampton (UHS) and the University of Southampton has acted quickly to address this need and use bioinformatics innovation, with the support of BC Platforms’ underlying system BC|INSIGHT, to integrate, stage and analyze real time clinical data in order to understand high level clinical presentation risk stratification and monitor the progression in COVID-19 patients.

This webinar will highlight insights gained while using a system to coordinate research studies in a single platform, and how this framework can be applied to the challenges associated with the burden of COVID-19.

Sponsored by


The FDA and CDC call for a pause in administering Johnson & Johnson's SARS-CoV-2 vaccine while reports of rare blood clots are looked into, reports the Wall Street Journal.

According to the Associated Press, a Swiss program aims to shepherd long-term science projects and diplomacy.

CNN reports that two new studies suggest the B.1.1.7 SARS-CoV-2 variant may be more transmissible, but may not lead to more severe disease.

In PNAS this week: analysis of pathway affecting acute kidney injury, parental-specific allelic expression in horse placenta, and more.

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