Presented by expert speakers, our webinars will give you advance insight into topics that will be covered at the event.

Can’t make the date? Still register to receive the webinar recording afterwards.

Genome Editing Webinar

How Animal Models Are Leading to Improve Gene-therapies in Humans

Tuesday 27th October 2020 | 14:00 - 15:00 GMT

Presented by Dr Guillaume Pavlovic, Head of Unit – Genetic Engineering and Model Validation Department, PHENOMIN-ICS – IGBMC

  • Genome editing tools (especially CRISPR/Cas9) have already revolutionized biomedical research. But what promise do they hold for clinical studies?
  • Several years of using genome editing in basic research have revealed the unpredictable nature and the uncertainty of the mutations that are obtained. While the bearing of off-target effects is widely known (& sometimes overestimated); on-target effects are less recognized and underestimated
  • This presentation will review recent work from animal and cell models that demonstrate the importance of extensive validation for the risk assessment of genome editing and its impact on cell integrity

Dr Guillaume Pavlovic is the Head of the mouse and rat model creation core (Genetic Engineering and Model Validation Department) at Institut Clinique de la Souris (ICS) – PHENOMIN. He direct the generation and validation of genetically rodent mutants for many academic laboratories, European consortia and pharmaceutical or biotech companies (more than 2,300 models achieved to date) and animal model microbiota research.

He leads R&D programs focusing on the development of new tools for genetic engineering and microbiota analyses, and is an expert in genetics and genome editing including the CRISPR/Cas9 system.

After a PhD in 2004, about bacterial mobile elements evolution, Guillaume Pavlovic worked at genOway, one of the leader company in the generation of customized and ready-to-use genetically modified mouse and rat models to develop the molecular biology activity. He joined ICS in 2007 as project manager in charge of the mouse model projects of its main industrial customers and was appointed at his present position one year later.

Digital PCR Webinar

Updating the Digital MIQE Guidelines: dMIQE2020

Tuesday 27th October 2020 | 10:00 - 11:00 GMT

Presented by Alexandra Whale, Science Leader, National Measurement Laboratory

  • Overview of what dMIQE is and what adoption by the scientific community will mean
  • Applications of dPCR with focus on specific factors for designing assays
  • Considerations for analysing experiments

The National Measurement Laboratory (NML) is the UK Designated Institute for chemical bio-measurement. Hosted at LGC we deliver underpinning chemical and bio-measurement science for the UK and form part of the UK National Measurement System (NMS), funded by the Department for Business, Energy and Industrial Strategy. The NML supports the work of the UK Government Chemist, a unique statutory function that provides expert opinion and advice to Government.

Single Cell Analysis Webinars

Advancements in Spatial Genomics Research - Oncology focus

Thursday 29th October 2020 | 15:00 - 16:00 GMT

Register for the webinar that includes three short presentations on Spatial Biology and one narrated poster. The illustrious presenters will share interesting insights on how to uncover biomarkers in situ and how to deconvolute scRNA data and spatial profiling results in situ.

Presentations Include:

Introduction | Agnese Winfield, PhD, Marketing Dir. NanoString
The 2 minutes introduction will be followed by:

Spatial Characterization of The Tumor-Immune Microenvironment Through Therapy in Breast Cancer | Christina Curtis, PhD, Associate Professor, Medicine – Oncology- Stanford University

The work presented is addressing the critical need to identify biomarkers of treatment response in early stage HER2-positive breast cancers. The Stanford team used NanoString’s GeoMx™ Digital Spatial Profiler (DSP) to quantify 38 tumor and immune proteins across multiple panCK-enriched regions from HER2-positive breast cancers, after different treatments, Important biological insights into the role of innate immune markers, ER status, and pam50 subtype on treatment response are presented.

Spatial Transcriptomics and Single-Cell Integration for In-Depth Localized Tissue Interrogation | Ioannis Vlachos, PhD, Assistant Professor of Pathology, Beth Israel Deaconess Medical Center

The talk will cover the method to integrate spatial information with single nucleus sequencing. The biology is focused on the characterization of lung tissue samples from COVID patients. The work carried out with the Whole Transcriptome Assay, on GeoMx DSP, to elucidate the genes and functional pathways associated immune response, and tissue damage and repair.

Highly Multiplexed Digital Spatial Profiling of the Tumor Microenvironment of Head and Neck Squamous Cell Carcinoma Patients Treated with Immune Checkpoint Therapy | Arutha Kulasinghe. PhD. NHMRC Research Fellow, Queensland University of Technology

In this study, the GemoMx™ Digital Spatial Profiler (DSP) was used to determine the immune markers and compartment specific measurements in a cohort of HNSCC tumours from patients receiving Immune checkpoint therapy.

Updating Immune Cell Deconvolution for the Spatial Genomics Era | Patrick Danaher, PhD Principle Statistician NanoString

The final part of the webinar is a poster presentation- Dr Patrick Danhart will share in less than 5 mins the deconvolution methodology for the integration of scRNASeq data in the tissue spatial context.

If you would like to receive copy of this poster, please contact awinfield@nanostring.com

An Integrated Cellular Atlas of Primary Human Breast Cancers

Tuesday, 10 November 2020 | 15:00 - 16:00 GMT

Presented by Dr Daniel Roden, Senior Research Officer, Cancer Division, Tumour Progression Laboratory Conjoint Lecturer, St Vincent’s Clinical School, Faculty of Medicine, UNSW Australia

Breast cancers are complex cellular ecosystems where heterotypic interactions play central roles in disease progression and response to therapy. However, our knowledge of their cellular composition and organization remains limited.

To systematically profile the cellular diversity of primary breast cancers, we integrated transcriptomes from over 100,000 individual cells, spanning all major molecular subtypes.  This provided a high-resolution characterization of the neoplastic, immune and stromal landscape of human breast cancers. To investigate neoplastic cell heterogeneity, we have developed a single cell classifier of intrinsic subtype (scSubtype) and reveal recurrent neoplastic cell transcriptional programs. Integration of immunophenotyping using CITE-Seq has revealed novel immune and stromal cell subsets which show a continuum of differentiation states with diverse predicted functions and cell surface protein expression. This has allowed us to generate a detailed taxonomy of the cells present in the breast tumour micro-environment.

Using this, we show that stromal and immune niches are spatially organized in tumours, offering insights into anti-tumour immune regulation. In particular, Nanostring spatial profiling, at whole-transcriptome resolution, was used to analyse T-cell rich regions of the tumour micro-environment in a subset of matching triple-negative breast cancers. Altered T-cell subset abundance was identified by tissue domain. Integration with our cellular gene signatures allowed deconvolution of the cell-type abundances of these specific tissue regions.

Finally, our single-cell derived signatures were used to deconvolute large breast cancer cohorts. We were able to stratify them into nine clusters, termed ‘ecotypes’, with unique cellular compositions and association with clinical outcome.

This work highlights the potential of atlas-scale single-cell projects to unravel the complex cellular heterogeneity within tumours and identify novel cell types and regulatory states underlying carcinogenesis. Such insights will guide the next generation of therapies, which will likely be based upon an integrated understanding of the cell states that define a tumour ecotype and inform treatment response

Next Generation Sequencing Webinar

Next Generation Solutions for Epigenetic Analysis

Thursday 19th November 2020 | 15:00 - 16:30 GMT

Presentations Include:

A New Way for DNA Methylation Analysis: Move Over Bisulfite | Vladimir Benes, Head of Genomics Core Facility, EMBL

For us in GeneCore, the opportunity to use the new EM-seq system launched recently by NEB has been a true game changer. In addition to its attractive features such as user-friendly workflow, it enables us to determine in a precise and DNA sparing way the cytosine methylation status, even with low integrity DNA. If bisulfite conversion were the only approach to apply, we would fail to generate relevant results. The biochemical approach the system is utilizing also opens new opportunities for analysis of cytosine methylation across the whole spectrum of DNA fragments: from very short cfDNA to intact long DNA fragments.

Targeted Epigenome Sequencing in Cell Free DNA to Improve Cancer Early Detection | Gahee Park, CRUK Early Detection Programme, Department of Oncology, University of Cambridge

The work presented is addressing the critical need to identify biomarkers of treatment response in early stage HER2-positive breast cancers. The Stanford team used NanoString’s GeoMx™ Digital Spatial Profiler (DSP) to quantify 38 tumor and immune proteins across multiple panCK-enriched regions from HER2-positive breast cancers, after different treatments, Important biological insights into the role of innate immune markers, ER status, and pam50 subtype on treatment response are presented.

Open Chromatin Profiling Using Nicking Enzyme Assisted Sequencing: NicE-seq | Chaithanya Ponnaluri, New England Biolabs

Chaithanya will describe his work developing NicE-seq (Nicking Enzyme assisted sequencing), a novel approach for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. In addition, he will introduce recent updates that allow sequencing of FFPE samples and a method for combined accessible chromatin visualization and sequencing.

Epigenetics is the study of heritable changes in gene expression that are not encoded in the DNA of the genome. In this webinar we will discuss two novel, enzyme-based methods for studying epigenetic changes, NEBNext Enzymatic Methyl-seq (EM-seq™) and NicE-seq, that are used to study DNA methylation and chromatin state respectively.

 

Bisulfite treatment has long been the gold standard for methylome analysis, specifically the identification of 5mC and 5hmC. However, this harsh chemical treatment damages DNA, resulting in DNA fragmentation and loss. Sensitivity of detection and confidence in results are also reduced by the bias introduced, including in GC coverage and over-representation of methylated regions. In response to the need for an alternative, New England Biolabs has developed NEBNext EM-seq, a conversion method that utilizes enzymatic treatment and minimizes damage to DNA. Because EM-seq uses enzymes, as opposed to harsh sodium bisulfite, it results in larger library insert sizes, minimal GC bias, uniform dinucleotide distribution, improved CpG coverage and greater mapping efficiency, all with a wide range of DNA inputs.

 

Another important factor controlling gene expression is chromatin accessibility – the measure of how “accessible” or “open” a region of the genome is to the access of transcription factors and other DNA binding proteins. Changes in chromatin accessibility are important epigenetic regulatory processes that govern cell or context-specific expression of genes. DNase hypersensitive assay, FAIRE-seq, NOMe-seq, and ATAC-seq are some of the methods used for interrogating chromatin accessibility. Nicking enzyme assisted sequencing (NicE-seq) is a novel method that captures and reveals open chromatin sites (OCSs) and transcription factor occupancy at single nucleotide resolution, even on fixed cells, coincident with DNase hypersensitive and ATAC-seq sites at a lower sequencing burden

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