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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

Pathologist,
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
Mon
Jun
1
1:00 pm2020
Sponsored by
LGC SeraCare Life Sciences

Germline Insights from NGS Somatic Testing: Clinical Challenges and Controversies

GenomeWebinar

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

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
Thu
Jun
4
11:00 am2020
Sponsored by
Ovation

COVID-19 Testing, Treatment and Future Outlook

GenomeWebinar

Chief Scientific Officer, Vikor Scientific

This webinar will discuss the current status of COVID-19 testing, treatment and other aspects of the current pandemic as they relate to getting this outbreak under control.  

Attendees of this webinar will learn about:

  • The role of PCR and antibody testing in the management of the pandemic;
  • The role of potential treatments for COVID-19 and future vaccines on the management of the pandemic;
  • Actions that need to be taken to mitigate the impact of future pandemics.
Sponsored by

Professor for Molecular Hematology,
Medical Faculty Carl Gustav Carus, Technical University of Dresden

The invention of novel high-throughput technologies, especially next-generation sequencing (NGS), has spurred our understanding of the development of human cancers and opened new avenues for rapid and comprehensive diagnosis. Especially in hematological malignancies, the availability of these novel high-throughput technologies has greatly enhanced our capabilities for the identification of disease, defining lesions and targets for tailored treatment. At the same time, these diagnostic tools have inherent aspects that make them vulnerable to false positives as well as false negatives. Major aspects are balanced coverage, the rate of detection of long insertions and deletions, as well as the sensitivity of the assay. 

Besides these technical aspects, the comprehensive and adequate interpretation of results, especially in the light of more recent discoveries regarding preleukemic, clonal hematopoiesis, such as clonal hematopoiesis with indeterminate potential (CHIP), adds an additional layer of complexity, which requires a substantial level of expertise to avoid over- as well as underinterpretation of results.

Nevertheless, the important information gained by using NGS-based evaluation of patients for the presence of mutations enables much more comprehensive analysis; identification of disease-defining lesions (e.g., mutations in genes like NPM1, CEBPA, SETBP1); and potential targets for treatment (e.g., cKIT, FLT3) and risk stratification (e.g., TP53, RUNX1 or ASXL1).

In this webinar, Dr. Christian Thiede, Professor for Molecular Hematology at the Technical University of Dresden will discuss the pros and cons of these methods, their appropriate and cost-effective use, as well as aspects to keep in mind for data interpretation will be discussed.

For Research Only. Not for use in diagnostics procedures.

Sponsored by
Tue
Jun
9
1:00 pm2020
Sponsored by
Illumina

Enabling Scalable Comprehensive Genomic Profiling from FFPE Samples

GenomeWebinar

Technical Director, Clinical Genomics,
Providence Cancer Center

Staff Product Manager,
Illumina

Senior Scientist,
Illumina

Comprehensive genomic profiling (CGP) is becoming standard of care for cancer and allows pathology labs to consolidate individual biomarkers into a single NGS assay. It enables the assessment of all key biomarkers cited in guidelines and clinical trials using a minimal amount of formalin-fixed, paraffin-embedded (FFPE) tissue while increasing the chance of finding a positive biomarker for every sample. 

Illumina’s TruSight Oncology 500 High-Throughput (TSO500 HT)assay enables labs to perform in-house CGP with scalability on a NovaSeq 6000 platform. 

In this webinar, Brian Piening of Providence Cancer Center will discuss why his team decided to implement in-house CGP and will share analytical performance data from their TSO500_HT runs. He will also provide details of the center’s end-to-end workflow, including the data analysis flow and how they build their final reports.

Attendees of this webinar will learn about: 

  • Providence Cancer Center’s implementation of in-house CGP
  • Illumina’s solution enabling in-house CGP
Sponsored by

Professor, Division of Cellular Immunology, La Jolla Institute for Allergy and Immunology & Head of Cancer Vaccines, Human Longevity Inc.

Medical Oncologist & Assistant Professor of Medicine, UC San Diego Health

 

T-cell receptor (TCR) therapy is a rapidly emerging adaptive cell therapy (ACT) method in the field of cancer immunotherapy. However, the process for developing effective T-cell receptors can be time consuming, particularly with regard to the rigorous functional testing needed prior to scale-up and patient infusion.

In this webinar, Stephen Schoenberger of the La Jolla Institute for Immunology discusses how he is leveraging an automated DNA assembly and cloning platform, the BioXp 3200, to achieve a 10-fold increase in the development of TCRs.

 

Sponsored by
Thu
Jun
11
11:00 am2020
Sponsored by
Stilla

Innovation in Digital PCR: Maximizing Data Output from Precious Samples

GenomeWebinar

Research Assistant,
National Institute of Biology

Director of Molecular Biology R&D,
Stilla Technologies

The commercialization of digital PCR platforms has sparked a revolution in quantitative nucleic acid detection over the past decade. Stilla Technologies’ Naica System, an established easy-to-use digital PCR platform, offers an innovative solution that quantifies in three colors while minimizing time to results.  

This webinar will present the features of the company’s new 6-color Crystal Digital PCR System and highlight a set of applications poised to greatly benefit from the increased multiplexing and high sensitivity of 6-color digital PCR. 

First, Alexandra Bogozalec from the National Institute of Biology in Slovenia will detail how her team has capitalized on the high-plex capacity of 6-color Crystal Digital PCR to simplify the time-consuming GMO quantification workflow and simultaneously quantify a set of genetically modified soybean lines at low target concentrations.  

This webinar will also discuss how the highly sensitive detection capability of 6-color Crystal Digital PCR benefits oncology applications. Allison Mallory of Stilla Technologies will present high-plex mutation detection in non-small cell lung cancer, colorectal and breast cancer samples and will show how 6-color digital PCR enables efficient therapeutic monitoring and early detection of treatment resistance through noninvasive liquid biopsy. 

Sponsored by
Mon
Jun
15
1:00 pm2020
Sponsored by
Thermo Fisher Scientific

Making the Case for Expanded Carrier Screening for Inheritable Genetic Disorders

GenomeWebinar

Vice President, Associate Dean, University of South Florida and Executive Medical Director,
Access to Expanded Carrier Screening Coalition

Advances in DNA sequencing technology have dramatically enhanced our ability to perform more comprehensive genetic risk assessments. Carrier screening protocols for the detection of serious and prevalent inheritable disorders have seen significant evidence-based advances but have experienced slow adoption, limited primarily by education of pregnant women and providers.  

Population demographics and variability in population ethnicity have redefined a couple’s risk for many inheritable autosomal recessive disorders. Advances like next-generation sequencing and sophisticated bioinformatics pipelines have provided insight into carrier frequencies in more diverse populations and identified the gaps that are created by current guidelines.

This webinar is the first in a three part series that will present cases that highlight the benefits of expanded carrier screening research for less well known inheritable conditions.

Join Dr. Brown in this webinar to learn about:

  • The evolution of expanded carrier screening  
  • Current guidelines and their role 
  • Cases highlighting the power of expanded carrier screening  
Sponsored by

Associate Professor,
Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph

All living organisms shed DNA into their environment, and these traces of DNA can now be profiled using next-generation sequencing. Thanks to a colossal effort around the world to sequence the molecular markers (e.g. DNA barcodes) of hundreds of thousands of eukaryotic species, we now have databases that allow us to match eDNA to its sources. By using the massive capacity of high-throughput sequencers, we can now survey the presence and dynamics of shifts in biodiversity in different environments and monitor it over time. 

Existing methods for environmental surveys are costly and time consuming, often relying on invasive or destructive sampling methods, and specialist expertise from taxonomists to correctly identify species. Metabarcoding promises to be a complementary alternative that will enable researchers, governments, and industry to gain more comprehensive insights into changes in biodiversity, and make more informed choices around conservation, environmental impact assessment, water quality monitoring, biosecurity, and more. 

This webinar will review recent research and validation experiments demonstrating the power of metabarcoding for a range of potential applications. 

Attendees of this webinar will learn about: 

  • Biodiversity markers and DNA barcoding
  • Metabarcoding and environmental DNA
  • Sample types and sampling regimes
  • Next-generation sequencing approaches for eDNA metabarcoding
  • Bioinformatics for taxonomic assignment and validation
  • Experimental design aspects from sample to data analysis and interpretation
  • Freshwater metabarcoding for water quality assessment
  • Soil metabarcoding for ecological surveys
  • Comprehensive biodiversity assessment in seawater using ultra-deep metabarcoding
Sponsored by

Application Scientist,
Lexogen

Chief Science Officer,
OnRamp Bio 

Epigenetic regulators are constituted by a great diversity of subunits, which are often redundant to varying extents. Novel experimental strategies including genome editing and small molecule-inducible systems allow for systematic dissection of multi-subunit complexes. While these approaches are ideal to assess the transcriptional consequences of combinatorial genetic perturbations to epigenetic pathways, the sequencing costs associated with gene expression analysis by RNA-seq quickly escalate as a function of sample number.

Lexogen QuantSeq facilitates increased multiplexing capacity without ramping up the sequencing costs by focusing on the 3’ ends of mRNAs. Such gene expression profiling approaches require only about 10 percent of sequencing depth compared to standard RNA-seq methods.

In this webinar, Jorge Zepeda from Lexogen will discuss a study conducted at the Institute of Molecular Biotechnology that used small molecule-inducible genetic perturbations in combination with transcriptional profiling by QuantSeq and chromatin immunoprecipitation sequencing (ChIP-seq) analysis to unravel the differential subunit requirements of polycomb repressive complexes 1 (PRC1) and 2 (PRC2), in maintaining robust silencing of lineage-specific genes and self-renewal capacity in mouse embryonic stem cells.

The second speaker, Jean Lozach from OnRamp Bio will demonstrate the capabilities of the OnRamp Bioinformatics discovery platform Rosalind to analyze and integrate multi-omics datasets like the QuantSeq and ChIP-seq used in this study and, will also show a new option for efficient collaboration between researchers.

Sponsored by
Tue
Jun
23
10:00 am2020
Sponsored by
Illumina

Building Global Startups: An Expert Panel on Entrepreneurship in Genomics

GenomeWebinar

Global Head, Illumina Accelerator

Co-founder & CEO, Biome Makers

Co-founder & CEO, Juno Bio

CEO, BioAmp

Co-Founder and Chief Operating Officer, 4baseCare

The decreasing cost of genomic technologies has democratized their use for many biotech and clinical breakthrough applications. Entrepreneurs are playing a key role in advancing these applications by translating scientific breakthroughs and ideas into commercially viable businesses that transcend borders.

Join the Illumina Accelerator and four global genomics startups in the biotech, clinical, and agricultural industries to discuss key trends in entrepreneurship; how to build a genomics startup from ideation to commercialization; how to access capital; and how to navigate and find opportunity in the current challenging climate.

Sponsored by
Wed
Jun
24
11:00 am2020
Sponsored by
NanoString

Implementing Digital Spatial Profiling as a Service: A Core Lab Case Study

GenomeWebinar

Research Scientist, Experimental Pathology; Division of Advanced Research Technologies, New York Langone Medical Center

An increasing number of technologies combine spatial discrimination with molecule identification, as has been done for decades through immunohistochemistry and in situ hybridization. The difference is that now a range of commercially available platforms promises to significantly increase the number of targets that can be identified on a single sample. These platforms also provide higher throughput in terms of the number of samples that can be interrogated, and some offer semi-automation with straightforward sample preparation.

These characteristics promise to make the new spatial profiling technologies attractive candidates for biomedical research facilities, but in order to discriminate between them, it is necessary to share real-world experiences using them in core labs.

This session will share the experience at New York University Langone Health using Nanostring’s GeoMx digital spatial profiling platform as a service for research laboratories. Dr. Valeria Mezzano of NYU Langone will discuss how her team approaches each project, interacts with clinical researchers, and performs the assays as an integrated network of core facilities.

Sponsored by
Thu
Jul
9
1:00 pm2020
Sponsored by
Illumina

Our Magic DRAGEN: A Sequencing Lab Case Study on Accelerated Bioinformatics

GenomeWebinar

Executive Director and Founder, Texas A&M AgriLife Genomics and Bioinformatics Service

Global Product Marketing Manager, Software, Illumina

In this webinar, Dr. Charlie Johnson, founder of the Texas A&M AgriLife Genomics and Bioinformatics Service, will share how his team is utilizing Illumina’s DRAGEN informatics platform in its high-throughput agrigenomics research program. 

Increases in sequencing power, laboratory automation, and bioinformatics have revolutionized agriculture genomics, but until the rise of the DRAGEN system, computing was the biggest roadblock for Dr. Johnson’s team. He will discuss how the platform has enabled his lab to reduce post-run data processing time from days to hours and in some cases minutes.

Dr. Johnson will also share how his team has expanded use of the DRAGEN system across the whole analysis pipeline, describe areas where the power of the platform’s hardware acceleration provides the best performance, and outline work being done to further improve efficiency.

Illumina’s Stephanie Black will review the DRAGEN technology, discuss key application areas, summarize recent advancements, and walk through the growing DRAGEN access points, both on-premises and in the cloud.

Sponsored by
Wed
Jul
22
12:00 pm2020
Sponsored by
Thermo Fisher Scientific

Advances in Genetic Testing for IVF Research: PGT-A, PGT-M, and Carrier Screening

GenomeWebinar

Scientific and Lab Director,
Bioarray & Journey Genomics

This webinar is the second in a three part series that will provide an overview of how cutting-edge genomic technologies based on next-generation sequencing (NGS) are streamlining in vitro fertilization research workflows*. 

Luis A. Alcaraz, cofounder of Bioarray and Journey Genomics, accredited diagnostic and research labs based in Alicante, Spain, will review how his teams use advanced genomic techniques for carrier screening research as well as for preimplantation genetic testing (PGT) in embryos for both aneuploidies (PGT-A) and monogenic disorders (PGT-M).

These technologies deliver greater efficiency to Bioarray and Journey Genomics, allowing faster delivery of meaningful results and reports for geneticists and researchers, which in turn is increasing their customer outcomes. 

In this webinar you will learn:

  • How to study PGT-A and PGT-M with NGS  
  • How expanded carrier screening with NGS screens for 420 genes in a single assay
  • How new molecular techniques are improving workflows at Bioarray and Journey Genomics

*For research use only. Not for use in diagnostic procedures.

Sponsored by

Kindai Nara University Hospital,
Department of Medical Oncology

This webinar will discuss a study that set to assess the efficacy and safety of osimertinib in EGFR T790M positive non-small cell lung cancer (NSCLC) patients identified by using plasma sample and cobas EGFR Mutation test v2. This is the first prospective study to use liquid biopsy upfront to evaluate osimertinib efficacy.

Takayuki Takahama of Kindai Nara University Hospital will share details of the study, which enrolled 276 patients with advanced or recurrent NSCLC with known TKI-sensitizing mutations of EGFR, had documented disease progression after treatment with at least 1 first- or second-generation EGFR TKI, and were positive for the T790M mutation in plasma.

Dr. Takahama will discuss the results, which demonstrate the utility of liquid biopsy for the detection of T790M with the cobas EGFR Mutation Test v2. Plasma genotyping with this assay is informative for treatment selection in clinical practice when tumor sampling is not feasible. 

Sponsored by
Thu
Sep
17
1:00 pm2020
Sponsored by
Thermo Fisher Scientific

Clinical Diagnosis of Developmental Disorders with Chromosomal Microarrays

GenomeWebinar

Senior Director, Cytogenetics Laboratory,
Greenwood Genetic Center

The prevalence of developmental disability among US children aged 3 to 17 years increased between 2009 and 2017, with as many as 1 in 6 children in the US reported to have a developmental disability diagnosis. Developmental delay/intellectual disability (DD/ID) is frequently accompanied with one or more congenital anomalies or dysmorphic features. 

Chromosomal microarrays (CMA) are an established technology that has demonstrated great sensitivity and specificity for detecting genome-wide copy number variants (CNVs) and now represents a robust technical platform for both medical genetics research and clinical services. The American Academy of Neurology, the American College of Medical Genetics, and the International Collaboration for Clinical Genomics recommend CMAs as the first-line test to aid in the diagnostic evaluation of intellectual disability.

CMA is replacing traditional karyotype and FISH as the first-line genetic test due to its greater sensitivity, higher resolution, genome-wide capability, and greater diagnostic yield. The CytoScan Dx Assay is the first FDA-cleared chromosomal microarray test to aid in the identification of the underlying genetic cause of developmental delay, intellectual disability, congenital anomalies, or dysmorphic features in children.

Join Barb Dupont from Greenwood Genetic Center to: 

  • Learn about the importance of CMA postnatal assessments for developmental delay, intellectual disability, congenital anomalies, or dysmorphic features
  • Discover the advantages of using a higher-resolution CMA solution when compared to conventional techniques such as karyotyping and FISH
  • Understand how CMA results from CytoScan Dx Assay can be used in conjunction with other clinical and diagnostic findings by healthcare professionals
Sponsored by
Recent GenomeWebinars

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
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

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

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

Technology Co-Inventor , IsoPlexis

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
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

Postdoctoral Scholar, Cellular Molecular Pharmacology,
University of California, San Francisco, School of Medicine

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

Professorial Fellow of Clinical Informatics and Healthcare Innovation, University of Southampton

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
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 discusses 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
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

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