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Genome Webinar

Co-Founder & CEO, LifeFoundry

This webinar discusses how an algorithm-driven synthetic biology system can enable engineering of biological systems for a range of applications.

Synthetic biology applies engineering principles to study biological systems through design-build-test cycles and offers great promise for applications in healthcare, the biochemical industry, as well as fundamental discovery. However, the workflows are still mainly driven by human scientists, making it slow, expensive, and prone to human error and biases.

Our speaker, Ran Chao of the University of Illinois, shares details of a fully automated and highly versatile biological foundry that allows algorithms to directly design biosystems, orchestrate workflows, and analyze data. Dr. Chao discusses the latest applications of algorithm-driven synthetic biology at the University of Illinois as well as at LifeFoundry, a synthetic biology startup. He also shares applications of Tecan liquid handling systems in high-throughput TALEN (transcription activator-like effector nucleases) synthesis as well as rapid strain development processes.

Sponsored by
Genome Webinar

Head of Molecular Biology and Cell Engineering, Cerevance

Product Manager, NuGEN

This webinar will highlight the use of high-throughput sequencing of post-mortem human brain tissue to identify neurodegenerative markers and identify potential drug targets.

Dr. Steve Sheardown, Head of Molecular Biology and Cell Engineering at pharmaceutical company Cerevance, will discuss a technology platform  called NETSseq (Nuclear Enriched Transcript Sort sequencing). Cerevance uses NETSseq to interrogate the molecular diversity of individual neuronal cell types in human tissue to understand their genetic complexity, the contribution that each of these make to circuit function, and, in the context of brain disorders, their potential for therapeutic intervention.

Cerevance is building an extensive collection of transcriptomes from cell types selected for relevance to human disease covering both sexes and spanning different ages from donor samples obtained from diseased populations. Since commencing clinical data collection in October 2017, Cerevance have already accumulated over 1,300 high quality individual transcriptomes. Using this unique resource, the company aims to identify and pursue novel drug targets to address areas of high unmet medical need within the field of central nervous system disorders.

Dr. Sheardown will discuss how his team has transformed NETSseq from a low-throughput proof of concept to a robust high-throughput process for generating deep sequencing libraries from limited quantities of fixed post-mortem tissue. To achieve this, Cerevance has rigorously tested a range of products at every stage of the process, focusing on yield, quality, reproducibility, and automatability.

Drawing on examples from the company's transcriptome dataset, Dr. Sheardown will illustrate the depth of information that his team can generate using its NETSseq platform.

Sponsored by
Genome Webinar

Instructor, Department of Pathology & Biomedical Data Science,
Stanford Medical School

Director of Product Management, Dovetail Genomics

This webinar discusses a proximity ligation-based method for studying structural variation in formalin-fixed paraffin-embedded (FFPE) tissue.

FFPE tissue produces highly fragmented, low-molecular weight nucleic acids, presenting a principal challenge to identifying relevant genetic variants with tumor sequencing. This sub-optimal input specimen was previously not thought to contain long-range (Mbp+) information needed to accurately and robustly identify balanced and unbalanced large-scale structural variation and phasing from these specimens.

This webinar highlights a proof-of-concept study for using Hi-C chromosome conformation capture methodology for FFPE tissue, called Fix-C, which yields phased read pairs spanning distances up to full chromosomes and enables unambiguous structural variation detection and variant phasing in archival specimens.

Join this webinar to:

  • Learn how proximity ligation technology works and proven applications for this multi-dimensional NGS datatype from structural variation detection to genome assembly
  • See how proximity ligation overcomes the main challenge of highly fragmented DNA for studying structural variation from FFPE samples with data from a proof of concept study
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April 26, 2018
Sponsored by
Thermo Fisher Scientific

Evaluation of a Pan-Cancer Cell-Free Assay to Meet Unmet Research Needs

Genome Webinar

Senior Director, R&D Unit, Senior ConsultantMolecular Pathology Unit, University Hospital Basel | Institute for Medical Genetics and Pathology 

In this webinar, the second in the “New Frontiers in Liquid Biopsy Research” series, Luca Quagliata, Senior Consultant in the Molecular Pathology Unit at University Hospital Basel, shares two specific unmet needs within his lab’s liquid biopsy research that led to the eventual evaluation, adoption, and implementation of the latest liquid biopsy Oncomine NGS solutions from Thermo Fisher.

Dr. Quagliata’s lab at University Hospital Basel’s Molecular Pathology Unit has established methodologies for the genomic analysis of circulating cell-free tumor DNA (cfDNA) for lung and colon cancer research. The team’s validated workflow includes cfDNA extraction from plasma followed by next-generation sequencing with commercially available or specific custom-made gene panels and clinical interpretation of results to support their study.

Dr. Quagliata discusses two challenges that his lab faced with early liquid biopsy assays: 1) they could not detect fusions, and 2) they could not detect mutations from multiple cancer types with one NGS assay. He shares details of how the Ion Torrent Oncomine Lung Cell-Free Total Nucleic Acid Assay addresses the first of these challenges and how the Ion Torrent Oncomine Pan-Cancer Cell-Free Assay addresses the second.

For information on all webinar in this series, click here.

Sponsored by
Genome Webinar

PhD Student,
Petrov and Hadly Labs, Department of Biology, Stanford

Director of Product Management,
Dovetail Genomics

Proximity ligation technology generates multi-dimensional next-generation sequencing data that is proving to solve unmet needs in genomic research. Learn about some of the applications for this datatype and specifically how it helps create high-quality assemblies to overcome challenges of working with non-model organism genomes.

This webinar highlights three projects where proximity ligation technology and scaffolding software were used to create high-quality and highly contiguous genome assemblies for different organisms. Our speakers will also discuss the scientific discoveries enabled by these high-quality genome assemblies.

View this webinar to:

  • Learn how proximity ligation technology works and the applications for this multi-dimensional NGS datatype from cancer research to genome assembly
  • Hear how proximity ligation overcomes one of the main challenges of studying non-model organisms: being able to easily generate high-quality and contiguous genome assemblies
Sponsored by
Genome Webinar

Head of Pathology, Hospital Del Mar, Spain 

Director, R&D, Clinical Next Generation Sequencing Division, Thermo Fisher Scientific

In this webinar, the first in the “New Frontiers in Liquid Biopsy Research” series, Bea Bellosillo, head of pathology at the Hospital del Mar, discusses her experience evaluating an early-access lung cancer panel that detects copy number variants and fusions.

Dr. Bellosillo’s research lab was previously using the Ion Torrent Oncomine Lung cfDNA Assay from Thermo Fisher when it enrolled as a test site for an early-access program for the new lung panel that detects CNVs and fusions. Preliminary testing with the Oncomine Lung cfTNA (circulating free total nucleic acid) Assay indicated the presence of a RET fusion, which had not been detected previously. The finding led to a retrospective study of that sample where the RET fusion on the primary tumor was confirmed by FISH.

Following Dr. Bellosillo’s talk, Kelli Bramlett, senior director of R&D at the Clinical Next- Generation Sequencing Division at Thermo Fisher Scientific, presents a new white paper that showcases the performance of the new variant types introduced in the Oncomine Lung cfTNA Assay that Dr. Bellosillo was evaluating.

 

For information on all webinars in this series, click here.

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Genome Webinar

Laboratory Specialist, Clinical Genetics, University Medical Center Utrecht (UMCU)

 

This webinar shares how clinical genetics labs can integrate cytogenetics and molecular data to assess abnormalities using a single sample on a single workflow platform.

The current standard of care in genomics diagnostics laboratories is advancing toward array testing and whole exome sequencing on a single sample. Additionally, labs are shifting to the analysis of all molecular events for a patient sample – whether structural (CNVs, deletions, duplications, LOH regions, translocations) or molecular (SNPs, insertions, deletions). Labs do this because they are confident the diagnostic yield of combined CNV / NGS analysis exceeds that of each individual assay type, making 1+1=3.

Moreover, historically, the cytogenetics lab and the molecular lab were separate domains, within different groups at the lab or hospital. Cartagenia Bench Lab software, which was acquired by Agilent in 2015, catered to these different customer types with separate applications. While labs that did both arrays and sequencing could make the modules talk together and collaborate, they were not tightly integrated.

Today, with Alissa Interpret, the next evolution of Cartagenia Bench Lab recently released by Agilent, array data and WES data can now be integrated for a single patient sample, allowing for combined CNV/SNV analysis on a single workflow platform.

In this webinar, Ellen van Binsbergen, a laboratory specialist in clinical genetics at the University Medical Center Utrecht (UMCU) in The Netherlands, shares how Alissa Interpret was used in a case of multiple skeletal abnormalities to assess data from CNV analysis via SNP array and from WES analysis. By jointly triaging, classifying, and curating molecular and structural variants, she shows how UMCU was able to pinpoint variants inherited from the father AND deletions in the maternal allele – all yielded from a single sample, on one platform.

Genome Webinar

Emery-Dreifuss Muscular Dystrophy Patient Advocate

Head of Lab; Clinical Genomics and Personalized Medicine Specialist,
Congenica

Deputy Head of Clinical Services,
Congenica

In this webinar, Jill Viles, an Iowa mother with no clinical training, shares her story of how she self-diagnosed her rare condition, a muscle-wasting disease caused by a mutation in the LMNA gene. She also discusses how she discovered that a mutation in the same gene is the underlying cause for the excess muscle phenotype exhibited by Canadian Olympic hurdler Priscilla Lopes-Schliep. 

Members of Congenica's clinical team also discuss their identification of a potential modifying gene, SMAD7, which may contribute to Jill’s alternative phenotype, and how these are being used to further research the cause of her disease.

This webinar will cover:

  • Jill's steps to discovery and how she first started working with Congenica
  • How Congenica found the potentially modifying variant
  • The SMAD7 gene mutation, and how Sapientia can be used to make similar diagnoses
  • How Jill is acting on this information and looking to the future
Genome Webinar

University of Vermont Health Network

College of Medicine, University of Vermont

Q2 Solutions, a Quintiles Quest Joint Venture

Genomenon

In this webinar, an expert panel discusses how they used a genomic search engine to mine the genomic literature for two key applications: variant interpretation and the development of evidence-based diagnostic gene panels.

Nikoletta Sidiropoulos and David Seward from the University of Vermont College of Medicine first discuss their approach and the tools used to quickly and thoroughly mine the scientific literature to interpret variants in somatic cancer cases.

Next, Victor Weigman from Q2 Solutions presents an evidence-based method that his team used to select the content for gene panels by mining millions of full-text genomic articles to identify disease-gene-variant relationships. Dr. Weigman discusses how he created an evidence-based gene panel in under a week with prioritized literature citations for each biomarker.

Finally, Mark Kiel, founder and chief scientific officer of Genomenon, discusses a comprehensive, evidence-based cancer panel that was produced using automated machine learning techniques. The pan-hematopoetic cancer panel is a comprehensive cancer panel of more than 300 genes supported by specific literature citations from among millions of research publications. Dr. Kiel discusses how his team used the Mastermind Genomic Search Engine software to objectively correlate genes and genetic variants with the quality and frequency of scientific literature citations.

January 25, 2018
Sponsored by
Thermo Fisher Scientific

Rethinking Healthcare with Better Tools, More Information, and Deeper Analysis

Genome Webinar

Founder & CEO, Sema4

This webinar discusses a predictive, multiscale framework that can be used to understand the health of an individual at the molecular, cellular, organ, organism and community scales in order to better diagnose, treat, and prevent disease at a highly personalized level.

One of the primary goals of precision medicine is the aggregation and interpretation of deep, longitudinal patient-specific data in the context of the digital universe of information, using advanced predictive analytics to better diagnose and treat patients, even down to tailoring individualized treatments.

The rapid advance of panomic technologies such as next-generation DNA sequencing and medical imaging technologies, as well as the vast array of wearable, implantable, and environmental sensors, all linked to personal smart devices, are transforming the scale, scope, and depth of data we can generate on patients.

In this webinar, Eric Schadt, Founder and CEO of Sema4 and Dean for Precision Medicine at the Icahn School of Medicine at Mount Sinai, discusses a predictive, multiscale framework his team has developed to better understand diseases such as coronary artery disease, inflammatory bowel disease, diabetes, asthma health, Alzheimer’s disease, cancer, and several other disease areas in addition to wellness.

In this webinar, Dr. Schadt discusses how his team is evolving this framework to accelerate the engagement of big data and predictive models by patients, physicians, healthcare professionals, and researchers in ways that transform how the medical community diagnoses, treats, and prevents disease.

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Genome Webinar

Scientific Manager, LabEx Milieu Interieur, Institut Pasteur, Paris

This webinar discusses a standardized whole-blood culture and stimulation system and its application to a range of multi-center immune response studies.

Our speaker, Darragh Duffy, Scientific Manager of the LabEx Milieu Interieur consortium at the Institut Pasteur, shares details of several projects using the TruCulture whole-blood syringe-based system, which permits point-of-care standardized immune stimulation.

Dr. Duffy's team recently completed a multi-center clinical study in seven Federation of Clinical Immunology Societies (FOCIS) Centers of Excellence across Europe to directly compare TruCulture to conventional peripheral blood mononuclear cell (PBMC) methods. The study found that the ex vivo TruCulture procedure preserved physiological cellular interactions to more accurately reflect the complexities of the human immune system.

Dr. Duffy also shares how his team has applied TruCulture stimulation to the 1,000-donor cohort of the Milieu Interieur consortium, the objective of which is to define the boundaries of a healthy immune response at both the proteomic and transcriptomic level.

Dr. Duffy also discusses a partnership with Myriad RBM to co-develop the 13-analyte OptiMAP Luminex panel to enable the dissection of intrinsic (age, sex), genetic, and environmental factors to diverse immune stimuli at the population level.

Sponsored by
Genome Webinar

Sean C. Murphy, MD, PhD, Assistant Professor, Department of Laboratory Medicine, University of Washington

This webinar discusses how new quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) tests can accelerate the discovery and development of much-needed anti-malarial drugs and vaccines.  

Novel anti-malaria drugs and vaccines are currently evaluated using the Controlled Human Malaria Infection (CHMI) model, in which human volunteers receive a candidate drug or vaccine and are "challenged" with live Plasmodium falciparum sporozoites. Participants are then followed closely during the ensuing month, and if investigators detect the presence of malaria parasites in peripheral blood, it can indicate that the drug or vaccine was ineffective.

Historically, the gold standard test for erythrocyte stage Plasmodium infection has been microscopic examination of thick blood smears (TBS), which is analytically sensitive to 5-10 parasites per microliter of whole blood under ideal conditions. Because participants can be symptomatic prior to becoming TBS-positive, CHMI studies traditionally housed participants in a hospital ward or hotel during the potential symptomatic period. 

More recently, qPCR/RT-qPCR-based tests have improved the analytical sensitivity of infection detection by several orders of magnitude and now permit pre-symptomatic infection detection. Such tests accelerate infection detection compared to TBS and enable CHMI studies to be conducted without domiciling participants.

In this webinar, Sean Murphy of the University of Washington discusses efforts to improve the limit of detection for Plasmodium 18S rRNA/rDNA assays to 10-20 parasites per milliliter of blood. His presentation describes how such tests have reduced the costs, complexity, and risks of CHMI studies by accelerating infection detection and will detail external quality assurance efforts between laboratories that corroborate these diagnostic improvements. 

Genome Webinar

Assistant Member, Fred Hutchinson Cancer Research Center, Clinical Research Division; Assistant Professor, University of Washington, Division of Oncology

This webinar discusses the benefits of genomically profiling the immune microenvironment of soft tissue sarcomas during neoadjuvant therapy.

Sarcomas are a group of more than 70 cancers of mesenchymal origin that together comprise approximately 1 percent of all cancers. On initial presentation, these tumors are often localized and curable. Surgery is the mainstay of therapy, but radiation and sometimes chemotherapy can also play an important role.

Unfortunately, even with state-of-the-art care, more than 50 percent of patients with large, high-grade tumors will develop advanced disease. Immunotherapy has the potential to cure many of these patients, but little is known about the changing immune microenvironment during neoadjuvant treatment for soft tissue sarcoma.

During this webinar, Seth M. Pollack of Fred Hutchinson Cancer Research Center discusses a study that used multiple approaches to generate a molecular profile of these cancers. He provides details of how Cofactor Genomics' Paragon assay was used to dissect the changing tumor immune microenvironment in soft tissue sarcoma during neoadjuvant therapy and share results from the study.   

Genome Webinar

Director of the Laboratory for Clinical Genomics & Advanced Technology, Dartmouth-Hitchcock Medical Center & Norris Cotton Cancer Center; Professor of Pathology & Laboratory Medicine, Audrey & Theodor Geisel School of Medicine at Dartmouth

Senior Member & Chair, Department of Anatomic Pathology, Moffitt Cancer Center;  Executive Director of Esoteric Laboratory Services, Morsani Molecular Diagnostic Laboratory & Scientific Director of the Moffitt Tissue Core

 Associate Professor of Pathology, Associate Director of the Residency Program, Medical Director of Cytogenetics Laboratory & Director Georgia Esoteric & Molecular Laboratory, Augusta University

Founder & Chief Biomedical Informatics Officer, PierianDx

This webinar discussed the adoption of a commercial gene panel for tumor profiling at several leading US cancer centers.

Our expert panel — Gregory Tsongalis from Dartmouth-Hitchcock, Anthony Magliocco from Moffitt Cancer Center, Ravindra Kolhe from Augusta University, and Rakesh Nagarajan from PierianDx — specifically discuss their experiences with Illumina’s TruSight Tumor 170 targeted cancer assay.

The TST170 next-generation sequencing-based panel targets single nucleotide variants, indels, gene amplifications, gene fusions, splice variants, mRNA expression, and mRNA isoform detection found in 170 cancer-related genes and also calculates metrics such as tumor mutation burden and determines evidence for microsatellite instability.

Our panelists discuss the design of the assay, data analytics, and reasons behind their selection of the TST170 assay, and share details of how it is being utilized within their organizations. 

Sponsored by
Genome Webinar

Sr. Director of Clinical Operations, 
Rady Children’s Institute for Genomic Medicine

Scientist, Fabric Genomics

This webinar discusses the critical role of genomic interpretation software for clinical labs looking to establish comprehensive NGS testing programs. Accurate and fast software for variant calling, alignment, interpretation, and clinical reporting is an essential component of genomic medicine, with the potential to significantly impact patient outcomes and improve healthcare economics.

In this webinar, Shareef Nahas of Rady Children’s Institute for Genomic Medicine (RCIGM) presents various case studies that demonstrate how Fabric Genomics’ Opal Clinical software helps achieve accurate and rapid whole-genome interpretation of disease-causing variants in critically ill children.

RCIGM’s goal is a 24-hour turnaround time from blood sample to clinical report. Dr. Nahas discusses key interpretation and reporting capabilities needed to launch and scale clinical NGS testing, including the need for advanced computational algorithms to maximize diagnostic yield.

Our second speaker, Vanisha Mistry of Fabric Genomics, addresses best practices for adoption, deployment, and scaling of genomic data analysis platforms in the clinical lab, including automation and streamlining NGS workflows. She will review sample workflows for panels, exomes, and genomes, and will demonstrate their value to clinical labs.

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