Novel Applications of NGS in Cancer DiagnosticsWed, 11/19/2014 - 12:00
This live online seminar will address new applications for next-generation sequencing in routine histopathological diagnostics and molecular pathology.
Reinhard Büttner, director of the Institute of Pathology at Cologne University Hospital, will discuss how his team is integrating genomic information into cancer classification.
His presentation will cover five key areas in which NGS is changing cancer diagnostics:
• Somatic genomic or epigenomic alterations acquired during carcinogenesis, which may be used for disease classification in combination with conventional morphological classifications.
• Oncogenic driver lesions, which provide molecular targets for prediction of effective and selective therapies.
• Genomic alterations in signal transduction cascades and gene expression patterns, which may be used as prognostic parameters for predicting the need and extent of adjuvant therapy.
• Genomic profiling for differentiating metastases from tumors of unknown primary and correct tumor staging.
• Mutational profiling of circulating tumor DNA, which may enable monitoring the response of tumors to therapy and the development of secondary resistance.
Vikram Devgan, head of Qiagen's Biological Research Content business, will follow Dr. Büttner's presentation with a short review of current NGS technologies and applications of Qiagen's NGS technologies for molecular and predictive cancer diagnostics. He will cover the general principles of targeted enrichment panels design for NGS and the key factors that determine a successful NGS run.
, Director, Institute of Pathology, Cologne University Hospital and Center for Integrated Oncology.
Dr. Büttner is Professor and Chairman of the Institute for Pathology at University Hospital Cologne and Co-founder and Chief Scientific Officer, Targos Germany. Previously, he was Dean of the Medical Faculty and Professor and Chairman for Pathology at the University of Bonn. He holds an MD degree from the University of Mainz-Germany following residencies at Rheinisch-Westfälische Technische Hochschule Aachen and the University of Regensburg, and post-doctoral work at the Gene Center Munich and MD Anderson Cancer Center. He is a co-founder of the Network for Genomic Medicine in Lung Cancer
, head of Biological Research Content, Qiagen.
Dr. Devgan is the head of Biological Research Content, Qiagen. He received his PhD in molecular biology and conducted post-doctoral research at Harvard Medical School before moving to the biotechnology industry. He received his MBA from the University of Wurzburg in Germany and spent more than seven years as a scientist in technology and product development in the life sciences.
Managing Genetic Data in the Clinical Diagnostic Lab: an Integrated Informatics Workflow for Interpretation and Reporting Thu, 10/09/2014 - 11:00
This online seminar provides a first-hand look at how one clinical diagnostic laboratory is addressing the data-management challenges associated with high-throughput clinical genomics.
Julie Jones, Director of the Clinical Genomic Sequencing Program at the Greenwood Genetic Center, shares insights on integration of next-generation sequencing data in clinical diagnostics.
Dr. Jones will address how variant assessment and reporting workflows are set up at GGC, with a focus on panels, on full-exome sequencing, and on integrating copy number variant and NGS data. The presentation will include concrete clinical cases to illustrate the diagnostic workflow. Dr. Jones also shares notes on how labs can address workflow automation, clinical validation, compliance, and accreditation through the adoption of a standardized software platform, and review how GGC uses Cartagenia’s Bench Lab software platform to automate and streamline the analysis, interpretation, and reporting workflow for next-generation sequencing data in a diagnostic laboratory.
Cartagenia's Bench Lab was developed to reduce turnaround time; generate clinical grade lab reports; manage increasing volumes of data; interact with referring physicians; and to allow labs to confidently interpret, report, and share genomic variants.
Julie Jones, Director of the Clinical Genomic Sequencing Program, Greenwood Genetic Center
Dr. Jones received her PhD from the University of Alabama at Birmingham, completed a research fellowship at Vanderbilt University Medical Center, and performed her clinical laboratory training in molecular genetics at the Greenwood Genetic Center.
She holds a specialty certification in Clinical Molecular Genetics from the American Board of Medical Genetics. Her primary focus is on the validation and implementation of exome sequencing in a clinical diagnostic setting.
Register for the on-demand recording here
The ABRF NGS Study: A Multi-Platform Assessment of Transcriptome Profiling by RNA-SeqMon, 09/29/2014 - 12:00
This on-demand webinar, recorded Sept. 29, 2014, details the results of the first phase of an ongoing study on next-generation sequencing (NGS) technologies being conducted by the Association of Biomolecular Resource Facilities’ (ABRF) Research Groups.
The goal of this study was to evaluate the performance of six next-generation sequencing platforms, including the Illumina HiSeq 2000/2500, Illumina MiSeq, Life Technologies Ion Torrent PGM, Life Technologies Ion Torrent Proton, Roche 454 GS FLX, and Pacific Biosciences (PacBio) RS.
The first phase of the study focused on transcriptome analysis and involved more than 20 core facility laboratories who used standard reference samples from the Microarray Quality Control Consortium to perform replicate RNA‐seq experiments on these platforms. A paper
describing the results of this phase of the study was recently published in Nature Biotechnology
The results from this phase of the study showed high intra‐platform consistency and inter‐platform concordance for expression measures, but also demonstrated highly variable rates of efficiency and costs for splice isoform detection between platforms. A comparison of alternative aligners for each platform was performed, which showed that algorithm choice affects mapping rates and transcript coverage more than gene quantification.
The speakers also provide an overview of the next phase of the ABRF NGS Study, which will focus on DNA reference standards, and will be done in close collaboration with the NIST Genome in a Bottle (GIAB) Consortium. They discuss the study's goal of establishing a community resource that will facilitate self-evaluation and improvement of NGS performance data as instruments and protocols change.
• Christopher Mason, Weill Cornell Medical College, ABRF Genomics Bioinformatics Research Group
• George Grills, Cornell University, ABRF Executive Board
• Don Baldwin, Pathonomics LLC, ABRF Genomics Research Group
• Scott Tighe, University of Vermont, ABRF Metagenomics Research Group
• Sheng Li, Weill Cornell Medical College, ABRF Genomics Bioinformatics Research Group
• Marc Salit, National Institute of Standards and Technology
Register here to download or view the recording
The Message in the Haystack: Screening Live Stem Cells Using RNA Detection ProbesThu, 09/25/2014 - 12:00
This on-demand webinar, recorded Sept. 25, 2014, provides an overview of new tools for screening stem cells — in particular, the use of RNA detection probes to detect pluripotency gene expression in live embryonic and induced pluripotent stem cells by fluorescence microscopy without the need for manipulation of the cells.
Since their introduction in 2012, EMD Millipore's SmartFlare RNA detection probes have been cited in numerous publications, for studying gene expression in individual, live cells. This technique is widely applicable in dissecting heterogeneous cell populations across multiple cell types and research areas, including oncology, immunology, and cardiovascular research.
In this webinar, Don Weldon (Lead Scientist, EMD Millipore) provides an overview of the SmartFlare technology and its ability to study the gene expression of population subsets. Next, Dr. Harald Lahm (Head of the Laboratory of Experimental Surgery, German Heart Center Munich) describes the detection of various pluripotency genes in live, murine embryonic stem cells using SmartFlare probes. The same probes were also successfully applied to iPS cells of murine, human and porcine origin.
You will also learn about Dr. Lahm’s use of SmartFlare probes as a live screening tool to identify truly reprogrammed murine iPS cells derived from murine tail-tip fibroblasts in situ, based on their fluorescence intensity.
, Head of Laboratory of Molecular and Cell Biology of Experimental Surgery, German Heart Center Munich
Harald Lahm holds a PhD in Biology from the German Cancer Research Center and is currently the head of the Laboratory of Experimental Surgery at the German Heart Center Munich where he leads a team focused on regenerative therapy research for cardiovascular conditions.
, Lead Scientist, Application Development, EMD Millipore
Don Weldon holds a Bachelor’s degree in Cellular and Molecular Biology from San Diego State University. He has worked in the biotechnology industry as a research scientist for more than 11 years with a focus on emerging technologies including gene targeting in mice and molecular analysis of transgenes using GFP variants at the single cell level. His current focus involves working on a novel technology for RNA detection in live cells.
Advances in Molecular Profiling: Implications of Gene Expression Signatures in Radiation OncologyThu, 08/14/2014 - 11:00
This online seminar, recorded Aug. 14, 2014, provides an overview of new developments in the use of genomic methods to discover tumor biomarkers, with a particular focus on the field of radiation oncology.
Our expert panel discusses the discovery and evaluation of gene expression signatures associated with cancer treatment outcomes. These presentations will provide an overview of the promise of tumor microenvironment profiling in the radiation oncology setting, as well as the challenges in applying genomic methods to biomarker discovery.
, professor of radiation biology at the University of Manchester, discusses a recent study investigating radiosensitivity gene signatures in cancer cell lines. Her group evaluated three gene signatures trained on the NCI-60 panel, which contains cell lines from multiple tissues of origin, but few tumor types where radiotherapy is an important part of treatment. Dr. West's team used cell line cohorts from cervix and head and neck cancers to derive gene signatures associated with response to radiation therapy. Her group's findings suggest that a common transcriptional signature can reflect the radiosensitivity of tumors of heterogeneous origins.
, resident physician in the department of radiation oncology at Moffitt Cancer Center, speaks about a gene signature his team is developing to predict distant metastasis in stage I lung cancer following local therapy with surgery or stereotactic body radiation therapy. Dr. Kim and colleagues used Moffitt Cancer Center's biorepository, which contains tumor microarray data linked to longitudinal clinical data, to identify a 35-gene signature associated with the risk of distant metastasis in these patients. This presentation will outline the discovery and evaluation of this signature, and discuss future steps, including the development of a scoring system to classify stage I lung adenocarcinoma patients into three groups: low risk, intermediate risk, and high risk for distant metastasis.
, Professor of Radiation Biology, Translational Radiobiology Group, Institute of Cancer Sciences, University of Manchester.
, Resident Physician, Department of Radiation Oncology, Moffitt Cancer Center.
to view the on-demand recording.
Standardized Assays for Personalized Immune Response MonitoringThu, 05/15/2014 - 12:00
This online seminar, recorded May 15, provides an overview of recent research published in the journal Immunity
that demonstrates progress in the standardization of assays for personalized immune response monitoring.
Matthew Albert, co-director and founder of the Center for Human Immunology at Institut Pasteur, shares findings from the Milieu Interieur Project, a population-based study that aims to identify the genetic and environmental determinants of immune phenotype variance and establish a path towards personalized medicine.
Dr. Albert and colleagues have developed a suite of whole blood, syringe-based assay systems that can be used to reproducibly assess induced innate or adaptive immune responses. By eliminating pre-analytical errors associated with immune monitoring, he and his team have defined the protein signatures induced by: (i) medically relevant bacteria, fungi and viruses; (ii) agonists specific for defined host sensors; (iii) clinically employed cytokines; and (iv) activators of T cell immunity.
Initial results provide healthy donor reference values for induced cytokines and chemokines and indicate that the failure to release interleukin 1 alpha is a common immunological phenotype. Dr. Albert discusses how observed naturally occurring variation of the immune response may help to explain differential susceptibility to disease or response to therapeutic intervention.
The results of this work indicate that the implementation of a general solution for point-of-care assessment of functional immune responses will support harmonization of clinical studies and data sharing.
Participants will learn about the following from this archived webinar:
• Standardization of whole blood immune assays
• Use of Luminex assays to assess stimulation-induced protein signatures
Director of the Department of Immunology; Co-Director and Founder of the Center for Human Immunology at Institut Pasteur; Adjunct Faculty at Cochin Hospital
Dr. Matthew Albert is an INSERM director of research and full professor working at Institut Pasteur, where he heads a mixed INSERM/Pasteur unit. He received his MD at Cornell University Medical College and his PhD in immunology at Rockefeller University. He trained in Clinical Pathology at New York Presbyterian Hospital and was a Clinical Scholar at Rockefeller University Hospital.
Dr. Albert’s laboratory is centered around a "bedside‐to‐bench" approach to translational research. This has helped him to stay firmly rooted in clinically relevant scientific questions, which has furthered the understanding of disease pathogenesis and helped to establish the proper scientific foundation for the identification of new therapeutic interventions.
He is currently co-coordinating, with Dr. Lluis Quintana-Murci, the Milieu Interieur Consortium, which aims to define the genetic and environmental determinants of immune phenotype variance.
Register here to view the archived recording.
Utility of an Automated SureSelect NGS Panel for Understanding Disorders Featuring Aortopathy Tue, 03/25/2014 - 11:00
This online seminar, recorded March 25, covers the use of next-generation sequencing panels to understand mutations in inherited disorders.
Dr. Whitney Wooderchak-Donahue of the University of Utah and ARUP Laboratories shares the findings from sequencing 200 samples using an aortopathy sequencing panel developed at ARUP laboratories.
Aortopathy is a group of disorders that includes aneurysms, dilation, and tortuosity of the aorta. Although the FBN1 gene plays a major role in pathogenesis, several other genes are known to be involved. Because of the phenotypic overlap and genetic heterogeneity of these disorders, ARUP developed a next generation sequencing panel to detect mutations in seventeen genes that cause thoracic aortic aneurysms.
Dr. Wooderchak-Donahue and colleagues used a Bravo automated liquid handling instrument and custom SureSelect capture enrichment probes from Agilent Technologies to target the seventeen genes associated with aortopathies. NGS results were analyzed using an internally developed program, and mutations were confirmed using Sanger sequencing.
This webinar details how the aortopathy NGS research panel enables the identification of mutations in genes from individuals with disorders featuring aortopathy, including Marfan and Marfan-like syndromes.
Adjunct Assistant Professor, Department of Pathology, University of Utah; research and development scientist, ARUP Laboratories
Dr. Wooderchak-Donahue received a Bachelor's degree in chemistry from Western Illinois University and a doctorate in biochemistry from Utah State University. Her current focus is designing and validating various molecular genetics assays and next-generation sequencing assays that will be used in the clinical diagnostic laboratory at ARUP. She recently developed a multi-gene next-generation sequencing panel for the diagnosis of Marfan syndrome and Marfan-like syndrome disorders featuring aortopathies. Her research interests include understanding the molecular genetics of vascular malformation syndromes such as hereditary hemorrhagic telangiectasia using exome and genome sequencing.
to view the archived recording.
The 'Perfect Pairing:' ICE COLD-PCR with cfDNA for Highly Sensitive Mutation DetectionThu, 03/13/2014 - 10:00
This online seminar, recorded March 13, 2014, shares examples of a study being carried out by Transgenomic and MD Anderson that demonstrates the benefits of using circulating free DNA as a surrogate for formalin-fixed, paraffin-embedded tumor tissue. We will demonstrate how combining a PCR technique known as ICP with the analysis of cfDNA can dramatically improve the detection, treatment, and monitoring of cancer patients in the future and potentially replace tissue biopsies.
While circulating cell-free DNA (cfDNA) has been known for more than 60 years, the use of cfDNA as a molecular diagnostic tool — or so-called “blood biopsy” — has only recently been exploited for use in cancer treatment and monitoring. cfDNA provides a unique window into a cancer patient’s molecular landscape, which, unlike the static sampling of DNA from an FFPE tumor, is dynamic. The dynamic nature of cfDNA provides real time mutational analysis of primary and metastatic tumors for determining treatment options for patients as well as for the monitoring of treatment effectiveness and disease reoccurrence. However, the challenge for this analysis is the low concentration of cfDNA found in a patient’s plasma or serum and the potentially low level of mutations in this low concentration of cfDNA.
Transgenomic has developed and optimized the technique known as ICP (Improved and Complete Enrichment COamplification at Lower Denaturation PCR) for enriched amplification of mutant DNA. The enrichment is due to the differences in denaturation temperatures between mutant DNA duplexes and normal “wild-type” DNA duplexes. Transgenomic believes the pairing of ICP with cfDNA provides oncologists with a tool to detect cancers earlier and more accurately, allowing personalized targeted drug therapy and treatment monitoring, and resulting in the best possible outcome for patients.
The use of ICP coupled with Sanger sequencing shows greater than 400-fold enrichment for the detection of mutations and is a cost-effective assay when interrogating cfDNA for a small number of mutations. Furthermore, ICP can now be multiplexed prior to mutation characterization on next-generation sequencing platforms. This has the potential to monitor greater than 600 mutations from the same sample of cfDNA. This webinar will demonstrate how cfDNA + ICP + NGS provides the sensitivity required to make the "blood biopsy" the methodology of choice for cancer patient care decisions, monitoring and surveillance.
Katherine Richardson, Vice President of Research & Development, Transgenomic
Dr. Richardson holds an SB degree in Life Sciences from the Massachusetts Institute of Technology and a PhD in Molecular Cellular and Developmental Biology from Iowa State University. Prior to joining Transgenomic, she worked for eight years as a scientist with OSI Pharmaceuticals, where she specialized in molecular biology research and development in the area of oncology. Previously Dr. Richardson was with Eli Lilly and Company for nine years as a senior toxicologist specializing in genetic toxicology and molecular carcinogenesis. At Eli Lilly, Dr. Richardson was part of the group that identified the link between the BRCA-1 gene and hereditary breast cancer.
Filip Janku, Assistant Professor, Investigative Cancer Therapeutics, University of Texas MD Anderson Cancer Center
Dr. Janku holds an MD and a PhD from Charles University Prague. His research interests include oncogenic mutations, next-generation sequencing, the PI3K/AKT/mTOR pathway, autophagy, and therapeutic targets and molecular aberrations in histiocytic disorders.
Register to view the recorded webinar here