Webinars Archive Page

Explore Our Webinars and see how the scientific community has used Ingenuity Software to create novel discoveries

2013 IPA Fall Release Product Introduction Webinar [34:11 minutes]
Presented by Dr. Stuart Tugendreich, Scientific Director, IPA
See the whole picture! Powerful functionality enables you to understand causal connections between molecules and diseases. This Fall 2103 release of IPA® from Ingenuity® Systems has exciting new capabilities which enable interactive visual exploration of causality between molecules and disease, functions, or phenotypes.
Life Long Changes in DNA Methylation & ncRNAs in Fetal Alcohol Syndrome (FAS) [54:54 minutes]
Presented By: Ben Laufer, PhD Candidate, Western University, Ontario, Canada
Fetal alcohol spectrum disorders (FASDs) are characterized by life-long changes in gene expression, neurodevelopment and behavior. What mechanisms initiate and maintain these changes are not known, but current research suggests a role for alcohol-induced epigenetic changes. We assessed alterations to adult mouse brain tissue by assaying DNA cytosine methylation and small noncoding RNA (ncRNA) expression, specifically the microRNA (miRNA) and small nucleolar RNA (snoRNA) subtypes. We found long-lasting alterations in DNA methylation as a result of fetal alcohol exposure, specifically in the imprinted regions of the genome harboring ncRNAs and sequences interacting with regulatory proteins. The findings of this study help to expand on the mechanisms behind the long-lasting changes in the brain transcriptome of FASD individuals.
Leveraging Ingenuity for Predictive Systems Biology: An Approach To Broad-Spectrum, Host-Directed Drug Target Discovery In Infectious Diseases [50:33 minutes]
Presented By: Dr. Ramon Felciano, Co-founder and Senior Vice President, Applied Research and Partnering, QIAGEN Silicon Valley
Knowledge of immune system and host-pathogen pathways can inform development of targeted therapies and molecular diagnostics based on a mechanistic understanding of disease pathogenesis and the host response. We used the Ingenuity plaform to investigate the feasibility of rapid target discovery for novel broad-spectrum molecular therapeutics was investigated through comprehensive systems biology modeling and analysis of pathogen and host-response pathways and mechanisms. We used this approach to identify and prioritize candidate host targets based on strength of mechanistic evidence characterizing the role of the target in pathogenesis and tractability desiderata that include optimal delivery of new indications through potential repurposing of existing compounds or therapeutics. We will describe our approach, experimental results, and the key technology innovations now publically available in IPA.
IPA the Fast Path to Toxicity Targets of Interest [36:55 minutes]
Presented by Dr. Aaron Erdely, Health Effects Laboratory Division, NIOSH
and Kaushal Parekh, Associate Staff Ontology Engineer, QIAGEN Silicon Valley
Metal-rich particulate matter inhalation exposure results in target organ toxicity but also adverse systemic effects including cardiovascular dysfunction and immunosuppression. As a preliminary search for induction of systemic mechanisms, generation of comprehensive transcriptome datasets by DNA microarray, along with gene network analysis, was performed from circulating whole blood cells, aorta, and lung then compared to determine related biological signaling following inhalation exposure.
Also demonstrated are some exciting new features in the new 2013 IPA Spring Release. Learn how IPA can help you quickly filter down to specific toxicity targets of interest
IPA 2013 Spring Release [48:24 minutes]
Presented by Dr. Stuart Tugendreich, Scientific Director, IPA
The 2013 IPA Spring Release is here! Powerful new functionality enables you to upload, find, and compare datasets, and understand causal connections between diseases, genes, and networks of upstream regulators. Stuart Tugendriech, PhD, Scientific Director, IPA from QIAGEN Silicon Valley gives an overview of the new IPA capabilities in the release, as well as a use case utilizing the new features and how IPA helps to Discover Causal Connections. Faster.
Improving Single Genome Annotation by Multi-Genome Analysis [37:32 minutes]
Presented by Gustavo Glusman, Senior Research Scientist, Institute for Systems Biology
This webinar discusses the analysis of whole genome sequence data in Alternating Hemiplegia of Childhood (ACH) samples using custom workflows and Ingenuity Variant Analysis platform to improve the sensitivity and specificity of genome interpretation.
Ingenuity Knowledge-Based Tools for Comprehensive Interpretation of Variant & Gene Expression Data [56:16 minutes]
Presented by Jean-Noel Billaud and Megan Laurance
Ingenuity Staff Scientists Jean-Noel Billaud and Megan Laurance present strategies for integrated analysis and interpretation of variant and gene expression data generated from cell lines representative of 2 breast cancer subtypes: Claudin-Low and Luminal. These subtypes represent different disease entities associated with specific molecular alterations and histo-clinical features. Interrogating these samples at both the variant and transcript level with Ingenuity's Variant Analysis and IPA software presents a powerful approach to drawing clear molecular paths from variants and gene expression changes to phenotypes relevant to these disease subtypes including Epithelial-to-Mesenchymal Transition and Metastasis.
A Bioinformatician's Guide to Lung Cancer: Wnt7a Signaling and Beyond [40:13 minutes]
Presented by Michael Edwards, Ph.D. Assistant Professor Division of Pulmonary Science and Critical Care Medicine. University of Colorado, Denver
This webinar discusses an important antitumor pathway in lung cancer (Wnt7a signaling) as a framework to explain the bioinformatic analysis process using IPA. Topics covered include biological function and pathway analysis, network construction, and identifying and interpreting upstream regulators.
Differential Expression of Focus Genes Associated Feed Efficiency [41:26 minutes]
Presented by Dr. Walter Bottje, Professor, Dept. of Poultry Science, University of Arkansas
Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated using microarray analysis. By using an overlay function of IPA in which canonical pathways can be projected onto a set of genes, differentially expressed focus genes were identified. We selected 130 out of 260 possible canonical pathways in the IPA program that would likely be associated with normal metabolic activities and did not select those that were obviously tissue or disease specific. The results of this study provide additional insight into gene expression in muscle associated with the phenotypic expression of feed efficiency in broilers.
The Role of microRNAs in Kidneys of Hypertensive Patients [23:09 minutes]
Presented by Aimee Jackson, Ph.D.
microRNAs are small, non-coding RNAs that function as central regulators of gene expression and development. These regulatory molecules have been implicated in a wide range of normal and pathological activities, including embryonic development, cancer, inflammation, cardiovascular disease and viral infections. We explored the possibility that microRNA dysfunction in the kidney might contribute to hypertension, a significant health issue. We analyzed mRNA and microRNA expression profiling data from kidneys of untreated hypertensive patients and normotensive patients to identify microRNAs, microRNA targets, and gene networks that are dysregulated in hypertension. The results of these analyses identify microRNAs and their targets that could be biomarkers or therapeutic targets for hypertension.
Whole Genome Sequencing for Rare Clinical and Consanguineous Familial Cases [37:16 minutes]
Presented by Christopher E. Mason, Ph.D., Assistant Professor, Department of Physiology and Biophysics and the Institute for Computational Biomedicine; Affiliate Fellow of Genomics, Ethics, and Law, ISP, Yale Law School
Learn how to use Ingenuity® Variant Analysis™ to analyze whole genome sequencing data. Chris Mason, Ph.D., presents a case study where Variant Analysis was used to analyze data from rare clinical cases with extreme phenotypes from the NIH's Undiagnosed Disease program and a consanguineous family with neural-tube defects. You will learn how to pinpoint likely genes causing disease phenotypes and see how an integrated systems biology approach that leverages biological analysis can contribute to advancements in personalized medicine.
Distinct Gene Expression Profile of Regulatory T Cells in Prostate Cancer [45:00 minutes]
Presented by Simo Arredouani, Assistant Professor of Surgery at Harvard Medical School
The inhibitory role of regulatory T-cells (Tregs) in cancer is now well established. Furthermore, inhibition of Treg function has been shown both experimentally and clinically to improve the immune response towards a variety of cancers. Developing new and more effective strategies interfering with the function of Tregs in cancer requires a deep understanding of Treg suppressor machinery, and a thorough dissection of the molecular elements that orchestrate their differentiation from T cells. This work paves the way for a better understanding of Treg biology in the context of prostate cancer and offers potential new avenues for Treg manipulation toward improving the outcome of immunotherapy.
Gene Expression Analysis Using Ingenuity iReport to Analyze Response to H1N1 Influenza [49:58 minutes]
Presented by Jamie L. Fornak, Ph.D. MPH
This webinar uses previously published data from an influenza study to demonstrate the ability of Ingenuity® iReport™ to correctly identify expected results and gain additional novel biological insights from gene expression data. Lee et al. originally performed gene expression analysis on human type-I like alveolar epithelial cells that were mock infected or infected with seasonal H1N1or pandemic H1N1. Two separate iReport analyses were generated from this dataset: one comparing mock infection to seasonal H1N1 infection and another comparing mock infection to pandemic H1N1 infection. See how iReport expanded the insights described in the original publication and provided additional genes of interest for potential follow up studies in the areas of transcription and mRNA transport.
IPA and Coronary Artery Disease: A Case Study from Harvard [36:23 minutes]
Presented by Dr. Jochen Danny Muehlschlegel, M.D., Harvard Medical School
See how IPA was used for the discovery of novel pathways of affected genes in coronary artery disease. Cardiopulmonary bypass (CPB) with cardioplegic arrest is associated with ischemia leading to metabolic substrate depletion, reperfusion injury, apoptosis and necrosis. The study hypothesized that human left ventricular (LV) myocardium responds differently to the stress of (CPB) depending on the presence or absence of coronary artery disease (CAD). Therefore, they assessed differences in gene expression in patients undergoing aortic valve replacement (AVR) with (CPB) prior to and after cardioplegic arrest using whole-genome transcriptional profiling.
A Combined Biological and Bioinformatic Analysis of Primary and Metastatic Tissues from NGS Ewing's Sarcoma Patients [58:00 minutes]
Presentation by Jean-Noel Billaud, Ph.D., QIAGEN Silicon Valley and and Sylvain Foissac, Ph.D., Integromics
The Ewing's Sarcoma family of tumors is a category of cancers that predominantly affects teenagers between the ages of 10 to 20. Learn how QIAGEN Silicon Valley' IPA software and Integromics' SeqSolve software were used to investigate Ewing's Sarcoma patient samples generated from Helicos' NGS technology. We will present a combined bioinformatic and biological analysis of Ewing's Sarcoma patient samples, focusing on the differences between primary and metastatic tissues. IPA was used to analyze the significantly regulated genes and Integromics' NGS SeqSolve software was used to prepare the RNA-Seq data. IPA's new transcription factor analysis tool and downstream effects map were used to help narrow down targets and visualize the biological networks.
Using IPA to Analyze Illumina RNA-Seq Data Reveals Abundance-Specific Biological Signatures in Alzheimer's Disease [33:44 minutes]
Presented by Darryl Gietzen, Ph.D., QIAGEN Silicon Valley
IPA was used to interpret Alzheimer's disease biology by comparing Illumina RNA-Seq data from Alzheimer's disease (AD) and normal brain samples. This analysis revealed very specific biological changes in certain classes of transcript expression, demonstrating how the unique benefits of RNA-Seq can help characterize disease changes. See how IPA maximizes RNA-Seq data analysis, how grouping and analyzing all significantly changed genes in RNA-Seq data can provide pathway level information, and how the sensitivity and accuracy of RNA-Seq enables pathway analysis on a subset of genes to elucidate more subtle biological changes.
Utilizing IPA for the Discovery and Development of New Pain Therapeutics [18:29 minutes]
Learn how Dr. Prysak utilized IPA to investigate the neuropathic pathways related to pain. In the United States, more than 39 million people suffer from neuropathic pain related to postherpetic neuralgia, trigeminal neuralgia, AIDS-related neuropathy, diabetic neuropathy, chronic low back pain, and cancer neuropathy. Unfortunately, neuropathic pain is often intractable and resistant to available drug therapies, none of which achieve clinical significance greater than 50%. To address this problem of great clinical need and poor therapeutic response, new mechanisms of action must be identified for future pain therapeutics. Aestus Therapeutics has undertaken a project to identify novel biological pathways involved in neuropathic pain using genome-wide expression data from a variety of sources and models. IPA, as well as other bioinformatics tools, helped Aestus identify seven novel biological pathways previously not associated with neuropathic pain. These seven novel pathways are being targeted for novel pain therapies. These potential therapeutics have been pre-clinically tested in animal models, validating both the pathways and the targets. The lead compound for the project, ATx08-001, was recently advanced into the clinic by Aestus, and is currently in a Phase 2 trial for the treatment of post-herpetic neuralgia. In this presentation, you will see how IPA was used to filter and explore existing data to investigate affected pathways and ultimately pathways for novel neuropathic pain therapies for patients.
NGS: Insights Into Prostate Cancer Mechanisms Via Integrated In Silico RNA-Seq Analysis of NGS Patient Data [14:07 minutes]
Presented by Sandeep Sanga, Ph.D.
This presentation explores some insights into the mechanisms of prostate adenocarcinoma, putative biomarkers and therapeutic targets by leveraging next generation sequencing (NGS) data through in silico RNA-seq analysis and interpretation using CLC bio and Ingenuity IPA®.
Biomarkers for Prostate Cancer: How IPA Can Help Explore Potential Biomarkers for a Complex Disease [39:31 minutes]
Presented by Dr. Jean-Noel Billaud
Dr. Billaud demonstrates IPA networks, gene views and canonical pathways for the exploration of molecular signatures of cancer. He utilizes the IPA Biomarker Filter, reagent view, functions & diseases overlay, and SNP data to help him identify the clinical aspects of prostate cancer. IPA allows you to overlap results from independent studies and this provides high value for the discovery and/or validation of biomarkers.
MicroRNA: Using IPA's microRNA Target Filter to Identify and Prioritize microRNA Targets for Melanoma [25:13 minutes]
In the rapidly evolving field of microRNA research, which still relies heavily on a variety of measurement techniques and prediction algorithms for target identification, the challenge is in identifying the most biologically relevant targets. To identify potential microRNA markers for disease progression from primary melanoma to metastatic melanoma, Ingenuity scientists applied biological information to prioritize mRNA targets, understand how these biomarker candidates contribute to disease progression, and design followup experiments to test their hypotheses. IPA®'s new microRNA Target Filter functionality enables prioritization of experimentally validated and predicted mRNA targets through the addition of biological information from the Ingenuity Knowledge Base and the ability to include experimental results in a single application.
Using IPA to Explore Pathways and Investigate Effects of Insulin Resistance on Human Adipose [25:19 minutes]
Presented by Aimee Jackson, Ph.D.
Learn how Dr. des Etages utilized IPA to investigate the metabolic and signaling pathways affected by insulin resistance in adipose tissue. Insulin resistance is a key component of Type II Diabetes. Essentially, it reflects the state in which peripheral tissues such as liver, muscle and adipose become less responsive to insulin. The increased insulin output required to maintain glucose homeostasis eventually leads to loss of pancreatic islet function and frank diabetes. Sears et al. published a study examining adipose and muscle samples extracted from insulin sensitive and resistant subjects at baseline, and then 3 months after thiazolidinedione (TZD) treatment. In this presentation, you will see how IPA was used to filter and explore existing data to investigate affected pathways and ultimately identify a transcription factor that may serve as a link between TLR2 signaling and adiponectin levels.
Biomarkers and microRNA: Integrative Analysis of microRNA and mRNA as Biomarkers for Ovarian Cancer [11:11 minutes]
This webinar discusses how IPA was used to identify microRNA biomarkers of ovarian cancer and explore their mRNA targets and possible roles in disease. IPA helped identify networks of microRNAs and their predicted targets, as well as the implicated pathways and cellular types affected by more aggressive tumors.
A Systems Toxicology Approach To Understanding Drug Toxicity And Compound Prioritization
Presented by Kevin T. Morgan, Old Dogs in Training, LLC Ke Xu, Department of Pharmacology, UNC Chapel Hill
[36:18 minutes] This webinar discusses how unfortunately, in spite of a massive investment in omics technologies (hardware and software), most Toxicogenomic studies receive inadequate interpretation due to (a) insufficient training of staff (wetware) in transcriptome physiology and pathophysiology, and (b) inadequate allocation of trained wetware resources to the task.