Upcoming GenomeWebinars

Standardized Assays for Personalized Immune Response Monitoring
Thu, 05/15/2014 - 12:00 | Register
This online seminar will provide 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, will share 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 will discuss 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 webinar:

• Standardization of whole blood immune assays
• Use of Luminex assays to assess stimulation-induced protein signatures


Matthew Albert

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.

Archived GenomeWebinars

Utility of an Automated SureSelect NGS Panel for Understanding Disorders Featuring Aortopathy
Tue, 03/25/2014 - 11:00 | Register
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.


Whitney Wooderchak-Donahue
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.

Register here to view the archived recording.

The 'Perfect Pairing:' ICE COLD-PCR with cfDNA for Highly Sensitive Mutation Detection
Thu, 03/13/2014 - 10:00 | Register
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.

Winning Westerns: Tips and Techniques for Improved Western Blotting Workflows
Tue, 11/05/2013 - 12:30 | Register
Western blotting is a powerful and sensitive technique used to detect low amounts of proteins in complex samples, or to monitor protein expression and purification by protein blotting and immunodetection. Difficulties with this technique arise from poor protein transfer and antibody performance, both complicated and critical parts to the procedure, but completely optimizable with some key knowledge on membrane and antibody mechanics. Please view this online seminar, recorded Nov. 5, to gain more technical insight on the science and optimization of Western blotting.

The first speaker, Dr. Tim Nadler, is a Western blot veteran. Running hundreds of Western blots per year and assisting with customer technical issues, his group has amassed a wealth of information on this technique. In his presentation, he shares some tips and techniques that may enhance your current capabilities to run "Winning Westerns."

Following his talk, Dr. Natalie Tronson discusses how the use of optimal detection reagents and systems has enabled her to speed up her Western blotting workflow.

Register to view the archived recording here.

Is Next Generation Sequencing Accelerating Your Cancer Drug Development and Clinical Trial Programs?
Thu, 10/03/2013 - 02:00 | Register
Next-generation sequencing has emerged as a powerful tool to illuminate "druggable" targets in oncology. Tumor heterogeneity and limitations in DNA quality and yield from formalin-fixed specimens, however, present formidable challenges to routine NGS analysis.

In this webinar, recorded Oct. 3, panelists Brian Dougherty and Gary Latham discuss the pre-analytical, analytical, and post-analytical hurdles for targeted NGS, and offer solutions using workflows that provide sensitive and accurate results for both discovery and downstream clinical applications.

The speakers also describe how these methods can accelerate drug development by enabling new insights into cancer biology that can inform targeted therapies and companion diagnostics and by guiding patient stratification and selection in clinical trials.

Results from a recent study published in Genome Medicine, "Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies," are also discussed.

Register to view the archived recording here.

Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection
Thu, 04/25/2013 - 07:00 | Register
Sponsor: EMD Millipore

Data presented in this webinar illustrates the value of live cell analysis at the single-cell level to identify differences in expression levels across populations of cells. The cells remain intact for downstream analysis. Our experts also discuss the use of SmartFlare RNA detection probes for the direct quantification of circulating miRNAs with rapid processing of blood plasma/serum, which is done without the use of enzymes. Using circulating miRNAs with established roles in cancer and quality control, we can accurately detect these miRNAs in plasma using a microplate fluorometer within an hour after plasma preparation.

On-demand recording is available here.

Optimization of NGS Library Preparation: Low Inputs and Fast, Streamlined Workflows
Thu, 02/07/2013 - 08:00 | Register
Sponsor: New England Biolabs

Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.

Available here.