GenomeWebinars

Thu
May
28
11:00 am2015
Sponsored by
PerkinElmer

Using RNA-seq to Study a Splicing-based Human Disease in a Model Organism

GenomeWebinar

Principal Investigator at Bellvitge Institut for Biomedical Research, Barcelona, Spain 

Bioinformatics Products Strategist & Manager, PerkinElmer, Madrid, Spain

This online seminar will demonstrate how RNA-seq analysis in a model organism can provide insights into human disease. 

In this webinar, Dr. Julian Ceron of the Bellvitge Institut for Biomedical Research in Barcelona, Spain, will present a system to model retinitis pigmentosa in the nematode Caenorhabditis elegans using RNA sequencing data. 

Retinitis pigmentosa (RP) is a rare degenerative disease that causes progressive blindness. Among the 50 genes that have been associated with RP, Dr. Ceron's team has studied six that are transmitted from parents to their children in a dominant manner. These six genes codify for well-conserved proteins that are involved in RNA splicing. 

Despite the more than 9,000 published scientific studies about RP, there is still no efficient treatment to avoid the blindness caused by this disease. This may be due to the diversity of genes that can be involved, so it's possible that a personalized medicine approach that identifies the mutation for each patient might be the best strategy to use. The genes that Dr. Ceron and colleagues are studying share the same cellular function, so it is highly possible that they would also share a similar treatment. 

Dr. Ceron will present the system his team has developed to model RP in C. elegans and will discuss how RNA-seq analysis with OmicsOffice guided his research to identify a novel cellular mechanism that can explain why the pathogenesis caused by excessive apoptosis takes place specifically in the retina of RP patients. 

Sponsored by
Tue
Jun
23
11:00 am2015
Sponsored by
PerkinElmer

The Unsung Hero: Automated Liquid Handling for Innovative NGS Workflow Strategies

GenomeWebinar

Automation Program Manager, Kapa Biosystems 

Senior Biomedical Research Services Officer, Food and Drug Administration 

This webinar will demonstrate how automated liquid handling workstations can reduce bottlenecks in library preparation for next-generation sequencing, enabling scientific advances in genomics research that were not possible five years ago. 

Advances in NGS tools have led to greatly reduced sequencing costs and widespread adaption of the technology, but manual library prep methods can be laboriously intensive and prone to errors, while increasing the cost and timeline of the workflow. These tasks can now be robotically performed, decreasing hands-on labor and sample-to-sample variance while reducing tracking errors. This has ultimately led to increased productivity and better quality data. 

This webinar will discuss next-generation applications that use automation to reduce bottlenecks in NGS library generation and informatics processing. 

Our first panelist, Dan Stovers, Automation Program Manager for Kapa Biosystems, will provide an overview of Kapa's HyperPlus kit, which streamlines the NGS workflow by carrying out fragmentation and library preparation in a single tube. The solution combines enzymatic fragmentation with the speed and convenience of tagmentation-based workflows, coupling the benefits of liquid handling with NGS library preparation robustness. 

Liberating researchers from the repetitive processes of NGS library preparation with standardized liquid-handling workstations has allowed for novel applications and data-mining of vast sequencing data sets. In line with this, our second panelist, Marc W. Allard, Senior Biomedical Research Services Officer with the Food and Drug Administration, will present the open-access genomic reference database GenomeTrakr. GenomeTrakr is a new approach to tracking pathogen sources that uses DNA sequence information from a network of laboratories across the country that collect samples from foodborne outbreaks, contaminated food products, and environmental sources. GenomeTrakr can be used to develop new rapid methods and culture-independent tests. Dr. Allard will discuss data acquisition, assembly, analysis, and storage, as well that the application and interpretation of the data. 

With standardized hardware configurations, open-platform reagent compatibility, and pre-validated protocols, PerkinElmer NGS workstations can provide the flexibility and quality control to support novel approaches and chemistries within the NGS process. 

Sponsored by
Recent GenomeWebinars
Wed
Apr
29
10:00 am2015
Sponsored by
Covance

Genomic Analysis of CTCs and cfDNA for Dynamic Monitoring of Tumors

GenomeWebinar

Professor of Medicine/Hematology, Adjunct Professor of Genome Sciences, Director of the Center for Cancer Innovation, Co-Director of the Institute for Stem Cell and Regenerative Medicine, University of Washington

Senior Technical Director, Genomic Services, Covance 

This on-demand webinar, recorded April 29, 2015, reviews case studies demonstrating the clinical utility of CTCs and cfDNA to define and characterize a variety of dynamic genomic changes throughout the course of cancer detection and treatment. 

As a non-invasive method to improve prognoses, circulating tumor cells (CTCs) provide insights on drug resistance and determine appropriate, targeted cancer treatments. As compared to analyzing a single metastatic biopsy, CTCs provide a more holistic evaluation of metastases; they often demonstrate the same genetic mutations found in metastasized tumors and also reflect intratumoral and intermetastatic heterogeneity. Analysis of CTCs further allows biological characterization of a tumor that is inaccessible or too risky to biopsy. In addition, when collected and evaluated over an extended period of time, the rise and fall of CTC counts can offer clues into the effectiveness of a treatment, indicate the progression of disease, and detect metastatic spread earlier. 

The promise of periodic CTC analysis to monitor and treat tumors dynamically can also be extended to cell-free DNA (cfDNA) released from dying tumor cells and CTCs. Like CTCs, tumor-derived cfDNA reflects the genomic alterations of tumors -- but also boasts a short half-life that can indicate tumor changes faster than imaging or conventional biomarkers. Studies have also shown that cfDNA levels can reveal treatment response; amounts increase as a result of disease progression and decline with effective therapies. Also, when coupled with CTC characterization, genomic analysis of cfDNA can provide complementary information to detect mutations, which is especially valuable if CTC counts are lowered from a positive treatment response. 

When used together, cfDNA and CTC analyses could lead to more accurate profiling of tumors to detect various mutations, determine markers of resistance, and ultimately design a custom panel for personalized therapies. 

Sponsored by
Wed
Apr
15
1:00 pm2015
Sponsored by
WaferGen

Clinical NGS Testing Strategies for Oncology and Rare Disease

GenomeWebinar

Director, Casey Eye Institute Molecular Diagnostic Laboratory, Oregon Health and Science University 

Sequencing Group Leader, Michael Smith Genome Sciences Centre

This on-demand webinar, recorded April 15,  highlights recent trends in applying next-generation sequencing in the clinical setting, with a particular focus on oncology and rare disease. 

John Chiang, Director of the Casey Molecular Diagnostics Laboratory at Oregon Health and Science University, discusses a novel targeted next-generation sequencing test for retinal dystrophy. The test has so far been used to interrogate the underlying molecular mechanisms involved in the presentation of RD in more than 700 patients. Dr. Chiang shares details on how the implementation of this test has not only improved his team's understanding of the genes contributing to RD, but has also led to improved patient care and given certain patients the opportunity to be enrolled in clinical trials. 

Richard Moore, Sequencing Group Leader at the British Columbia Cancer Agency's Michael Smith Genome Sciences Centre, discusses the use of targeted sequencing at the GSC. In addition to production sequencing for research projects, the GSC recently implemented a College of American Pathologists-accredited diagnostic sequencing pipeline, currently offered for hereditary cancer with other panels under validation. 

This webinar is sponsored by WaferGen. Information on the company's targeted resequencing solutions is available here

Sponsored by

Principal Investigator, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital 

Chief Medical Officer, SomaLogic

In this on-demand webcast, Robert Gerszten of Massachusetts General Hospital will describe an ongoing project that is integrating metabolic and proteomic profiling to gain a better understanding of cardiometabolic disease.

In previous studies, Dr. Gerszten and his colleagues identified and validated metabolite profiles of those destined to develop overt diabetes mellitus. The strongest predictors of future diabetes included specific amino acid and lipid species, as well as 2-aminoadipic acid. These metabolites were found to predict diabetes mellitus above and beyond clinical risk factors and biochemical markers.

By integrating metabolite data with genome-wide scans, Dr. Gerszten and colleagues have identified 23 novel genetic determinants of human metabolism, including 8 loci previously implicated in human diseases.

More recently, Dr. Gerszten's group is complementing these mass spectrometry-based small molecule studies by integrating the Somascan apatamer-based proteomic technology into the work. Dr. Gerszten discusses how this approach is expected to lead to a more systematic understanding of cardiometabolic disease.

Sponsored by
Thu
Feb
19
11:00 am2015
Sponsored by
Lucigen

Finishing Genomes with Long Span NGS Reads

GenomeWebinar

Research Project Leader, Institute of Experimental Botany, Olomouc, Czech Republic 

Doctoral Candidate, Harrison School of Pharmacy, Auburn University

Founder and Chief Scientific Officer, Lucigen

This online seminar describes new technology capable of generating mate-pair sequencing reads up to 50 kb in length, enabling de novo genome assembly, closure, and finishing on the Illumina or Ion Torrent next-generation sequencing platforms. 

Despite advances in NGS technology, true closure and finishing of genomes or bacterial artificial chromosomes remains extremely difficult. NGS instruments produce gigabases per run, but the short read lengths and small size of sequenced fragments result in gaps, misassembled contigs, collapsed repeats, and missing sequences, leaving these regions to be finished manually, if at all. 

With new long span NGS read technology, however, user-defined 2-8 kb mate-pair or 10-20 kb mate-pair libraries can be produced with bead-based or gel purification protocols, with the potential for up to 100 kb mate-pair libraries in the future. Featured speakers will highlight real-world applications of this technology and the utility of long-span mate-pair libraries for genome closure. 

Sponsored by

Dr. Büttner is Professor and Chairman of the Institute for Pathology at University Hospital Cologne and Co-founder and Chief Scientific Officer, Targos Germany. He is a co-founder of the Network for Genomic Medicine in Lung Cancer.

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.

This online seminar, recorded November 19, addresses 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, discusses how his team is integrating genomic information into cancer classification.

His presentation covers five key areas in which NGS is changing cancer diagnostics:

      1. Somatic genomic or epigenomic alterations acquired during carcinogenesis, which may be used for disease classification in combination with conventional morphological classifications.
      2. Oncogenic driver lesions, which provide molecular targets for prediction of effective and selective therapies.
      3. 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.
      4. Genomic profiling for differentiating metastases from tumors of unknown primary and correct tumor staging.
      5. 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, follows 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 of the Clinical Genomic Sequencing Program, Greenwood Genetic Center 

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.