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Webinar/Video Library

July 14, 2015
Sponsored by
Agilent Technologies

Molecular Barcoding and NGS to Detect Somatic Mosaicism in Primary Tumors

GenomeWebinar

Associate Professor, Department of Human Genetics, McGill University 

This online seminar outlines a recent example of the use of molecular barcoding in combination with next-generation sequencing to detect somatic mosaicism in cancer patients. 

Ioannis Ragoussis, associate professor in the Department of Human Genetics at McGill University, will discuss the study, which confirmed that somatic mosaicism was the cause of a rare cancer syndrome in four children. 

The children presented with multiple primary tumors associated with DICER1 syndrome, an inherited disorder characterized by pleuropulmonary blastoma along with other rare childhood sarcomas and dysplasias. The patients were each found to carry a specific DICER1 “hotspot” RNase IIIb mutation in multiple tumor biopsies from different sites. However, the mutations were not detected in the patients’ germline using conventional technology, leading to the suspicion of somatic mosaicism. 

Dr. Ragoussis and colleagues investigated and characterized the suspected mosaic origin of the DICER1 RNase IIIb mutations by deep sequencing both tumor and normal tissues from the four patients. 

An in-house, custom made DICER1 PCR-based array and a HaloPlexHS panel incorporating molecular barcodes were used prior to next generation sequencing on the Illumina HiSeq at high coverage. Using the molecular barcoding technology, the relative abundance of the previously identified mutations was assessed between tumor and non-tumor samples from the respective patients with the aim of confirming or refuting the hypothesis of a mosaic origin. 

Using this approach, the team confirmed its hypothesis that DICER1 RNase IIIb mosaicism was the cause of the rare DICER1-associated tumors in these children. Dr. Ragoussis will provide details of how the sensitivity of the HaloplexHS panel improved the ability to detect rare low-frequency mosaic mutations.

Sponsored by
GenomeWebinar

Automation Program Manager, Kapa Biosystems 

Senior Biomedical Research Services Officer, Food and Drug Administration 

This on-demand webinar, recorded June 23, demonstrates 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 Stover, Automation Program Manager for Kapa Biosystems, provides 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, presents 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 discusses 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
GenomeWebinar

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

Bioinformatics Products Strategist & Manager, PerkinElmer, Madrid, Spain

This online seminar demonstrates 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, presents 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 presents 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
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
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
GenomeWebinar

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
February 19, 2015
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
GenomeWebinar

This online seminar details the results of the first phase of an ongoing study being conducted by the Association of Biomolecular Resource Facilities' Research Groups that aims to evaluate the performance of six next-generation sequencing platforms: Illumina HiSeq 2000/2500, Illumina MiSeq, Roche 454 GS FLX, Life Technologies Ion Torrent PGM, Life Technologies Ion Torrent Proton, 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 study was recently published in Nature Biotechnology.

This webinar will discuss the findings from this phase, which 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. The speakers will also describe a comparison of alternative aligners for each platform, which showed that algorithm choice affects mapping rates and transcript coverage more than gene quantification.

The speakers will also provide an overview of the next phase of the study, which is focused on DNA reference standards, and will discuss the study's goal of establishing a community resource that will allow users of sequencing technologies to easily compare performance data as instruments and protocols change.

Panelists: 

  • George Grills, Cornell University, ABRF Executive Board
  • Scott Tighe, University of Vermont, ABRF Nucleic Acid Research Group
  • Christopher Mason, Weill Cornell Medical College, ABRF Genomics Bioinformatics Research Group
  • Don Baldwin, Pathonomics LLC, ABRF Genomics Research Group
  • Marc Salit, National Institute of Standards and Technology

Pages

The FDA and CDC call for a pause in administering Johnson & Johnson's SARS-CoV-2 vaccine while reports of rare blood clots are looked into, reports the Wall Street Journal.

According to the Associated Press, a Swiss program aims to shepherd long-term science projects and diplomacy.

CNN reports that two new studies suggest the B.1.1.7 SARS-CoV-2 variant may be more transmissible, but may not lead to more severe disease.

In PNAS this week: analysis of pathway affecting acute kidney injury, parental-specific allelic expression in horse placenta, and more.

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