GenomeWebinars | GenomeWeb


Medical Director, Molecular Diagnostic Center, Knight Diagnostic Laboratories 

Adjunct Associate Professor, Genomic Medicine Initiative, University of California, San Francisco 

This webinar will outline the 2015 ACMG interpretation framework and demonstrate how the recommended variant scoring and classification rules may be applied to standardize reporting on sequencing test results within and across institutions.

Our first speaker, Sue Richards, Molecular Diagnostic Center medical director at Knight Diagnostic Laboratories, chaired the joint workgroup that devised the ACMG Standards and Guidelines to minimize differences in how laboratories interpret genetic variants and report on sequencing tests. Dr. Richards will discuss how the evidence-based system was developed for clinical labs to provide a systematic process to classify genomic variants. Dr. Richards will walk through the ACMG classification scheme and demonstrate how greater concordance of reporting may be achieved when using the standards.

Jeanette McCarthy, adjunct associate professor of Duke University and the Genomic Medicine Initiative at UCSF, will discuss the logic of the ACMG evidence framework, including the types of evidence and how the strength of such evidence is weighed when assessing variants.

While the ACMG guidelines were developed to enable consistent, reliable interpretation of genetic variants, for many clinical labs, implementing the variant scoring rules into a standardized workflow has proven difficult with available tools. Dr. McCarthy will demonstrate how the ACMG system was adapted as a rules-based software engine in Omicia’s Opal Clinical genome interpretation platform. The Opal Clinical scoring system provides guided assessment with yes/no evaluations that automatically generate classification recommendations based on the ACMG guidelines or customizable scoring rules. In addition, Dr. McCarthy will explore how labs can manage citations for segregation and functional evidence to support classification.

Information on Omicia’s variant interpretation solutions for clinical testing and translational research is available here.

Sponsored by
11:00 am2016
Sponsored by
Agilent Technologies

Defining Minimal Genomics Content for All Tumor Types


Assistant Professor in the Division of Cancer Biology in the Department of Radiation Oncology at Emory University. 

This online seminar will discuss the use of a hybrid capture-based FFPE DNA sequencing methodology with the potential for advancing precision oncology studies.

The goal of precision oncology is to identify and target molecular events that give rise to tumor growth and progression. Although the overall success of this approach for all tumor types is debated, it is clear that in some instances this approach has yielded dramatic results. The mutation spectrum of cancers encompasses driver missense and indel mutations, copy number abnormalities and coding fusions, many of which are still routinely analyzed with independent molecular pathology and cytogenetic assays. Moving forward, it is clear that if we are to improve the outcomes of the majority of patients with recalcitrant tumors, we need to update the histological diagnostic standards to incorporate molecular markers to propose more rational approaches to combined therapies.

This webinar will focus on the use of a hybrid capture-based FFPE DNA sequencing methodology to move toward this goal. Research into the technical feasibility, cost-effectiveness, and bioinformatics analysis workflows will be described.

Sponsored by

Scientific Director, Cytogenetics; Technical Director, Molecular Pathology/FISH; Legacy Health, Oregon

Product Director, NGS, Qiagen

Clinical Research Insights from the GeneReader NGS System

While next-generation sequencing has proven to be a very useful tool in basic research, two major hurdles remain for its broad adoption in the clinical research setting: lack of seamless workflow for routine clinical research use and truly relevant content to guide clinical research activities.

This webinar will discuss Qiagen's approach to address these two issues. The Qiagen proprietary Knowledge Base was used to design a tumor panel to identify aberrations of value for clinical research. The GeneReader NGS System was then used to deliver clinical research insights in a laboratory setting. Testing was conducted with a set of colorectal cancer samples, and results confirmed with alternative testing platforms.

Our first speaker, Yassmine Akkari, Scientific Director of Molecular Pathology at Legacy Health, will share her experience of NGS panel-based testing, and some of the challenges. She is also going to speak about the Qiagen Actionable Insights Panel design process, and how this unique process led to robust content focused on variants of clinical significance.

Yi Kong, Marketing Director, NGS, Qiagen, will then share some of the data generated using the Actionable Insights Tumor Panel and the GeneReader NGS System, as part of a collaboration between Qiagen and the Broad Institute.

The Qiagen GeneReader NGS System is a fully integrated sequencing workflow, engineered specifically for clinical research purposes. This turnkey solution is purpose-built, focusing on the assays that matter most. Learn more about the GeneReader NGS System here

Sponsored by
11:30 pm2016
Sponsored by
Core Informatics

How Mount Sinai Uses LIMS to Support Clinical & Research Genomics Workflows


Managing Director, Mount Sinai Genetic Testing Laboratory 

Applications Manager, Genomics, Core Informatics

Selecting and deploying a laboratory information management system is not a trivial task. This webinar will discuss some of the criteria that the Mount Sinai Genetic Testing Laboratory used to develop and implement a highly configured LIMS for clinical and research genomics workflows in a high-throughput sequencing facility. 

Dr. Todd E. Arnold, Managing Director of the Mount Sinai Genetic Testing Lab, will share details of his team’s experience deploying a LIMS from Core Informatics. The Mount Sinai lab posed some unique challenges to the Core Informatics team, including a very large number of samples, stringent traceability requirements for CLIA and CAP compliance, research and clinical sample handling, a variety of input materials, diverse workflow elements, and the need to interface with multiple report templates. 

In his presentation, Dr. Arnold will describe his site, his team’s charter, detail around the implementation process, and the performance of the Core LIMS in his team’s hands. 

Sponsored by
Recent GenomeWebinars
11:00 am2016
Sponsored by
Agilent Technologies

A Metagenomic Assay to Study the Role of the Microbiome in Cancer


Professor of Microbiology, Radiation Oncology, and Vice Chair for Research of Otorhinolaryngology, Perelman School of Medicine, University of Pennsylvania 

Array & Dx Applications Manager, Genomics R&D, Agilent Technologies 

This on-demand webinar discusses a metagenomic assay to identify viruses and other pathogenic microorganisms in human tumor samples, with the aim of gaining a more comprehensive understanding of the role of the microbiome in cancer development and treatment. 

Erle Robertson, a professor of Microbiology at the University of Pennsylvania's Perelman School of Medicine, discusses the PathoChip, a 60,000-probe comparative genomic hybridization microarray that was developed to target viral, prokaryotic, and eukaryotic genomes. 

Dr. Robertson and his colleagues recently used the PathoChip technology to identify viruses, bacteria, fungi, and parasites associated with triple negative breast cancer. The study used formalin-fixed paraffin embedded archival tissues and the results were validated by PCR and next-generation sequencing. Hierarchical clustering analysis identified two signature patterns, one predominantly bacteria and parasites and the other predominantly viruses. 

The contribution of these microbial signatures has yet to be determined. It's possible that the microbes play a causative role, contributing something to the cellular microenvironment that helps damaged cells become malignant, or they may just find tumor tissue to be a favorable environment. Nevertheless, their association with the disease indicates that they may have diagnostic potential. 

Dr. Robertson also discusses how his team used the PathoChip to rapidly identify a zygomycetous fungi, Rhizomucor pusilla, in a case of a patient with acute myelogenous leukemia, highlighting the value of the chip as a tool to identify microorganisms to the species level, especially those that are difficult to identify for most microbiology laboratories. 

Sponsored by

Associate Professor, Department of Medicine, University of British Columbia 

Co-founder and Chief Scientific Officer, MSK/dx

Senior Director, Marketing, Assays and Reagents, HTG Molecular Diagnostics 

This webinar discusses potential clinical applications for miRNA signatures and a novel, extraction-free miRNA profiling technology for advancing biomarker discovery. 

MicroRNAs — small, non-coding RNA molecules ranging from 18 to 25 nucleotides — have recently demonstrated potential as markers for diagnostic or prognostic applications due to their resilience to degradation, comprehensive annotation of more than 2,000 transcripts, and a deeper understanding of how miRNAs play a role in human disease. However, application of miRNA biomarkers has been limited by the difficulty of extracting quality product from clinically relevant sample types, the biases associated with preparing small, non-coding RNAs for next generation sequencing, and the data complexity caused by the sequencing of random fragments. 

In this online seminar, panelists will discuss two projects that are seeking to optimize miRNA profiling for eventual clinical applications. 

Scott Tebbutt, associate professor in the Department of Medicine at the University of British Columbia, will share his team's work developing tissue- and blood-based miRNA signatures of acute heart failure. Currently, there are no well-defined response biomarkers that can be used to monitor treatment or evaluate recovery in patients with severe inotrope-dependent acute heart failure. Dr. Tebbutt will present details from a study that is characterizing miRNAs as tissue and circulating biomarkers of heart failure in these patients over the first 30 days of medical management or mechanical circulatory support. 

Don Baldwin, co-founder and chief scientific officer of MSK/dx, will discuss a project that is exploring miRNA profiling to identify biomarkers associated with bone fractures, with the goal of developing tests to help reduce the comorbidities and costs of treating complicated fracture cases. Dr. Baldwin will introduce a Latin square set of synthetic miRNAs developed by the Association of Biomolecular Resource Facilities that was used to demonstrate quantitative responses and specificity of the HTG EdgeSeq platform. The MSK/dx team then performed molecular profiling with the HTG EdgeSeq system to study circulating miRNAs in whole blood and serum from orthopedic trauma patients. 

Sponsored by
2:00 pm2015
Sponsored by
Oracle Health Sciences

Building a Scalable Precision Medicine Infrastructure: Penn Medicine’s 'Life Lessons'


Associate Vice President of Health Technology and Academic Computing, Penn Medicine

Director of Business Development and Strategy, Oracle Health Sciences 

Are you thinking about establishing a precision medicine program and wondering how to build the right infrastructure? Has your institution put plans in motion to integrate genomic data with traditional clinical data from the EHR for research or clinical purposes? Are you committed to building a scalable precision medicine program but want to avoid the challenges associated with being on the leading edge? Are you struggling to understand the cost/benefit ramifications of running a precision medicine program? 

If you answered "yes" to any of these questions, you should attend this live webinar, where Brian Wells, Associate VP of Health Technology and Academic Computing at Penn Medicine, will discuss his experience putting these issues into practice. Penn Medicine has successfully blended millions of patient records and billions of genetic variant data points into a single system that researchers and clinicians alike are accessing on a daily basis to move precision medicine forward. 

Attendees will gain insight about how to plan for and build a scalable IT infrastructure that will enable clinicians and researchers to efficiently stratify patients and uncover new biomarkers. You will also learn how to empower a wide range of users to access and mine unstructured medical data, bio-bank samples, and readily blend clinical trial management system data into your EHR record. 

Brian will detail how Penn has successfully leveraged its "PennOmics" integrated healthcare data warehouse to accelerate clinical trial recruitment at the point of care, accept data from wearables, and do it all in a secure, HIPAA- and research-compliant fashion. 

Sponsored by

Associate Professor, Department of Biological Sciences, Auburn University

Research Geneticist, US Department of Agriculture Agricultural Research Service 

Professor of Laboratory Medicine & Pathology, Mayo Clinic

This webinar will focus on a range of research and clinical applications enabled by improvements in mate pair technology for whole genome sequencing. 

Speakers will discuss their use of Lucigen's NxSeq long mate pair library kit for a number of applications, including closing and finishing microbial genomes, resolving complex plant organelle genomes, and characterizing genetic alterations in cancer. 

Mark Liles, associate professor at Auburn University, will describe his use of the technology to finish multiple bacterial genomes using a single 10-20 kb mate pair library in conjunction with a conventional 600 bp paired end fragment library. His presentation will address the implications of this approach for assembling repeat-rich, complex genomes from fungi, mitochondria, chloroplasts, plants, and animals. 

Bob Klein, research geneticist at the US Department of Agriculture's Agricultural Research Service, will share details of a project to sequence and assemble the mitochondrial and chloroplast genomes of sorghum. De novo sequence assembly of these large, repeat-rich interrelated genomes is complicated by significant lateral gene transfer between the organelles, but his team was able to use a new long span mate pair library construction strategy to unambiguously assemble both genomes. 

Finally, David Smith, professor of laboratory medicine and pathology at the Mayo Clinic, will discuss the use of next-generation sequencing in cancer management In particular, he will focus on the use of mate pair sequencing to characterize genomic alterations in an individual cancer and how this knowledge can be used to both monitor the cancer through treatment regimens and to develop the most appropriate clinical regimen for that cancer.

Sponsored by
11:00 am2015
Sponsored by

Rapid High-Risk Diagnostic Testing for Newborns Using Targeted NGS

Partner Webinar

Adjunct Professor of Pediatrics, Medical University of South Carolina

Director, Clinical and Client Services, Parabase Genomics 

This webinar will discuss the benefits of a rapid targeted next-generation sequencing (TNGS) panel, using dried blood spots, for second-tier newborn metabolic and hearing loss screening and its immediate utility for high-risk diagnostic testing in the neonatal intensive care unit. Speakers will share case reports on the application of TNGS for inherited metabolic disorders. 

While newborn screening has dramatically reduced infant morbidity and mortality for some genetic disorders, these improvements have not had a significant impact on most NICUs, where almost 478,000 infants are admitted each year. It's estimated that between 10 percent and 25 percent of all NICU admissions are the result of a genetic disease, with infants staying in the hospital approximately 40 percent longer than non-genetic cases. 

Due to the non-specific presentation of many of these genetic disorders, many infants are unable to receive a definitive diagnosis in a timely fashion or are misdiagnosed completely. 

This online seminar will discuss a rapid targeted NGS panel that can be used with standard dried blood spots in order to expand molecular diagnosis and precision medicine for hundreds of genetic diseases. 

The speakers will discuss the development of this methodology, its application for high-risk diagnosis in the NICU, and specific panels for second-tier newborn metabolic and hearing loss screening. Speakers will present results of routine screening and details from actual case reports.

Sponsored by
11:00 am2015
Sponsored by
Personal Genome Diagnostics

High-Sensitivity Plasma Testing for Non-small Cell Lung Cancer


Interim Director, Sidney Kimmel Comprehensive Cancer Center

Vice President, Research & Development, Personal Genome Diagnostics 

This webinar highlights the key considerations and applications of next-generation sequencing for managing non-small cell lung cancer patients using plasma-based approaches. 

NSCLC is the most common type of lung cancer, accounting for about 80 percent of all lung cancer cases. Approximately 35 percent of NSCLC patients do not have sufficient tissue biopsy material for informative NGS testing due to late-stage diagnosis and difficulties associated with repeat biopsy for real-time monitoring. 

Circulating free DNA (cfDNA) has been proposed as an alternative approach for the detection of actionable mutations in NSCLC. Recent advances in next-generation sequencing of plasma allow for the rapid and affordable identification of driver mutations in NSCLC patients, which have a profound impact on clinical management. 

This online seminar will detail the clinical considerations of NGS-based plasma testing for managing NSCLC patients. 

Sponsored by
11:00 am2015
Sponsored by
Swift Biosciences

Lowering the Limits for Epigenetic Methylation Analysis


Research Associate, Salk Institute of Biological Studies 

Research Scientist, Swift Biosciences

This webinar discusses a new library preparation method that enables complete methylome characterization from only about 20 starting cells.

A key limitation to epigenetic studies has been the amount of starting material that is required to perform DNA sequencing of bisulfite-converted samples. Swift Biosciences has addressed this with a new method that dramatically reduces the amount of required starting material.

The Accel-NGS Methyl-Seq DNA Library Kit for Illumina platforms is based on Swift's Adaptase technology, a molecular biology method compatible with single-stranded DNA. Researchers can use Adaptase technology to create next-generation sequencing libraries after bisulfite treatment, thereby generating high-quality DNA sequencing data from five hundredfold less input DNA than other commercially available kits.

In this online seminar, Chongyuan Luo of Joseph Ecker’s lab at the Salk Institute details a comparison of the Swift Biosciences method with traditional methylC-seq and will also discuss several projects that have pushed the limits of the technology. He will show comparable coverage and strand evenness of a complex methylome library prepared from 1 ng of Arabidopsis DNA as compared to methylC-seq results. Additionally, the lab has successfully prepared ‘direct’ methylome libraries by fragmenting DNA solely with bisulfite conversion and thus removing the need of physical DNA fragmentation. Finally, methylome libraries were prepared from 10 mammalian neuron nuclei by combining bisulfite conversion and DNA purification into one step. This novel approach allows for efficient methylome library preparation from tissues and preserves precious DNA from minute amounts of starting cells.

Sponsored by

Chief Scientific Officer, Personalis

Bioinformatics Applications Manager, Personalis

This online seminar will outline a targeted enrichment technology to improve next-generation sequencing assays for cancer research and clinical applications.

NGS is increasingly being used to support cancer clinical trials, translational research, and immuno-oncology, but these NGS cancer solutions often suffer from a number of limitations, including sequence biases, gaps in coverage over cancer genes, narrow cancer footprint, limited validation studies, no support for paired tumor/normal analysis, and lack of RNA integration. 

Personalis addresses these issues using its Accuracy and Content Enhanced (ACE) technology to improve cancer panel, exome, and transcriptome sequencing. ACE fills in systematic NGS sequencing gaps through the company’s proprietary targeted enrichment approach, which optimizes sample prep and targeted capture in difficult-to-sequence regions such as those with high GC content.

The ACE extended cancer panel and ACE cancer exome capture more than 1,600 cancer genes and immuno-oncology genes as well as key non-coding regions. DNA data at high coverage provides sensitive detection of small variants and CNVs at low allele frequencies. RNA data from the same sample, targeted to the same gene set, is used to detect gene fusions, confirm allelic expression, and quantify gene expression.

This webinar will discuss the technical performance of these assays, as well as the company’s CLIA validation studies and tumor/normal support. Speakers will also outline the benefits of these assays for immunology studies that require broad neoantigen detection and gene expression to complement DNA variant analysis.  

Sponsored by

Director of Molecular Diagnostics, Children's National Medical Center 

Director of Clinical and Client Services, Parabase Genomics

Vice President, Products, Omicia 

This online seminar will provide examples of how commercial and hospital-affiliated clinical labs are successfully developing and deploying high-throughput next-generation sequencing-based testing services for genetic diseases. 

Our first speaker, Sean Hofherr, director of the Molecular Diagnostic Lab at Children’s National Medical Center, will discuss how his lab moved from outsourced NGS testing to an in-house offering. 

After years of sending requests for NGS testing out to independent specialty laboratories, Children’s National decided to bring genomic testing in-house. Dr. Hofherr will discuss how the lab developed a comprehensive NGS testing service with predefined panels, as well as customized patient-specific panels. He will detail how bringing NGS testing in-house enabled Children’s National to reduce lab costs in addition to providing accurate, comprehensive, and cost-effective diagnostic testing for patients. 

Our second speaker, Julie Rousseau, director of clinical and client services at independent testing lab Parabase Genomics, will detail how Parabase deploys its NewbornDx diagnostic test to sequence more than 500 genes in order to identify causative variants associated with newborn-related disorders and facilitate a turnaround time from sample collection to clinical report in 7-10 days. 

In addition, Charlene Son Rigby, Omicia’s vice president of products, will illustrate how labs can use Opal Clinical to streamline and optimize their NGS testing programs. Omicia developed Opal Clinical to meet the increasing need for intuitive tools to rapidly deploy and analyze NGS tests. The system provides labs with standardized interpretation and reporting workflows for gene panels, exomes, and whole genomes. 

Sponsored by

Center for Medical Genetics, Ghent University

Improved nucleic acid quantitation from precious samples is a key driver for the concept of liquid biopsy. By quantifying miRNA from serum/plasma samples as well as biofluids, such as cerebral spinal fluid, key biomarkers can be detected without the need for invasive tissue-based biopsy. 

In this online seminar, Jo Vandesompele of the Center for Medical Genetics at Ghent University will discuss methods for improving the analysis of microRNA expression from a range of samples. 

Dr. Vandesompele was a co-author of the microRNA quality control (miRQC) study, published in 2014. In this study, investigators analyzed the sensitivity, reproducibility and dynamic range of multiple technologies, including small RNA sequencing, reverse transcription–quantitative PCR, and microarray hybridization. The researchers determined that qPCR was the gold standard for the quantification of miRNA. 

Dr. Vandesompele's presentation will provide an overview of the use of preamplification and minimum sample inputs to maximize the dynamic range of miRNA expression studies. 

Sponsored by
11:00 pm2015
Sponsored by
Agilent Technologies

Molecular Barcoding and NGS to Detect Somatic Mosaicism in Primary Tumors


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

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
11:00 am2015
Sponsored by

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


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
10:00 am2015
Sponsored by

Genomic Analysis of CTCs and cfDNA for Dynamic Monitoring of Tumors


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
1:00 pm2015
Sponsored by

Clinical NGS Testing Strategies for Oncology and Rare Disease


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
11:00 am2015
Sponsored by

Finishing Genomes with Long Span NGS Reads


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. 

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