GenomeWebinars | GenomeWeb

GenomeWebinars

Thu
Oct
6
1:00 pm2016
Sponsored by
Agilent Technologies

Sequencing Pathogens Directly from Sputum: Promise, Progress, and Challenges

GenomeWebinar

Co-director of the Division of Infection and Immunity at University College London; Clinical Lead for Virology,
Great Ormond Street Hospital for Children

This webinar will discuss recent advances toward sequencing pathogens directly from sputum via novel enrichment methods.

Antimicrobial resistance in pathogens such as Mycobacterium tuberculosis has risen over the last decade, driving interest in methods to more rapidly and accurately detect resistance. Whole-genome sequencing of M. tuberculosis samples would allow simultaneous identification of all known resistance mutations as well as markers for monitoring transmission, but this process currently takes weeks because it requires prior bacterial enrichment by culturing.

In this webinar, Judith Breuer of University College London will discuss an effort to enable rapid whole-genome sequencing of hard-to-culture pathogens directly from sputum using a new enrichment technology. The UCL team compared direct WGS of M. tuberculosis for determining resistance with standard phenotypic culture methods well as rapid molecular tests and the recently developed mycobacterial growth indicator tube (MGIT) enriched sequencing method.

Data from the study show that, using enriched methods, the time to drug resistance profile is between 24 and 96 hours depending on the extent of sequencing and the method used. The results also indicate that direct sequencing is both sensitive and specific for M. tuberculosis first- and second-line drug resistance and that whole-genome sequencing provides sufficient genetic data to identify transmission clusters. Furthermore, direct sequencing from sputum provides more information on population diversity than sequencing of MGIT enriched cultures.

For Research Use Only. Not for use in diagnostic procedures. 

Sponsored by

Director, Partners Healthcare Laboratory for Molecular Medicine; Medical Director, Broad Institute Clinical Research Sequencing Platform; Associate Professor of Pathology at Brigham & Women's Hospital and Harvard Medical School

This webinar will provide an overview of how clinical labs can use variant interpretation software to scale their genetic testing efforts and improve reporting.

Dr. Heidi Rehm, Director of Partner’s Healthcare Laboratory for Molecular Medicine, will discuss how her lab is using the GeneInsight software solution as part of its testing workflow.

GeneInsight has been in continuous clinical use for more than eight years at the Partners Healthcare Laboratory and has been used to produce more than 50,000 clinical reports. During this webinar, Dr. Rehm will share how her team has used the software platform to scale its genetic testing program from small panels to whole-exome sequencing, as well as how GeneInsight facilitates variant data sharing and variant management.

Sponsored by
Thu
Oct
13
1:00 pm2016
Sponsored by
Personal Genome Diagnostics

NGS Plasma Sample Collection Best Practices and Demonstrated Utility of ctDNA

GenomeWebinar

Director, Meningioma Center; Associate Professor of Neurosurgery, John Hopkins Medicine 

Technical Lead, Product Development, Personal Genome Diagnostics

This online seminar will discuss sample collection challenges associated with tumor sequencing, with a particular focus on somatic variant testing in plasma. The session will also feature recent evidence demonstrating that circulating tumor DNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.

Liquid biopsies are emerging as a non-invasive alternative to tumor tissue testing and are likely to be rapidly incorporated into clinical care. Applying next-generation sequencing to liquid biopsies allows the detection of multiple gene mutations in ctDNA extracted from plasma without prior knowledge of the mutation(s) that may be present. NGS analysis of ctDNA in plasma holds much promise for improving cancer diagnosis and monitoring.

In this webinar, Chetan Bettegowda of Johns Hopkins University School of Medicine will discuss a study that evaluated the ability of ctDNA to detect tumors in 640 patients with various cancer types. Dr. Bettegowda will detail the findings of the study, which found that ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities.

This webinar will also discuss the sample requirements for somatic variant testing in plasma and metrics for measuring sample quality in plasma. This is of central importance when attempting to detect minute fractions of tumor-derived DNA.

Sponsored by
Thu
Oct
27
1:00 pm2016
Sponsored by
Agilent Technologies

Lowering the Stakes to Raise the Bar: Building an NGS Panel to Meet the Needs of Clinicians

GenomeWebinar

Clinical Director, Center for Personalized Diagnostics, University of Pennsylvania Perelman School of Medicine

Genomics Technologist, Center for Personalized Diagnostics, University of Pennsylvania Health System

In this online seminar, speakers from the Center for Personalized Diagnostics at Penn Medicine will discuss the design and technical validation of a custom next-generation sequencing panel to detect mutations in a wide array of tumor types.

Next-generation sequencing of tumor-derived DNA has revolutionized clinical cancer genomic diagnostics by directing molecularly targeted therapies. The accurate detection of mutations at low allele frequencies is essential to wider adoption of this approach due to high levels of stroma and tumor-infiltrating lymphocytes diluting the detectable alterations.

Dr. Jennifer Morrissette's lab at the Center for Personalized Diagnostics began clinical NGS of solid tumors in 2013 utilizing a 47-gene NGS panel covering clinically relevant genes and hotspots. This was an early success with over 3,500 solid tumors sequenced in the laboratory over three and a half years.

However, the clinical demand to increase gene content and to detect mutations in a wider array of tumor types led the team to explore molecular barcoding to decrease duplicate reads and detect lower variant allele frequencies. Dr. Morrissette and her colleague Karthik Ganapathy will share details of this work as well as key considerations for the design, technical validation, and data analysis of a custom 154 gene Agilent HaloPlex NGS panel.

Sponsored by

Director, Transgenic Core Facility, University of Nebraska Medical Center 

Director, Gene Editing Institute, Christiana Care Health System’s Helen F. Graham Cancer Institute & Research Center 

This webinar will outline new strategies for genome editing in mammalian cells using CRISPR/Cas9, with talks focused on point mutation repair in human cell lines and the design of knock-in animal models.

During this webcast,Dr. Eric Kmiec will discuss a new approach to the correction of point mutations using single-stranded oligonucleotides and a partially synthetic form of CRISPR/ Cas9, a ribonucleotideprotein (RNP) complex. The experimental design, including the process of RNP assembly and the workflow, will be presented.

Dr. Kmiec will share details of a case study in which a point mutation in an integrated copy of the mutated eGFP gene in a human cell line is corrected using this approach, and a reaction pathway that is likely distinct from that of homology-directed repair. The use of short single-stranded oligonucleotides may be a strategy of choice when the desired endpoint is correction of point mutations in chromosomal genes.

Our second speaker, Dr. CB Gurumurthy,will discuss the latest trends and CRISPR tools available for animal genome editing, with a particular emphasis on strategies for increasing the homology-directed repair mechanism to enable insertion of longer sequences at the Cas9 cut sites. A few examples of designing knock-in animal models and the workflow of generating the models will be presented. 

This webinar is the second on gene editing under the GenomeWeb/ABRF 2016 Webinar Series. The first webinar on gene editing is available on demand here

Sponsored by
Thu
Nov
3
1:00 pm2016
Sponsored by
BioFire Diagnostics

Molecular Syndromic Testing in the ER: Assessing the Impact on Pediatric Care

GenomeWebinar

Director, Clinical Microbiology Laboratory, Children’s Hospital Los Angeles,
Assistant Professor, Clinical Pathology, Keck School of Medicine, University of Southern California

The FilmArray Gastrointestinal Panel tests for identification of 22 different pathogens, including bacteria, parasites, and viruses from stool specimens in Cary Blair transport media. In this webinar, Jennifer Dien Bard from Children’s Hospital Los Angeles will discuss how the FilmArray GI Panel affects patient outcomes for children with gastroenteritis presenting to emergency departments.

BioFire’s FilmArray® System uses syndromic testing to identify infectious diseases and is used in combination with assay-specific reagent panels. The system combines a broad grouping of probable pathogenic causes into a single, rapid test. This allows physicians to easily choose the right test, the first time. Requiring only two minutes of hands-on time, the FilmArray has a turnaround time of about an hour.

Dr. Dien Bard will discuss ongoing work to assess whether this rapid turnaround time allows clinicians to more rapidly diagnose GI illness and recommend the appropriate therapy. 

Sponsored by
Recent GenomeWebinars

Chief Operating Officer, Molecular Pathology Center, Jewish General Hospital

Senior Scientist II and Group Leader, Asuragen, Inc.

This webinar described the design, development, and evaluation of a new gene panel for targeted RNA sequencing of formalin-fixed, paraffin-embedded lung cancer samples.

Dr. Richard Blidner, Senior Scientist II and Group Leader at Asuragen, first provided an overview of Asuragen's QuantideX NGS RNA Lung Cancer Kit. This product integrates reagents, controls, and bioinformatics software for sensitive, targeted NGS of RNA or total nucleic acid from challenging tumor biopsies.

Dr. Blidner briefly presented the kit design, workflow, and sample input requirements, and compared and contrasted the approach with other NGS methods. He also discussed supporting data and implications for low-copy number analytical sensitivity that can be achieved with the technology. Finally, he described the features and benefits of the companion QuantideX NGS Reporter software for fast and simple bioinformatic analysis that can be deployed on a conventional desktop computer.

Our second speaker, Dr. Léon van Kempen, Scientific Director of the Dubrovsky Molecular Pathology Center at the Jewish General Hospital, shared how his lab evaluated the QuantideX NGS RNA Lung Cancer Kit in a lung cancer study.

Dr. van Kempen and colleagues used the kit to analyze a cohort of 30 total nucleic acid isolates derived from FFPE residual tumor biopsies and cancer cell lines. Sequencing was performed on Illumina's MiSeq platform and data was analyzed using the QuantideX NGS Reporter software suite.

Dr. van Kempen discussed the results of the evaluation, which yielded 100% agreement for fusion and splice variant calling across 11 ALK fusions, 1 ROS1 fusion, 1 FGFR3 fusion, 1 MET exon 14 skipping and 16 negative samples.

The detection of 3’/5’ ALK expression imbalances in known fusion-positive samples indicated potential utility for the detection of fusions not explicitly targeted by the panel.

Sponsored by
Thu
Sep
22
1:00 pm2016
Sponsored by
PerkinElmer

New Technologies for Finding the 'Hidden Gems' in Genomic Research

GenomeWebinar

Team Leader, Platforms and Pipelines Team, Earlham Institute

Staff Scientist, 10x Genomics

This webinar discussed new technologies that are enabling researchers to uncover previously hidden aspects of the genome, including a novel approach to expand the analysis capabilities of next-generation sequencing data and a method for the quantitation of minute sample volumes using microfluidic analysis.

The first technology presentation, from Adrian Fehr of 10x Genomics, addressed a major obstacle of current short-read sequencing technologies, which often miss critical information such as phasing, structural variants, and the ability to map highly repetitive regions. Without this information, only a partial structure of the genome is realized and many mutations and variants are not identified. The 10x Genomics Chromium platform addresses this challenge by preserving relevant information over distances greater than 150 kilobases by linking the short reads to a larger DNA fragment by use of a barcode. The generated libraries are currently compatible with all short-read sequencers, enabling this hidden information to be accessed without the need to invest in a new sequencing infrastructure.

Additional technological advances have propelled a shift in the input concentration requirements for current next-generation sequencing technologies. The trend towards lower input sample concentrations necessitates initial accurate concentration values. In our second presentation, Leah Clissold from the Earlham Institute (formerly the Genomic Analysis Centre) shared results of a new assay for DNA analysis, which enabled accurate sizing/concentration assessment of difficult, precious sample types. The Earlham Institute is focused on the application of state of the art genomics and bioinformatics to advance plant, animal and microbial research to promote a sustainable bioeconomy. 

Sponsored by
Thu
Sep
15
1:00 pm2016
Sponsored by
Agilent Technologies

Custom Targeted RNA Sequencing of FFPE Biopsy Specimens

GenomeWebinar

Associate Professor of Pathology & Laboratory Medicine and Biomedical Informatics, Emory University

This webinar discussed a customized protocol for RNA sequencing that was developed enable focused RNAseq analysis of formalin-fixed paraffin-embedded biopsies for biomarker discovery in prostate cancer.

Our speaker, Carlos Moreno, Associate Professor of Pathology & Laboratory Medicine and Biomedical Informatics at Emory University, provided an overview of a custom RNA-seq panel his team developed using the Agilent SureSelect capture system.

In previous work, Dr. Moreno and colleagues used FFPE-derived radical prostatectomy RNA samples to identify a set of 24 mRNAs that could be used to discriminate between prostate cancer with and without biochemical recurrence (BCR) using whole transcriptome RNA-seq analysis. However, a more relevant point to assay for biomarkers is at the point of positive biopsy to ascertain whether active surveillance is needed.

To enable focused RNA-seq analysis of FFPE biopsies, Dr. Moreno and his team developed a customized protocol using the Agilent SureSelect capture system. So far, they have successfully sequenced a panel of 295 genes using FFPE RNA from 102 biopsies and 24 matching prostatectomies. Analysis of biopsy and prostatectomy-derived RNAseq data indicates that the data from both sources are strongly correlated. Analysis of multiple biopsies from the same source was able to detect a change in RNA signal due to tumor heterogeneity. The 256 gene panel also detected differences between African-American and Caucasian prostate cancer samples.

Dr. Moreno outlined the details of this work, which indicated that targeted RNA-seq of FFPE biopsies is feasible, increasing the available tissue resources for biomarker discovery.

Sponsored by
Tue
Sep
13
1:00 pm2016
Sponsored by
New England BioLabs

GenomeWeb/ABRF Webinar Series: Advancing Clinical Metagenomics via CLIA/CAP Accreditation

GenomeWebinar

Assistant Professor, Baylor College of Medicine,
Sequencing Director, Alkek Center for Metagenomics & Microbiome Research

Assistant Professor,Alkek Center for Metagenomics & Microbiome Research 

Clinical metagenomics is still in its infancy, and maturation of the field requires an appropriate accreditation program to ensure quality testing and patient safety. This webinar provided an overview of how one metagenomics lab — the Alkek Center for Metagenomics & Microbiome Research (CMMR) at Baylor College of Medicine — is pursuing CLIA/CAP accreditation.

An integral component of the accreditation process is proficiency testing (PT), which utilizes pre-established criteria, or measurement standards, for inter-laboratory comparisons. To date, commercially available metagenomic PT offerings are not available, which puts the burden on individual laboratories to develop an alternative assessment. In order to address the need for PT in metagenomics, the CMMR utilized a combination of previously sequenced samples (e.g. “blinded generous donor samples”), synthetic DNA standards, and mock communities to evaluate microbial DNA extraction, library preparation, and sequencing.

In addition to developing PT specific to metagenomic analyses, the CMMR developed a quality system with standard operation procedures (SOPs), competency testing, a laboratory information management system (LIMS), and asset management software in compliance with CLIA/CAP standards.

The complexity of metagenomic analyses are compounded by a limited understanding of the sources of variance and their impact on downstream analyses. Therefore, it is critical that the community adopt a universal set of standards for PT. Common sets of standards will enable identification of variation introduced by lab processes, thus allowing for the safe adaptation to clinical use.

This webinar is the second on metagenomics under the GenomeWeb/ABRF 2016 Webinar Series. The first webinar in the series is available on demand here.

Sponsored by
Tue
Aug
9
1:00 pm2016
Sponsored by
Sapio Sciences

Deploying an NGS LIMS for Complex Research and Clinical Environments

GenomeWebinar

Project Manager, Sample Receiving and LIMS Development, Memorial Sloan Kettering Cancer Center, Center for Molecular Oncology & Integrated Genomics Operation

This webinar highlights how next-generation sequencing labs can deploy laboratory information management systems to meet the challenges of complex workflows and sample tracking in both research and clinical environments.

Our speaker, Katelynd Vanness, LIMS manager for Memorial Sloan Kettering's Integrated Genomics Operation, discusses why LIMS configurability and adaptability is critical to a successful LIMS project and how Exemplar LIMS from Sapio Sciences aligned with their goals.

The MSKCC team was seeking the ability to retain a large degree of flexibility in its LIMS along with the need to create complex workflows on the fly as research needs change. Katelynd Vanness will discuss the complex challenges that this posed to the rollout of a LIMS within the core laboratory, as well as example pipelines implemented in Exemplar LIMS that addressed these requirements.

The talk also briefly covers how the MSKCC Integrated Genomics Operation maintains two separate instances of the LIMS, one of which is CLIA (HIPAA) certified, and how both Exemplar systems interface with many other systems within MSKCC.

Sponsored by
Thu
Aug
4
11:00 am2016
Sponsored by
New England BioLabs

GenomeWeb/ABRF 2016 Webinar Series: A Hypothesis-Driven Lean Management Tool for Core Labs

GenomeWebinar

Chief Information Officer, University of Virginia Medicine & Physicians Group

Professor of Medicine, Immunology & Cancer Biology, University of Virginia School of Medicine

This online seminar provided an overview of A3 problem solving, a lean management tool that can be used to improve efficiencies in life science core labs.

Developing a culture of continuous improvement in the core lab involves winning the hearts and minds of researchers and administrators and aligning their efforts around delivering value to the customer as quickly, cost-effectively, and flawlessly as possible. Along the way, performance gaps present themselves. The A3 lean approach — so-called because it limits all documentation to a single piece of 11 x 17 inch, or A3, paper — offers a consistent and effective means by which to address these gaps.

Using a hypothesis-driven approach, the A3 tool guides inquiry into the root cause of performance gaps, and the identification of proposed countermeasures and targets to improve. It also serves as a means by which to monitor progress toward goals and share results with others so that all may benefit from what has been learned.

Panelists in this webinar described how the A3 tool works, and how your organization can benefit from its adoption and use.

This webinar is the second on lean management for the core lab under the GenomeWeb/ABRF 2016 Webinar Series. The first webinar in the series is available on demand here.

Sponsored by

Head of the Molecular Diagnostic Department
Firalis and TcLand Expression

This webinar outlined an ongoing project to develop personalized treatment strategies for rheumatoid arthritis patients using miRNA profiling.

Millions of patients with rheumatoid arthritis are treated with TNF-α inhibiting agents, but the response rate to these therapies is low (30 percent to 40 percent) and no tool exists to predict treatment response.

During the study being discussed, Dr. Eric Schordan, Head of the Molecular Diagnostic Department at Firalis and TcLand Expression, led a project that aimed to address this via miRNA profiling in RA patients.

Using the HTG EdgeSeq platform, Dr. Schordan and colleagues first identified sets of miRNAs that discriminate responders from non-responders to anti TNF-α therapy and then developed a panel called RABIOPRED that includes more than 2,100 mRNAs identified as predictors of anti TNF-α therapy.

In a study that enrolled 67 RA patients, Dr. Schordan and his team determined that miRNA profiling using the HTG EdgeSeq platform served as a useful tool for biomarker discovery and enabled them to build predictive models for response to anti-TNF-α drugs.

During the webinar, Dr. Schordan discussed the details of that study, as well as his team's plans to validate the panel in a multicentric prospective clinical study of 600 patients.

Sponsored by

Professor and Chair Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic

Global Product Manager, NGS Solutions, Qiagen

This online seminar focused on the design of a large cohort study for assessing breast cancer risk and how using an innovative digital sequencing approach is able to solve the previously unmet challenges of this type of NGS study design.

Our speaker, Dr. Fergus J. Couch of the Mayo Clinic, presented on the design of this NCI-funded project, which comprises the sequencing of 60,000 samples to assess the risk of breast cancer through association with targeted genes.

The design and size of the study requires an accurate, robust, and high-throughput sequencing method. The investigators are using a digital DNA sequencing approach from Qiagen that incorporates molecular barcodes to tag and remove PCR duplicates and increase NGS assay sensitivity. The approach also uses proprietary chemistry that enables uniform sequencing to efficiently utilize sequencing power and deliver optimized results.

Viewers of this webinar will be able to ask Dr. Couch questions about the study design and methodology during a live Q&A session.

Information on Qiagen's universal NGS solutions is available here and Qiagen's GeneReader NGS system is available here

Sponsored by
Tue
Jul
19
1:00 pm2016
Sponsored by
New England BioLabs

GenomeWeb/ABRF 2016 Webinar Series: The Emergence of Gene Editing as a Standard Lab Tool

GenomeWebinar

Director, Gene Editing Institute, Christiana Care Health System's Helen F. Graham Cancer Center Research Institute

Director, Transgenic Core Facility, University of Nebraska Medical Center

This online seminar, part of the GenomeWeb/ABRF 2016 Webinar Series, covered the history of gene editing methods like TALENs and CRISPR/Cas and provided an overview of various gene editing technologies.

The emergence of these new technologies in the last decade "has triggered a veritable revolution as laboratories worldwide have begun to introduce or correct mutations in cells and organisms with the level of ease and efficiency not previously possible,” the Journal of the American Medical Association noted in 2015.

During the webinar, Eric Kmiec, Ph.D., of Christiana Care Health System’s Helen F. Graham Cancer Center & Research Institute and Channabasavaiah Gurumurthy of the University of Nebraska Medical Center, discussed some of the origins of gene editing and how the field emerged from a series of basic science observations to the dynamic fast-paced field dominating research journals today.

Kmiec and Gurumurthy also discussed some of the factors that can influence the frequency and efficacy with which gene editing takes place, including cell cycle progression, and the introduction of specific double-strand breaks at specified sites relative to the target.

The second part of the webinar focused on the latest developments in genome editing technologies: specifically, different genome editing technologies will be compared with a special emphasis on the CRISPR/Cas system.  

Sponsored by
Tue
Jun
21
1:00 pm2016
Sponsored by
The Jackson Lab

CRISPR/Cas9 Strategies for Disease Modeling and Drug Discovery

GenomeWebinar

Research Fellow, UCSF Fellows Program, Clinical Fellow, Division of Infectious Diseases, UCSF Medical Practice 

Associate Director, Genetic Engineering Technologies, The Jackson Laboratory 

This online seminar outlined emerging applications for the CRISPR/Cas9 system in disease modeling and therapeutic discovery.

CRISPR/Cas9 is a revolutionary approach that enables rapid, economical model generation through precise genome editing. Every day, new studies continue to leverage the potential of CRISPR to generate novel strategies for modeling diseases and assessing therapeutic intervention.

During this webinar, our panelists discussed

  • Strategies for high-throughput generation of mouse models (KO/KI) using CRISPR/Cas9 
  • Special considerations for the use of the CRISPR/Cas9 system 
  • Genetic manipulation of primary human T cells using CRISPR/Cas9
Sponsored by

Associate Professor, Weill Cornell Medical

Chair ABRF Metagenomics Research Group and Extreme Microbiome Project, Manager Massively Parallel Sequencing Facility, University of Vermont Cancer Center

This online seminar, part of the GenomeWeb/ABRF 2016 Webinar Series, provided an overview of experimental and computational standards for metagenomics that have been developed as part of the Genomes in a Bottle standards consortium.

Over the last decade, major advances in sequencing technology have led to a surge in large-scale metagenomics and microbiome studies. As these studies continue to grow both in number and in scope, researchers face methodological and computational challenges for experimental design and interpretation. Recently, several groups have come together to address these challenges and develop standardized samples and methods for DNA sequencing, including the Association of Biomolecular Resource Facilities Research Groups on next-generation sequencing and metagenomics, the Food and Drug Administration, and the National Institute of Standards and Technology, all of whom work together in the Genome in a Bottle standards consortium. These efforts encompass multiple stages of genomics and metagenomics work including study design, sample collection, DNA extraction, library preparation, sequencing, and computational analysis.

During this webinar, Christopher Mason of Weill Cornell Medical College and Scott Tighe of the University of Vermont provided an overview of metagenomics standards that leverage a titrated mixture of known bacteria and eukaryotes. These have been sequenced across multiple next-generation sequencing platforms and characterized with ten different algorithms for taxonomic classification. The consortium members have also aggregated a set of 30 control samples for additional classification.

Dr. Mason and Dr. Tighe reported on a number of findings from the project, including the fact that sites of cross-algorithm agreement can lead to the most accurate estimate of the number of species from a new sample. They also presented an online resource for these tools, methods, and data sets; all of which are freely available. These methods and standards can help the many large-scale metagenomics projects around the world (and even some in space).

About the GenomeWeb/ABRF 2016 Webinar Series: GenomeWeb has partnered with the Association of Biomolecular Resource Facilities to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. More information about ABRF and its activities is available here. Please check GenomeWeb's webinar schedule for future webinars in this series. The series is sponsored by New England BioLabs.

Sponsored by
Thu
Jun
2
11:00 am2016
Sponsored by
Agilent Technologies

Methyl-Seq Studies in Rodents and Humans Identify Stress-Related Epigenomic Changes

GenomeWebinar

Assistant Professor, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University

This webinar discussed the use of the Methyl-Seq platform in mouse, rat, and human studies to demonstrate how chronic exposure to stress and glucocorticoids can modify the epigenome in ways that may be relevant to disease.

During this webinar, Dr. Richard Lee, assistant professor in the Department of Psychiatry and Behavioral Sciences at Johns Hopkins University, discussed a series of studies in rodents and humans intended to elucidate the epigenomic changes linked to stress.

Dr. Lee and colleagues first sought to identify epigenomic targets of blood and brain in mice treated with glucocorticoids using the mouse SureSelect Methyl-Seq Target Enrichment platform and bisulfite pyrosequencing. They then designed and implemented a rat version of the Methyl-Seq to identify DNA methylation changes associated with stress in adolescent rats exposed to chronic variable stress for three weeks.

Dr. Lee outlined the details of these studies and their findings, which indicate that both glucocorticoids and stress can modify the epigenome.


For Research Use Only. Not for Use in Diagnostic Procedures.

Sponsored by
Tue
May
24
1:00 pm2016
Sponsored by
Abbott Informatics

Translating 'Big Data' into Therapies, Diagnostics, and New Insights into Disease

GenomeWebinar

Director, Institute for Computational Health Sciences and Professor of Pediatrics, University of California, San Francisco & Executive Director for Clinical Informatics, University of California Health Sciences and Services

Manager, Global Strategy, Abbott Informatics

This webinar discussed how laboratory information management systems can help analyze big data in biomedicine in order to advance precision medicine.

There is an urgent need to take what we have learned in the “genome era” and use it to create a new system of precision medicine, delivering the best preventative or therapeutic intervention at the right time, for the right patients. Dr. Butte's lab at the University of California, San Francisco, builds and applies tools that convert trillions of points of molecular, clinical, and epidemiological data -- measured by researchers and clinicians over the past decade and now commonly termed “big data” -- into diagnostics, therapeutics, and new insights into disease.  Several of these methods or findings have been spun out into new biotechnology companies.  

Dr. Butte, a computer scientist and pediatrician, highlighted his lab’s recent work, including the use of publicly-available molecular measurements coupled with samples in public and private biorepositories and discovering new diagnostics including blood tests for complications during pregnancy. 

Learning Objectives

  • What is the nature of public molecular data?
  • How can publicly available molecular measurements be used to find new uses for drugs, or new diagnostics for diseases?
  • What is big data in biomedicine and how can we utilize a LIMS to analyze this data and help with diagnostics, prognostics and precision medicine?
  • How can we use samples in biorepositories to validate data-driven predictions and launch discoveries in novel diagnostics?

By registering for this webinar, you agree that the sponsor may contact you.

Sponsored by
Thu
May
19
11:00 am2016
Sponsored by
HTG Molecular

Expression-based Profiling of Challenging FFPE Tumor Samples

GenomeWebinar

Professor of Pathology & Deputy Director, Hamon Center for Therapeutic Oncology, UT Southwestern Medical Center 

Assistant Professor, Hamon Center for Therapeutic Oncology, UT Southwestern Medical Center 

Medical Director, Molecular Oncology Diagnostics Lab, Hamon Center for Therapeutic Oncology, Ottawa Hospital 

This online seminar focused on recent advances in gene expression profiling of challenging formalin-fixed, paraffin-embedded tissue samples for cancer research and clinical practice. Presentations covered studies in non-small cell lung cancer and pancreatic cancer. 

Our first speakers, Adi Gazdar and Luc Girard from UT Southwestern Medical Center, discussed an expression-based assay for the pathological classification of non-small cell lung cancer. 

Most NSCLCs are diagnosed from small specimens, and classification using standard pathology methods can be difficult. This is of clinical relevance as many therapy regimens and clinical trials are histology-dependent. Dr. Gazdar and Dr. Girard developed a 62-gene mRNA expression signature as an adjunct test for routine histopathological classification of NSCLCs, which includes many genes used in immunostains for NSCLC typing. 

In order to demonstrate the clinical practicality and cost-effectiveness of the classifier, they developed a research-use, custom assay based on the HTG EdgeSeq technology. The classifier can be applied to small FFPE samples and core-needle biopsies, demonstrating the potential for deployment of routine RNA testing in standard clinical practice. 

Next, Bryan Lo of the Ottawa Hospital discussed a method for gene expression profiling of pancreatic cancer precursors directly from FFPE tissues without nucleic acid extraction. 

Gene expression analysis of pancreatic intraepithelial neoplasia’s (PanINs), the classical pancreatic cancer precursor, has been challenging because extracting and purifying RNA from pancreatic tissue is difficult. Since the pancreas is rich in ribonucleases and PanINs are typically very small lesions, attempts to purify RNA of sufficient quality and quantity for microarray or RNAseq are usually unsuccessful. This is especially true if the starting material is FFPE tissue, where the fixation process introduces further degradation of the RNA. 

Dr. Lo and colleagues have shown in a pilot study that they can use the HTG EdgeSeq Oncology Biomarker Panel to profile approximately 2,500 genes from a cohort of microdissected low- and high-grade PanIN lesions from human pancreatic cancer resections that have been archived as FFPE tissue blocks. 

Dr. Lo and colleagues believe that most of these PanIN lesions would not have been amenable to other gene expression methodologies and that the PanIN data collected using the HTG EdgeSeq technology will contribute to a better understanding of the molecular pathways that underlie pancreatic cancer. 

Sponsored by
Tue
May
17
1:00 pm2016
Sponsored by
New England BioLabs

GenomeWeb/ABRF 2016 Webinar Series: Three Lean Management Tools for the Life Science Lab

GenomeWebinar

Director, Antibody & Protein Resource, Vanderbilt University Medical Center

This online seminar provided a practical approach to implementing lean management tools in the life science laboratory. 

Unlike some management trends and tools, the scientific method is deeply engrained in lean management, making it an effective strategy for lab workflows. 

During this webinar, Robert Carnahan, associate professor of cancer biology at the Vanderbilt University School of Medicine, outlined three simple lean techniques that his team has implemented for project management, inventory and ordering, and equipment maintenance. 

Viewers of this webinar will learn about specific tools to begin implementation in their own working environment. 

About the GenomeWeb/ABRF 2016 Webinar Series: GenomeWeb has partnered with the Association of Biomolecular Resource Facilities to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. More information about ABRF and its activities is available here. Please check GenomeWeb's webinar schedule for future webinars in this series. The series is sponsored by New England BioLabs.

Sponsored by
Thu
May
5
11:00 am2016
Sponsored by
Personal Genome Diagnostics

Liquid Biopsy Approaches in Drug Development: A Case Study

GenomeWebinar

Director Biomarker Strategy, Bayer Healthcare 

Manager, Research Services, Personal Genome Diagnostics 

This online seminar provided insight into the use of liquid biopsy approaches to monitor drug response and resistance. 

Tumor heterogeneity and the molecular evolution of resistance are tightly linked concepts that are important factors for understanding how and why cancer patients respond to anti-cancer therapies. Circulating tumor DNA (ctDNA) and non-invasive serial liquid biopsies are tools that allow for a temporal molecular understanding of therapeutic response and resistance. Liquid biopsy approaches offer a considerable advantage for analyses of cancer patients as they allow for the non-invasive detection of somatic genetic alterations in multiple metastatic lesions throughout the course of therapy. 

During this webinar, Michael Teufel, director of biomarker strategy at Bayer HealthCare, shared lessons learned from digital PCR and next-generation sequencing analysis of ctDNA. Michael’s talk detailed how liquid biopsy-based approaches address the limitations of tissue-based testing. He also discussed the head-to-head comparison results of NGS and digital PCR approaches on samples from two clinical trials. 

Sponsored by
Thu
Apr
21
11:30 am2016
Sponsored by
Core Informatics

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

GenomeWebinar

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 discussed 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, shared 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. 

During the presentation, Dr. Arnold described 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

Senior Scientist, Product Development, Qiagen

Associate Professor, Tisch Cancer Institute, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

This webinar discussed the relationship between microRNA concentration and target regulation, as well as the biological implications of this association.

MicroRNAs are important regulators of gene expression. More than 800 different microRNAs are encoded in the human genome, and each cell type and even cell state appears to express a unique battery of microRNAs, which are estimated to control over half of the cell’s coding transcriptome.

MicroRNA profiling is now widely used to identify the microRNA complement of a cell, but it is not clear how to interpret microRNA expression as it relates to biology and function. An open question is how microRNA concentration influences target regulation.

In this webinar, Dr. Brian Brown, Associate Professor In the Department of Genomic Sciences at the Icahn School of Medicine at Mount Sinai, discussed emerging data that suggests that only abundantly expressed microRNAs have significant biological activity within a cell, and that even highly expressed microRNAs are subject to post-transcriptional control mechanisms that regulate the activity of the microRNA.

Dr. Brown discussed the implications of this understanding for identifying functionally relevant microRNAs, and for understanding how microRNAs function.

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 discussed 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, shared her experience of NGS panel-based testing, and some of the challenges. She also spoke 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, Product Director, NGS, Qiagen, shared 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
Thu
Mar
3
11:00 am2016
Sponsored by
Agilent Technologies

Defining Minimal Genomics Content for All Tumor Types

GenomeWebinar

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

This webinar discusses 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 focuses 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 are described. 

Sponsored by