GenomeWebinars | GenomeWeb

GenomeWebinars

Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology

Director, Technical Support,
NuGEN

This webinar will discuss a project that sought to understand the parent-of-origin epigenetic mechanisms that regulate seed development in plants, with a particular emphasis on differentiating the maternal or paternal origin of epigenetics marks. Parental-specific epigenetic marks are established in the gametes and maintained after fertilization, resulting in parental epigenetic asymmetry. Epigenetic asymmetry causes parent-of-origin-specific gene expression, a phenomenon termed genomic imprinting. Imprinted genes play an important role in animal and plant development. In plants, genomic imprinting occurs in the seed, particularly in the endosperm, an ephemeral tissue that supports embryo growth similarly to the nourishing role of the mammalian placenta.

To study the mechanisms that maintain epigenetic asymmetry, Jordi Moreno-Romero and his colleagues at the Department of Plant Biology at the Uppsala BioCenter generated endosperm-specific genome-wide profiles of histone modifications (using chromatin immunoprecipitation followed by high throughput sequencing, ChIP-seq) and DNA methylation (using bisulfite-seq) at an early stage of seed development. By crossing two Arabidopsis accessions that differ in large numbers of sequence polymorphisms the researchers were able to differentiate the maternal or paternal origin of epigenetics marks.

In this webinar, Dr. Moreno-Romero will discuss the findings of the study, which found that Polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is localized to DNA hypomethylated regions, linking DNA demethylation and H3K27me3 to imprinted gene expression.

Sponsored by
Thu
Mar
2
1:00 pm2017
Sponsored by
VelaDx

An NGS Workflow for HCV and HIV Resistance Testing

GenomeWebinar

Assistant Professor, Virology  University of Paris-Est-Creteil 

Chief Scientific Officer, VelaDx

This online seminar will highlight recent advances in the use of next-generation sequencing to detect drug-resistant mutations in patients with HIV or HCV.

Sanger sequencing and PCR have been the standard molecular methods in clinical diagnostics for decades, but NGS is now swiftly becoming a routine method in different areas of clinical diagnostics, including treatment management for viral diseases.

Vela Diagnostics has developed an automated qPCR and NGS workflow called Sentosa for targeted sequencing of human and viral DNA. Our speakers will discuss practical examples of the use of this workflow to aid clinical decision-making and patient management.

Gerd Michel, Chief Scientific Officer of VelaDx will discuss examples of how the Sentosa workflow may be applied to HIV and HCV, delivering accurate genotyping information and in the detection of drug-resistant mutations.

Christophe Rodriguez of the University of Paris-Est-Creteil, will discuss how his team used this automated workflow for HCV resistance testing. His presentation will outline how deep sequencing technology shows better performance than population sequencing in direct-acting antiviral-experienced patients awaiting retreatment.

Sponsored by
Recent GenomeWebinars
Thu
Dec
15
1:00 pm2016
Sponsored by
PierianDx

NGS Roundtable: Ask the Experts about the Future of Clinical NGS Testing

GenomeWebinar

Professor of Pathology, University of Utah; Medical Director, Genomics and Bioinformatics, ARUP Laboratories;
Chair, CAP Next Generation Sequencing Project Team

Assistant Professor of Pathology, University of Utah; Medical Director, Surgical Pathology and Molecular Oncology, ARUP Laboratories

Chief Biomedical Informatics Officer, PierianDx

This interactive roundtable discusses established and emerging regulatory, scientific, and medical topics related to next-generation sequencing in the clinical setting. An expert panel of leading pathologists, medical geneticists, and researchers will address genomic testing advances in two thematic areas: 1) scientific and clinical trends in reporting, and 2) clinical lab operations and quality management.

Topics covered by the expert panel include the importance of proficiency testing, both from the regulatory and quality perspective, and technical and clinical advances in using NGS to predict effective immunotherapy and determine tumor mutation load. 

Sponsored by
Tue
Dec
13
1:00 pm2016
Sponsored by
Agilent Technologies

Combining CNV and SNV Detection in a Single Test: An Alternative to Whole-Genome Sequencing

GenomeWebinar

Lyon University Hospital 

This webinar discusses a genomic strategy that detects single nucleotide variants and copy number variants in a single assay. This approach serves as a cost-effective alternative to whole-genome sequencing and shows promise for the field of cytogenetics.

Our speaker, Nicolas Chatron of Lyon University Hospital, shares the results of a study using Agilent Technologies’ OneSeq target enrichment panel, which includes a chromosomal backbone of probes mimicking the design of microarray-based comparative genomic hybridization with a theoretical 300kb resolution.

In the study, Dr. Chatron and colleagues first tested 29 control samples using OneSeq followed by next generation sequencing. All CNVs larger than 300kb were detected and only two out of seven CNVs below 300 kb were missed. The investigators next performed a blinded analysis of 32 samples comparing OneSeq data with chromosomal microarray data. Dr. Chatron discusses the results of the blinded study during his presentation.

Sponsored by

Director, Molecular Genetics Laboratory, Lifelabs 

This webinar discusses a partnership model for noninvasive prenatal testing that enabled LifeLabs Genetics, a genetic testing lab based in Toronto, Ontario, to implement NIPT in house.

LifeLabs implemented on-site testing of the Natera Panorama test service in October 2015 in Toronto, where funding is provided for chromosome aneuploidy testing under selected high-risk criteria set out by the Ontario Ministry for Health and Long-Term Care. Patients have the option of self-pay if they do not meet risk criteria. On-site testing capacity includes microdeletions as of July 2016.

In this webinar, Ronald Carter, Director of the Molecular Genetics Laboratory at LifeLabs, shares how licensing Natera’s technology permitted a rapid and seamless transition to in-house testing and enhanced the implementation of indigenous NIPT test capacity. Dr. Carter outlines a detailed analyses of laboratory test results showing that the performance of the LifeLabs partner laboratory is equivalent to the reference testing provided by Natera in California.

Dr. Carter also outlines the sequence of transfer of test capacity, describes the operational requirements for partnering, and reviews the impact of NIPT funded services on the provision of prenatal care services in Ontario. Analysis of all clinical outcomes from NIPT services provided in Ontario will be used to guide future development of guidelines for care.

Sponsored by

Executive Director, Clinical Genomics, Genoptix

Field Application Scientist, Clinical Applications Division, Agilent Technologies

This webinar provides specific use cases from a molecular pathology lab demonstrating how an automated bioinformatics pipeline can improve somatic variant assessment and reporting.

Next-generation sequencing of tumor samples is becoming increasingly common in the molecular pathology setting, but the adoption of this technology brings challenges in data management and clinical interpretation, and requires bioinformatics tools to analyze, interpret, and database the large number of variants originating from NGS assays. In a high-throughput context, the delivery of actionable results from NGS data needs to be clinically robust (informed, traceable and reproducible). Moreover, in a cancer diagnostics setting, fast turnaround times are essential for patient care.

In this online seminar, Matthew J. McGinniss, Executive Director of Clinical Genomics at cancer diagnostics firm Genoptix, shares how his team validated an automated pipeline for somatic variant assessment and reporting in a high-throughput diagnostic setting. This pipeline supports the interpretation of genomic alterations including copy number variants and translocations and allows clinical molecular geneticists and molecular pathologists to provide quality clinical laboratory services to oncologists, pathologists, and clinicians. To conclude, Dr. McGinniss shares some clinical use cases demonstrating the variant assessment pipeline.

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

This webinar covers an ongoing study to assess whether a rapid PCR-based gastrointestinal panel can improve health outcomes in the emergency room setting. 

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 discusses 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 discusses ongoing work to assess whether this rapid turnaround time allows clinicians to more rapidly diagnose GI illness and recommend the appropriate therapy. 

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

Bioinformatics Specialist
Penn Medicine, University of Pennsylvania Health System

During this webinar, speakers from the Center for Personalized Diagnostics at Penn Medicine 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 for wider adoption of this approach due to high levels of stroma and tumor-infiltrating lymphocytes diluting the detectable alterations.

The Center for Personalized Diagnostics began clinical NGS of solid tumors in 2013 using a 47-gene 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 demand to increase gene content and to detect mutations in a wider array of tumor types led the team to explore molecular barcoding to bioinformatically eliminate duplicate reads and detect variants at lower allele frequencies. The team developed a custom 153 gene Agilent HaloPlexHS NGS panel to address this need. Dr. Jennifer Morrissette and her colleague Karthik Ganapathy share details of this work and discuss key considerations for the design, technical validation, and performance of this panel. Ashkan Bigdeli, an informaticist in the CPD demonstrates that in addition to Agilent’s SureCall software, a lab can choose to write a custom script for the analysis of HaloPlexHS NGS data.

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 discussed sample collection challenges associated with tumor sequencing, with a particular focus on somatic variant testing in plasma. The session also featured 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.

During the webinar, Chetan Bettegowda of Johns Hopkins University School of Medicine discussed a study that evaluated the ability of ctDNA to detect tumors in 640 patients with various cancer types. Dr. Bettegowda detailed 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 also discussed 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

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 provided 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, discussed 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 shared 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
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 discussed 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.

During the webinar, Judith Breuer of University College London discussed 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 shows 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

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
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.

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