GenomeWebinars

CEO, OneCodex

This webinar will provide a comparison of several next-generation sequencing (NGS) approaches — including short-read 16S, whole-genome sequencing (WGS), and synthetic long-read sequencing technology — for use in microbiome research studies.

NGS is a powerful method for characterizing complex microbial mixtures, but both short-read 16S and WGS methods have their shortcomings. While short-read 16S data is inexpensive, it only enables family- or genus-level identification, is not comparable across different variable regions, and provides poor relative abundance estimation. WGS, meanwhile, offers more accurate relative abundance estimation and greater specificity, but at increased cost and complexity.

Another approach, LoopSeq synthetic long-read sequencing technology from Loop Genomics, offers an intermediate solution by providing species-level identification and significantly improved relative abundance estimation over short-read 16S data. LoopSeq uses unique molecular identifiers to generate synthetic long reads on short-read Illumina sequencing instruments. 

In this webinar, Nick Greenfield of OneCodex will discuss a comparison study of short-read 16S, WGS, and LoopSeq data for four samples – two known composition-positive controls, including a 20-organism bacterial mixture from ATCC, and two complex microbiome samples.

He will share details from this comparison as well as demonstrate how to analyze these datasets on the One Codex software platform.

Sponsored by

CEO, OneCodex

This webinar will provide a comparison of several next-generation sequencing (NGS) approaches — including short-read 16S, whole-genome sequencing (WGS), and synthetic long-read sequencing technology — for use in microbiome research studies.

NGS is a powerful method for characterizing complex microbial mixtures, but both short-read 16S and WGS methods have their shortcomings. While short-read 16S data is inexpensive, it only enables family- or genus-level identification, is not comparable across different variable regions, and provides poor relative abundance estimation. WGS, meanwhile, offers more accurate relative abundance estimation and greater specificity, but at increased cost and complexity.

Another approach, LoopSeq synthetic long-read sequencing technology from Loop Genomics, offers an intermediate solution by providing species-level identification and significantly improved relative abundance estimation over short-read 16S data. LoopSeq uses unique molecular identifiers to generate synthetic long reads on short-read Illumina sequencing instruments. 

In this webinar, Nick Greenfield of OneCodex will discuss a comparison study of short-read 16S, WGS, and LoopSeq data for four samples – two known composition-positive controls, including a 20-organism bacterial mixture from ATCC, and two complex microbiome samples.

He will share details from this comparison as well as demonstrate how to analyze these datasets on the One Codex software platform.

Sponsored by
Recent GenomeWebinars

Associate Professor, Pediatric Infectious Diseases
Cincinnati Children’s Hospital

This webinar discusses the use of shotgun metagenomics to identify children at risk of hospital-acquired infection.

Our speaker, David Haslam of Cincinnati Children's Hospital, details methods used to eradicate colonization with pathogenic organisms and hopefully prevent bloodstream infections. He also discusses how bacterial whole genome sequencing and shotgun metagenomics can be used to track and prevent transmission of hospital-acquired infections.

Dr. Haslam shares how this work fits within his lab's goal of identifying risk factors for invasive infection due to multidrug resistant bacteria. His team is applying next generation sequencing and metagenomic analysis to identify changes in the microbiome that correlate with risk for invasive infection and is currently developing this assay into a clinically actionable test.

Vice President, TRAD,
Rhythm Pharmaceuticals

Founder and Chief Science Officer,
Genomenon

Rhythm Pharmaceuticals and Genomenon will discuss their efforts to assemble a database of mutations associated with rare genetic disorders of obesity, and how this was optimized to facilitate a deep understanding of the variant landscape of melanocortin-4 receptor (MC4R)-pathway genes. This database may help identify MC4R-pathway deficient individuals who might benefit from future precision therapies.

WHY ATTEND? Developing an evidence-based view of the genetic contributors to human disease can help improve the diagnosis of rare disorders and drive important advances in precision drug development. Learn how Rhythm Pharmaceuticals partnered with Genomenon to inform their understanding of rare genetic disorders of obesity and help identify patients who might be appropriate for participation in clinical trials.

DETAILS: By indexing over 6 million full-text genomic articles using the Mastermind Genomic Search Engine, 120 genes and over 10,000 variants were identified as being associated with obesity in the medical literature. Each individual variant was interpreted using the evidence assembled through an automated technical process. This novel semi-automated approach to variant identification and annotation was accomplished via the Mastermind genomic database and vetted using American College of Medical Genetics and Genomics (ACMG) guidelines.

Join Alastair Garfield, PhD, Vice President, Translational Research & Development (TRAD) at Rhythm Pharmaceuticals and Dr. Mark Kiel, Founder and Chief Science Officer at Genomenon, as they share how a database of genes and variants associated with obesity was developed in less than 60 days, including scientific evidence complete with literature citations and ACMG interpretations for each mutation. The machine-learning driven process replaced several years of manual research of the scientific literature to find obesity-related mutations.

You will learn:

  • The importance of published genetic evidence in ensuring the success of a drug candidate
  • How to rapidly assemble a comprehensive biomarker database of this genetic evidence using data available in Mastermind
  • Why automated approaches are required for such disease-variant projects
Tue
Dec
4
11:00 am2018
Sponsored by
Sophia Genetics

Clinical-Grade Exome Analysis for Complex and Unsolved Case Investigations

Genome Webinar

Laboratory Director, Chief Genetic Officer, Co-founder,
Genotypos Science Labs

Clinical Application Product Manager
Sophia Genetics

This webinar will discuss the use of clinical-grade exome analysis application in complex case investigations.

Dr. Pantelis Constantoulakis of Genotypos Science Labs will first discuss the utility of Clinical Exome Solution by Sophia Genetics in routine clinical research and diagnostics. He will also share details of the application’s efficacy in investigating complex and unsolved clinical cases. 

Next, Dr. Georgios Stamoulis of Sophia Genetics will introduce new features in Sophia DDM dedicated to prioritization and filtering strategies of variants detected with exome-size applications.

Sponsored by
Mon
Dec
3
1:00 pm2018
Sponsored by
Advanced Cell Diagnostics

Application of a Novel ISH Approach to Elucidate Splice Variants in Schizophrenia

Genome Webinar

National Institutes of Health Graduate Student Partnership Program

Senior Image Analysis Scientist,
ACD

This webinar will demonstrate how a research team at the National Institutes of Health evaluated a novel in situ hybridization approach and applied it to study splice variants related to schizophrenia.

The neurotrophic factor neuregulin-1, as well as its neuronal receptor ErbB4, are risk factors for schizophrenia. Distinct ErbB4 isoforms are generated by alternative splicing, and the levels of specific receptor isoforms are altered in postmortem brains of patients.

Because of these splice variants differ functionally, it is important to identify the cells that express distinct isoforms. However, traditional molecular analysis tools such as qRT-PCR and RNA sequencing require the disruption of dissected tissue to isolate RNA. To investigate in different cell types the relative amounts of the four ErbB4 variants in morphologically conserved brain tissue, the NIH team used the BaseScope in situ hybridization system with specific oligonucleotides targeting single exon/exon boundaries and fluorescence signal amplification.

This webinar will outline how the NIH researchers first determined the specificity and sensitivity of the BaseScope system and then used it to identify regional and cell-type specific expression of ErbB4 isoforms in the brain. The presentation will also explain how the NIH team quantified both the BaseScope and RNAscope assay signals using the freeware CellProfiler combined with an in-house analysis pipeline.

Sponsored by

Vice President, R&D Amyris

This webinar will discuss how Amyris, a biotechnology company that develops renewable products for a broad range of applications and industries, uses large-scale microbial engineering to support its manufacturing processes.

Organisms offer unparalleled molecular diversity that can be tapped into for a wide array of practical and commercial applications, but there are numerous challenges associated with realizing the full potential within this molecular diversity. Microbes can be engineered to produce many biological targets, but optimizing this process requires repeated iterations of the design-build-test-analyze microbial engineering cycle. The rate at which each phase of the cycle can be executed, as well as the magnitude of strain improvement obtained from each iteration, directly affect the overall development time — and cost — for any product.

Amyris scientists have developed advanced tools for strain engineering, high-throughput screening, analytics, and bioinformatics that accelerate microbial engineering by improving and reducing the number of cycle iterations needed. Central to these capabilities has been the availability of large volumes of low-cost, but high-quality synthetic DNA, which enables the efficient interrogation of a diverse set of hypotheses.

The presentation will cover:

  • How Amyris uses Twist DNA for large scale microbial engineering
  • The automated platforms that enable Amyris scientists to rapidly cycle through a data-driven strain improvement process
  • The role that Amyris biotechnology plays with commercial partners in diverse industries by providing a sustainable, cost-effective alternative to traditional manufacturing practices
Mon
Nov
5
11:00 am2018
Sponsored by
Sophia Genetics

Overcoming Challenges in Solid Tumor Testing with Advanced AI

Genome Webinar

Molecular Biologist, Dijon University Hospital

Clinical Application Product Manager
Sophia Genetics

With the Next Generation Sequencing (NGS), genome sequencing has been democratized over the last decades with the detection of genomic alterations.

This webinar will discuss the different steps taken by the CHU de Dijon to move from a non-NGS lab to an experienced NGS lab and how Sophia Genetics has successfully accompanied the lab to use different diagnostic molecular applications to address their clinical needs in a short turnaround time using Sophia artificial intelligence (AI).

In the first part of the webinar, Dr. Caroline Chapusot will cover the set-up program used to implement the Solid Tumor Solution by Sophia Genetics in the lab and the advantages of this solution over previous lab’s tests.

Then, Dr. Chapusot will discuss two specific clinical cases addressed using STS and Sophia DDM platform for the analysis and the interpretation of the data.

Finally, Dr. Chapusot will discuss the vision of the CHU de Dijon over the NGS applications used for clinical and research purposes and their impact on the reimbursement system.

In the last part of the webinar, Dr. Shirine Benhenda of Sophia Genetics will briefly introduce a solution that will soon be launched to detect gene fusions, beside SNVs, Indels, MSI and gene amplifications in FFPE samples from various solid tumors.

The Solid Tumor Solution by Sophia Genetics is a molecular application that bundles a capture-based target enrichment kit with the analytical power of Sophia AI with and full access to Sophia DDM platform. The application is designed to accurately characterize the complex mutational landscape of solid cancers associated with lung, colorectal, skin and brain cancers using FFPE samples.

Sponsored by
Wed
Oct
24
11:00 am2018
Sponsored by
Thermo Fisher Scientific

What's the Best Technology for Rare Allele Detection in Pathology Research?

Genome Webinar

Head, Laboratory for Diagnostic Genome Analysis, Department of Pathology;
Medical University of Graz

A variety of technology choices are emerging as potential solutions for the identification of mutations in formalin-fixed, paraffin-embedded tumor samples and cell-free DNA for liquid biopsy analysis.

In this on-demand webinar, Dr. Karl Kashofer, head of the diagnostic genome analysis laboratory at the Medical University of Graz, describes an evaluation of digital PCR and targeted next generation sequencing for potential use in biomarker discovery and monitoring of pathology research samples.

Dr. Kashofer details his laboratory’s learnings, including:

  • What should you consider when choosing technology for pathology investigations?
  • How should you handle data interpretation for rare allele detection in samples with large deletions?
  • How do you optimize sensitivity in FFPE and cfDNA samples?
  • What are the key differences observed in digital PCR, Ion AmpliSeq, Ion AmpliSeq HD, and Oncomine cfDNA assays?

For research use only. Not for use in diagnostic procedures. 

Sponsored by

CEO, Girihlet

This webinar will address a range of methods for optimizing small RNA library preparation.

Anitha Jayaprakash, co-founder of T-cell receptor sequencing firm Girihlet, will provide her perspectives on sequencing small RNAs and its utility in the study of various applications, including miRNA profiling in various systems and other small RNAs such as piRNAs in the germline.

Dr. Jayaprakash will discuss challenges and complications that can occur during small RNA-seq library prep and ways to avoid them. She will review the various steps in small RNA-seq library construction and discuss how protocol optimization can improve results and increase user friendliness. She will also discuss the 4N sequencing method, which uses randomized adapters to reduce the ligation bias associated with small RNA sequencing.

Sponsored by

Medical Director, Clinical Pathways, Dana-Farber Cancer Institute; Senior Physician, Thoracic Oncology Program, Dana-Farber Cancer Institute & Assistant Professor, Harvard Medical School

Business Development, Philips Oncology Informatics

This webinar will provide a first-hand look at how the Dana-Farber Cancer Center is adapting its oncology care strategy in light of the rapidly evolving molecular landscape.

With advances in the understanding of tumor biology and drug development, oncologists must now incorporate patient factors and preferences, tumor characteristics and genomics, and treatment toxicities and cost. In this struggle to keep pace with scientific evidence and provide best-practice care for patients, a new approach to cancer care pathways is needed. 

In this webinar, David Jackman from Dana-Farber will discuss how his team considers evidence, how clinicians make on- and off-pathway treatment decisions at the point of care, and how varying genomic alterations in a patient’s tumor can be married to a drive towards enhanced clinical quality and an appropriate reduction in variation of treatment decisions, while maintaining a granular and “personalized” view of each patient.

Dr. Jackman will also review how Dana-Farber uses analytics and real-world evidence alongside clinical experience and published evidence in a continuous-learning framework. 

Hospital Practitioner, Laboratory of Molecular Genetics, Arnaud de Villeneuve Hospital

 

This webinar will discuss the use of new software tools to support the diagnosis of CTFR-related disorders using next-generation sequencing.

Molecular diagnosis of cystic fibrosis and CFTR-related disorders is based on the detection of mutations in the CFTR gene. A wide range of techniques is still used to identify CFTR gene sequence variations. While there is no gold standard or preferred method for routine testing, the rapid adoption of NGS technologies in diagnostics laboratories is enabling a range of new approaches. 

In this webinar, Caroline Raynal of the Laboratory of Molecular Genetics at Arnaud de Villeneuve Hospital will describe how her team tested a new data analysis software in combination with a diagnostic amplicon-based CFTR assay for NGS.

The lab re-analyzed 13 runs in which 158 individuals were included (patients, relatives, partners, and fetuses suspected to have CF) and assessed the assay with the new software.

This webinar will provide details on the findings of this study as well as how amplicon-based solutions for NGS in diagnostics can provide reliable results.

Director of Molecular Pathology, Carolinas Pathology Group

Director of Molecular Pathology, Phenopath Laboratories

In the last few years several molecular testing methodologies — such as immunohistochemistry, PCR, and sequencing — have been approved by the US Food and Drug Administration to aid in the management of patients with lung cancer.  

In this webinar you’ll learn how these very different technologies serve specific needs and how creating a testing strategy that employs many of these different methodologies can provide the information clinicians need to make the best treatment decisions for critically ill patients.

Our two speakers, Dr. John Longshore from the Carolinas Pathology Group and Dr. Harry Hwang from Phenopath Laboratories, will share their experiences from both the large healthcare system and reference laboratory perspectives.