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Webinar Archive

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Introducing Nextera™ Flex for Enrichment

Nextera™ Flex for Enrichment is the fastest and most flexible targeted sequencing solution for DNA in the Illumina library prep portfolio:

  • A time-saving solution that is 85% faster than the standard Illumina library prep and enrichment
  • Integrated DNA extraction protocols for blood and saliva
  • Optimized performance using bead-based library prep chemistry for reliable results
  • Compatibility with custom, fixed, or whole exome panels from Illumina or 3rd party oligo vendors

Nextera Flex for Enrichment uses a fast, user-friendly workflow. On-bead tagmentation chemistry is combined with a simplified, single hybridization protocol to reduce total workflow time. From DNA input and extraction to library normalization, enrichment, and post-enrichment amplification, the total assay time is ~ 6.5 hours, and total hands-on time is ~2 hours.

Nextera Flex for Enrichment supports a broad DNA input range (10-1000 ng high-quality genomic DNA or 50 ng FFPE DNA) and multiple sample types, including blood, saliva, genomic DNA, and formalin-fixed, paraffin-embedded (FFPE) tissue. The Flex Lysis Reagent Kit enables fast DNA extraction from blood and saliva samples to go directly into library prep, reducing the number of required quantification steps to maximize cost-effectiveness.

While accommodating various study requirements, the Nextera Flex for Enrichment solution delivers consistent insert sizes, uniform coverage, optimized performance, and highly reproducible data across all Illumina sequencing systems.

Grace DeSantis, Ph.D. Director, Product Development , Illumina, Inc.
Topic: Oncology
Nextera Flex: A Robust and Self-Normalizing Enzymatic Library Prep Technology

Library preparation for Illumina sequencing consists of DNA fragmentation and adapter-tagging. DNA fragmentation can be achieved using enzymatic or mechanical methods. Enzymatic methods are typically more convenient but can create challenges around sensitivity to DNA quantitation, and/or require extensive optimization to achieve robustness.  

Nextera Flex is a novel bead-linked-transposome technology, which addresses these shortcomings whilst retaining the convenience of enzymatic fragmentation. Nextera Flex is compatible with a wide range of DNA inputs, providing new levels of robustness while minimizing the requirement for quantitation post-library prep for an input range of 100-500ng for whole genome sequencing and 50-1000ng for targeted enrichment. In addition, the underlying technology will normalize the libraries to give a consistent yield and insert size from a range of DNA inputs. When paired with the Nextera Flex lysis kit, customers can employ a quantification-free workflow to enable normalized library creation from raw samples such as blood and saliva. This new technology offers customers a novel, easy-to-use, fast, and simple solution for library preparation. 

Andrew Slatter and Joshua Burgess , Illumina
Topic:
Performing In-Depth Microbiome Analysis with the One Codex Bioinformatics Platform

Microbiome research is quickly becoming one of the most exciting fields in the life sciences, driven by the power of next-generation sequencing (NGS). One Codex is a leading platform for rapid, accurate microbiome and metagenomics analysis and is used by researchers across major academic, commercial, and clinical institutions. In this webinar, we will walk through a gut microbiome experiment including sample collection, sequencing, bioinformatics, and analysis.

On the bioinformatics side, we will show how you can easily analyze NGS datasets with the One Codex database of >80,000 whole microbial genomes. We will review several types of microbiome analyses from taxonomic classification to building predictive machine learning models. Finally, we will demonstrate how it can all be performed in a scalable, repeatable fashion, ensuring that your microbiome research is reproducible whether it involves 10 samples or 10,000.

Nick Greenfield , One Codex
Topic: Microbial Genomics
Human and Environmental Microbial Health: A Global Perspective

Understanding the microbial ecosystem dynamics of our planet is central to our role as custodians of the planet. The Earth Microbiome Project aimed to characterize the microbial diversity of the diverse ecosystems across our world, which we have used to model the ecosystem dynamics of these environments. Integrating these models with agricultural policy provides a framework on which to determine how climate change and shifting policy will influence the microbial metabolic dynamics, which will affect our ability to modulate system scale outcomes. In concert with this global perspective we are also characterizing the human microbiome, which has become a key part of patient care, provide new avenues to diagnose and treat human disease. The immune system controls our interaction with the microbial world, and yet the microbial communities in our bodies are central to modulating the immune response. Changes in the human microbiome have substantial influence on atopy, neurological disorders, metabolic disorders, and a range of complex conditions and disease states. We will discuss evidence of these mechanisms of interaction and how we have started to disturb the delicate balance of the immune-microbe equilibrium, impacting the development and function of our immune systems. Central to this disturbance is the distance we have placed between our children and the microbial world, which has been demonstrated to have a substantial influence on their physiological, immunological, neurological and even endocrinological development. Applying new strategies to identify how the microbial ecosystem correlates with diseases states and treatment efficacy through Microbiome-Wide Association Studies (MWAS) is altering the trajectory of precision medicine, and providing a new framework for facilitating patient care. 

Jack Gilbert

Jack Gilbert is the Faculty Director of the Microbiome Center, a Professor in the Department of Surgery at the University of Chicago Medicine, Senior Scientist (Adjunct) at Marine Biological Laboratory, and Group Leader in Microbial Ecology at Argonne National Laboratory. Gilbert's research is focused on the ecology, evolution, and metabolic dynamics of microbial ecosystems from myriad environments including built environments, oceans, rivers, soils, air, plants, animals, and humans. His primary interest is in using omics technologies (metagenomics, metatranscriptomics, metabolomics) to capture longitudinal dynamics in microbial ecosystems and then model how these interactions relate the environmental variables, be those variables disease onset and immunology in humans or chemical transformations in plants and soils. Gilbert is developing unifying principles which govern how microbial communities assemble. He founded the Earth Microbiome Project, and co-founded the American Gut Project, and is the editor-in-chief of the journal mSystems.

Jack Gilbert, Faculty Director , Microbiome Center
Topic:
Immunotherapy and genomics innovation advance Illumina’s vision for precision oncology

Genomics is facilitating a deeper understanding of cancer biology and through clinical research, new biomarkers are emerging that pave the way for next-generation therapeutics to help fight cancer in a more personalized way. 

In this webinar, Sandip Patel, MD will provide a review of biomarker research and discoveries in the field of Immunotherapy and Garret Hampton, PhD will discuss Illumina’s vision for Oncology and share how genomics will enable broader availability of comprehensive tumor sequencing to explore complex biomarkers and assess tumor mutational burden.

 

Sandip Patel, MD, Medical Oncologist, Assistant Professor of Medicine, University of California, San Diego , Garret Hampton, PhD, Executive Vice President of Clinical Genomics at Illumina
Topic: Cancer Research
Introducing the iSeq™ 100 Sequencing System—our latest solution for fast and efficient low-throughput sequencing for virtually any lab

Explore our smallest and most cost-effective sequencer ever. Join Bellal Moghis and Gary Schroth as they introduce our newest system—iSeq 100. They’ll walk through installation and also review applications and methods. Find out how you can make the most of your new lab partner.

Bellal Moghis, Senior Product Marketing Illumina and Gary Schroth, Distinguished Scientist Illumina , Illumina
Topic:
CosmosID Metagenomics for Public Health, Food/Water Safety, and Epidemiology

With the dramatically increasing amount of sequence data generation and the significant reduction of sequencing costs, rapid, easy, and accurate data analytics becomes the critical bottleneck in adopting next-generation sequencing (NGS) in the public health sector. To this end, CosmosID has developed a cloud-based microbial genomics platform featuring with world’s largest curated genome databases and scaling computational power to keep pace with the ever-increasing amount of data generation. The platform brings together the most comprehensive and ultrafast “sequence to answer” workflow for easy, accurate, and highly resolved profiling of cross-disciplinary microbiome data. In this webinar, various aspects of the platform will be presented with reference to recent studies on water and wastewater treatment, food safety, molecular epidemiology, and multi-kingdom microbiome profiling and characterization. Key technologies that will be showcased include strain-level metagenomics, metatranscriptomics, metagenomic assembly, and molecular sub-typing.

Rita R. Colwell, Ph.D., D.Sc - University of Maryland Institute of Advanced Computer Studies and John Hopkins University Bloomberg School of Public Health , Manoj N. Dadlani, CosmosID
Topic: Microbial Genomics
AmpliSeq™ for Illumina®—fast, simple, robust targeted library prep chemistry for Illumina sequencing systems

See what happens when a leading library prep is optimized to run on next-generation sequencing (NGS) systems from Illumina. Join Mitu Chaudhary and Claire White as they present data to demonstrate the robust performance of AmpliSeq for Illumina from a wide variety of sample types.

Mitu Chaudhary, Manager Illumina Core Library Prep Product Marketing and Claire White, Global Product Manager, Illumina Clinical Genomics , Illumina
Topic:
High-volume sequence analysis with BaseSpace Sequence Hub and Edico Genome DRAGEN apps

The latest sequencing technologies enable unprecedented throughput and redefine limits for many labs. To adapt, these labs must redefine how they work – by automating tasks to reduce touchpoints and by simplifying workflows with integration and robust analysis tools. In this webinar, we describe BaseSpace™ Sequence Hub and how the newest features support high throughput, high-volume sequencing. We demonstrate how customers can progress from flowcell loading to variant analysis with zero touchpoints by using the Whole Genome Sequencing or Edico Genome DRAGEN apps. Additionally, we describe how the integration with BaseSpace™ Variant Interpreter enables users to interpret and generate reports of identified variants.

Casey Geaney, Senior Product Manager and Ilya Chorny, Associate Director, Product Marketing, Illumina , Rami Mehio, VP of Engineering and Shyamal Mehtalia, Director of Operations, Edico Genome
Topic:
Enabling efficient Discovery and Clinical Research in drug response: Application of a targeted Next-Generation Sequencing Assay for Pharmacogenetics

Pharmacogenetic (PGx) testing enables researchers to understand a person’s genetic propensity for a therapeutic response or an adverse reaction to particular medications. Recently the NIH’s Precision Medicine Initiative has begun a nationwide effort to individualize a subject’s treatment program, while the FDA has already included PGx information in over one hundred drug labels. Serious drug reaction events are likely to become more prevalent as more drugs become available and the number of pharmaceuticals each person is taking increases. To understand the occurrence of these events, sequencing genomic regions associated with metabolism of a wide-spectrum of drug classes can help inform clinical researchers, and better characterize the frequency of known and novel haplotypes within validated genes involved in drug metabolism pathways.

In this presentation, we will describe a method and workflow for targeted pharmacogenetic gene sequencing using Kailos’ TargetRichTM PGxComplete assay.

Julie Collens, Associate Director, Market Development, Illumina , Troy Moore, Chief Scientific Officer and Founder, Kailos Genetics
Topic:
The Effective Implementation of NIPT into a Busy Practice: An Obstetrician Perspective

Medical societies now recommend that all women, regardless of age, be offered screening and diagnostic testing for aneuploidy during pregnancy.1-2 Noninvasive prenatal testing (NIPT) is a newer screening option that utilizes the presence of cell-free DNA in a pregnant woman’s blood originating from the pregnancy. Whole-genome sequencing-based NIPT can screen for common aneuploidies (trisomy 21, trisomy 18, trisomy 13, and certain sex chromosome aneuploidies) with greater accuracy than other available screening modalities, resulting in a significant reduction in false positive rates and, subsequently, potential reduction in invasive procedures in healthy pregnancies.3


In this webinar, Tina Ziainia, MD, FACOG, an Obstetrician-Gynecologist affiliated with Sharp HealthCare, provides insight and expertise on successfully implementing NIPT into a busy practice. Having been in practice for over 17 years and having offered NIPT since 2013, she’ll also discuss prenatal screening options, review the latest ACOG and ACMG screening guidelines, and identify helpful resources for both you and your patients.

 

References: 

1. Practice Bulletin No. 163: Screening for Fetal Aneuploidy. Obstet Gynecol. 2016;127(5):979-981.

2. Gregg AR, Skotko BG, Benkendorf JL, et al. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics. Genet Med. 2016: doi:10.1038/gim.2016.97.
3. Bianchi DW, Rava RP, Sehnert AJ. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014;371(6):578.

Tina Ziainia, MD, FACOG , Sharp HealthCare
Topic:
iDTECT Blood, a sample-to-report next-generation sequencing (NGS) solution for precision diagnostics in infectious diseases

This webinar will provide an overview of the development, validation and clinical evaluation of PathoQuest’s iDTECT Blood. This CE IVD test represents an application of NGS-based shotgun metagenomics to the field of infectious disease diagnosis. The test provides microbiologists and clinicians a precision diagnostics tool allowing individualized antimicrobial treatment decisions in patients where current microbiological methods frequently fail to identify a responsible pathogen. Both the sample preparation and the bioinformatic pipeline have been optimized to provide high sensitivity and accuracy and an actionable report. Clinical results from a prospective study recently published in Clinical Microbiology and Infection will also be discussed.

Helene Peyro-Saint-Paul, MD - Chief Medical Officer , PathoQuest
Topic:
The Human Microbiome: lessons and challenges in deciphering the microbiota in health and disease

Mechanisms of microbial pathogenicity have been extensively analyzed using a broad spectrum of methods, which are driven largely by the technologies available at that time. As animal experimentation gave way to in vitro methods, specific pathogens were systematically investigated as individual dominant clones and colonizers. With the arrival of next-generation sequencing, microbiomes of very diverse habitats are being described. Thus, the microbiome of newborns versus those of the elderly are now prescribed, also the transition and shift in complexity and specificity of bacteria from the oral cavity through to the gut compared to the skin and respiratory are now cataloged and mapped across communities and in response to stress and stimuli.  This tremendous leap in deciphering the human microbiome has ushered a new era of microbiology in which formidable challenges in establishing the foundation of taxonomy, dynamics and function of the residential microbial communities dominate.  

This talk will present the progress made in metagenomics and the use of largely unassembled sequences in constructing the microbial communities forming the human microbiome. The knowledge assembled from microbial whole genome sequences, and the metabolic traits of the human flora are perhaps the most significant framework for the construction of reference microbiomes that can drive research into how transient pathogens establish in new niches and drive the shift from health to disease. 

Professor Saheer Gharbia , Head of Genomics Research Unit Public Health England
Topic:
CosmosID Metagenomics for Rapid Detection of Enteric Pathogens and Characterization of Antimicrobial Resistance in Health and Disease

Abstract: High throughput sequencing, combined with a high resolution bioinformatics platform, provides a powerful tool for  researching enteric diseases and for agricultural and environmental applications. Results of a case control study, comprising samples of known and unknown disease etiology, as well as healthy individuals showed the intestinal microbiome could potentially be used in differentiating healthy, diseased, and asymptomatic carriers, as well as individuals in early stages of infection. Other examples include microbiology of wastewater reuse demonstrating the power of metagenomics to identify the microbial community of pathogens, indicator organisms, and natural microbiota to determine the safety of drinking water derived from recycled wastewater. The CosmosID system provides identification to species and strain within minutes, offers information on antibiotic resistance and pathogenicity factors, and provides relative abundance. The system has been used in analyzing over 25,000 samples to date.

 

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

Rita R. Colwell, Ph.D., D.Sc. , Distinguished University Professor University of Maryland Institute of Advanced Computer Studies, Johns Hopkins Bloomberg School of Public Health, and CosmosID
Topic:
Metagenomic Applications for Microbiome-Related Studies of Complex Disease

Dr. Petrosino is exploring the comprehensive taxonomic and functional changes in the microbiome between birth and Type-1 Diabetes onset in over 22,000 samples from 820 cases and controls (1:1 match) in the TEDDY (The Environmental Determinants of Diabetes in the Young) international prospective cohort.

Advanced analyses of 16S rRNA gene, and bacterial/viral metagenomic data will be presented in this webinar. 

 

Joe Petrosino, PhD, Associate Professor, Baylor College of Medicine
Topic:
Development and Validation of Automated Methods for Metagenomic Analyses

Next Generation Sequencing (NGS) methods are arguably responsible for the establishment of the field of metagenomics. Significantly lower nucleic acid input requirements have made it possible to sample microbial communities that would have been deemed undetectable just a few years ago. In addition to technological advancements, the continued decline in the cost of sequencing has made it feasible to survey the thousands of samples necessary for metagenomic analyses. To meet the throughput demands of these studies, we have automated NGS sample processing methods from nucleic acid extraction, through library normalization, and pooling.

Here, we will present automated methods for 16S rDNA amplicon and whole genome shotgun sequencing as well as discuss the impact of automation on quality. The resulting sequencing reads from both approaches were compared for quality metrics using our standard quality matrix (Q30, Cluster Density, number of mapped reads, etc.)

Subsequently, sequencing reads were used for taxonomic identification and a comparative analysis. Although both automated methods offer a significant benefit in throughput, we found the reduction in the risk of human error far outweighs all other benefits. Furthermore, utilization of automated liquid handling reduces the risk of contamination.

Russell Carmical, PhD, Assistant Professor , Baylor College of Medicine
Topic:
Development and Validation of Automated Methods for Metagenomic Analyses

Next Generation Sequencing (NGS) methods are arguably responsible for the establishment of the field of metagenomics. Significantly lower nucleic acid input requirements have made it possible to sample microbial communities that would have been deemed undetectable just a few years ago. In addition to technological advancements, the continued decline in the cost of sequencing has made it feasible to survey the thousands of samples necessary for metagenomic analyses. To meet the throughput demands of these studies, we have automated NGS sample processing methods from nucleic acid extraction, through library normalization, and pooling.

Here, we will present automated methods for 16S rDNA amplicon and whole genome shotgun sequencing as well as discuss the impact of automation on quality. The resulting sequencing reads from both approaches were compared for quality metrics using our standard quality matrix (Q30, Cluster Density, number of mapped reads, etc.) 

Subsequently, sequencing reads were used for taxonomic identification and a comparative analysis. Although both automated methods offer a significant benefit in throughput, we found the reduction in the risk of human error far outweighs all other benefits. Furthermore, utilization of automated liquid handling reduces the risk of contamination. 

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

Russell Carmical, PhD Assistant Processor , Baylor College of Medicine
Topic: Microbial Genomics