Webinar Archive

Webinar Archive

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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: Microbiology & Infectious Disease : Software : Informatics
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 Genomics
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: Sequencing
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: Microbiology & Infectious Disease : Software
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: Sequencing
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: Human Genetics & Genetic Disease : Software
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: Sequencing : Diagnostics : Customer
The Yin and Yang of NGS HLA typing

The Webinar Series will feature HLA laboratory directors presenting case studies from samples prepared with TruSight™ HLA, sequenced with Illumina next-generation sequencing (NGS) MiSeq or MiniSeq systems, and analyzed using TruSight HLA Assign software. Presentations will be followed by an interactive question and answer session. 


The webinar will offer participants:

  • Advanced sequencing data analysis and data interpretation in Assign software
  • Continuing education in current and relevant topics in Histocompatibility and Immunogenetics
  • An opportunity to share best practices and troubleshooting tips in data analysis and HLA typing by NGS
  • A forum for interaction with other NGS users    
Maria P. Bettinotti, PhD, (ABHI), FACMG, Director, Immunogenetics Laboratory, Johns Hopkins University School of Medicine
Topic: HLA Typing
Next-generation solutions for the next era of sequencing

The latest NovaSeq advancements have arrived—delivering unprecedented scalability and flexibility for next-generation sequencing (NGS). Discover how the S4 flow cell allows you to use the NovaSeq 6000 System to take your research to the next level.

Join Gary Schroth, Illumina Distinguished Scientist, to learn about these latest advancements with the NovaSeq 6000 System. See how the S4 can provide you the highest throughput of any sequencer. Finally, with the new NovaSeq Xp workflow, you can expand your research, giving you more flexibility than ever before.

Gary Schroth and Aboli Rane, Illumina
Topic: Sequencing
NGS HLA Typing for Solid Organ Transplantation: The New Frontier

The Webinar Series will feature HLA laboratory directors presenting case studies from samples prepared with TruSight™ HLA, sequenced with Illumina next-generation sequencing (NGS) MiSeq or MiniSeq systems, and analyzed using TruSight HLA Assign software. Presentations will be followed by an interactive question and answer session.

The webinar will offer participants:

  • Advanced sequencing data analysis and data interpretation in Assign software
  • Continuing education in current and relevant topics in Histocompatibility and Immunogenetics
  • An opportunity to share best practices and troubleshooting tips in data analysis and HLA typing by NGS
  • A forum for interaction with other NGS users
Annette Jackson, PhD, (ABHI), Director, Division of Immunogenetics and Transplantation Immunology, Johns Hopkins University School of Medicine
Topic: HLA Typing
Unambiguous High Resolution HLA typing by Next-Generation Sequencing (NGS): Breakthrough Enhancements and Clinical Research Utility in Solid Organ Transplantation

Dr Dolly Tyan will present on the Stanford Immunogenetics labs’ experience validating TruSight® HLA v2 for NGS HLA typing and validation of automation for TruSight HLA library prep. Dr Tyan will also share a case study to illustrate the utility of NGS HLA typing test results in solid organ transplantation research.


This presentation is part of the TruSight HLA Webinars Series which features HLA lab directors presenting case studies from samples prepared with TruSight HLA, sequenced with Illumina next-generation sequencing (NGS) MiSeq® or MiniSeq® systems, and analyzed using TruSight HLA Assign™ software.

Dr Dolly Tyan, Professor of Pathology, Stanford University Medical Center
Topic: HLA Typing
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.



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: Reproductive & Genetic Health
Implementation of HLA Next-Generation Sequencing (NGS) Platform Using Robotics

The Webinar Series will feature HLA laboratory directors presenting case studies from samples prepared with TruSight HLA, sequenced with Illumina next-generation sequencing (NGS) MiSeq or MiniSeqvsystems, and analyzed using TruSight HLA Assign software. Presentations will be followed by an interactive question and answer session.

The webinar will offer participants:

  • Advanced sequencing data analysis and data interpretation in Assign software
  • Continuing education in current and relevant topics in Histocompatibility and Immunogenetics
  • An opportunity to share best practices and troubleshooting tips in data analysis and HLA typing by NGS
  • A forum for interaction with other NGS users


Edgar Milford, MD, Director Tissue Typing Lab, Associate Professor, Harvard Medical School, Brigham and Women's Hospital
Topic: HLA Typing
Dissecting the genetic basis of Brugada Syndrome

Brugada Syndrome belongs to a family of rare inherited cardiac disorders that can lead to sudden cardiac death. Rare genetic variants in the SCN5A gene can be identified in ~20%* of cases with Brugada Syndrome, while the genetic basis in the others remains unresolved.

Ongoing studies, combining data from multiple genomic methods, are helping to elucidate the genetic basis of Brugada Syndrome and other complex cardiac disorders with the aim of improving patient care in the future.

Register for the webinar to hear Professor Connie Bezzina present data from her laboratory and ongoing collaborative studies with the Brugada Syndrome Genetics Consortium.

Professor Connie Bezzina, Professor of Molecular Cardiogenetics, Academic Medical Center, University of Amsterdam
Topic: Human Genetics & Genetic Disease
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: Human Genetics & Genetic Disease : Microbiology & Infectious Disease
Illumina TruSight HLA Case Study: Implementation of HLA (Human Leukocyte Antigen) typing by Next-Generation Sequencing

The Webinar Series will feature HLA laboratory directors presenting case studies from samples prepared with TruSight HLA, sequenced with Illumina next-generation sequencing (NGS) MiSeq or MiniSeq systems, and analyzed using TruSight HLA Assign software. Presentations will be followed by an interactive question and answer session.

The webinar will offer participants:

  • Advanced sequencing data analysis and data interpretation in Assign software
  • Continuing education in current and relevant topics in Histocompatibility and Immunogenetics
  • An opportunity to share best practices and troubleshooting tips in data analysis and HLA typing by NGS
  • A forum for interaction with other NGS users
Gerald Morris, MD, PhD, Director Immunogenetics & Transplant Lab, UCSD Center for Advanced Laboratory Medicine
Topic: HLA Typing
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: Human Genetics & Genetic Disease : Microbiology & Infectious Disease
Illumina TruSight HLA Case Study Webinar Series HLA typing of buccal swabs using TruSight HLA

The Webinar Series will feature HLA laboratory directors presenting case studies from samples prepared with TruSight HLA , sequenced with Illumina next-generation sequencing (NGS) MiSeq or MiniSeq systems, and analyzed using TruSight HLA Assign software.

Eric T. Weimer, PhD, D (ABMLI), University of North Carolina at Chapel Hill School of Medicine
Topic: HLA Typing
See the NovaSeq Series in action

Discover a new era of sequencing with the NovaSeq Series. Join us for a live webinar event to see firsthand how we are redefining what is possible with high-throughput sequencing. Built from the ground up to fulfill your scientific visions, the NovaSeq Series gives you the flexibility and scalability to complete projects faster and more economically than ever before across a broad range of applications.

Webinar at a glance

  • Overview of instrument and consumables
  • Demonstration from run setup through data analysis
  • Data analysis using BaseSpace® Sequence Hub
Brian Steffy, David Miller, and Aboli Rane, Illumina
Topic: Sequencing
Partnering Big Data Solutions from Illumina and Elsevier: Combining Genomic and Literature Data-Driven Analysis

Illumina BaseSpace Correlation Engine and the Elsevier Pathway Studio are two separate big data mining solutions for two different and highly complementary data problems: unlocking the molecular findings in the ever-growing genomic data repositories and staying up to date on the latest domain-specific scientific literature at the same time. Correlation Engine lets you query a repository of more than 128,000 experimental gene signatures as well as computed disease, compound, and genetic perturbation signatures. Pathway Studio gives you access to one of the world’s largest automatically curated literature databases, updated weekly, and generated using its proprietary NLP MedScan technology.

Joe Delaney Manager, Scientific Research Illumina , Chris Cheadle, Director of Genomics Research Elsevier
Topic: Informatics
The Future Reimbursement Environment for NGS for Oncology

Next-generation sequencing (NGS) is providing new tools to that are aimed at developing products to comprehensively profile cancer samples. However, as with any truly novel technology, payers likely will question the clinical utility of NGS and scrutinize testing coverage. Join us to hear Charles Mathews, Vice President of Boston Healthcare, review how reimbursement is likely to play out in the future for key applications of NGS technology in the oncology space. 

Charles Mathews, Vice President, Boston Healthcare
Topic: Cancer Genomics
Emerging methods: Driving transcriptome and epigenetics discovery with RNA-Seq and Methyl-Seq

As researchers seek to understand how the transcriptome shapes biology, RNA-Seq is
becoming recognized as one of the most significant and powerful tools in modern science. With RNA-Seq, researchers can detect the fine architecture of the transcriptome, such as transcript isoforms, gene fusions, single nucleotide variants, and other features—without prior knowledge. In addition to RNA-Seq, methylation sequencing can provide insights into the regulation of RNA and the temporal and spatial expression of gene products. By combining both RNA and methylation sequencing, researchers who study complex disease, cancer, and other biological systems will have a more complete picture of the transcriptome and its underlying regulatory features.

In this live webinar, we discuss the RNA-Seq and Methyl-Seq workflows that can help researchers drive breakthroughs and understanding in the area of gene expression and gene regulation. Join our gene expression and methylation experts as they review how researchers are driving discovery and learn how our workflows can help your lab leverage the power of next-generation sequencing.

Fraz Syed, Market Manager & Britt Flaherty, PhD, Sr. Sales Specialist, Illumina
Topic: Human Genetics & Genetic Disease : Sequencing
The Power of a Whole-Genome Sequencing Assay for Noninvasive Prenatal Testing

It is important for health care professionals who offer noninvasive prenatal testing (NIPT) to understand the advantages and disadvantages of various assays currently used for NIPT. During this webinar, Dr Yuval Yaron will provide insight on the unique features of a whole-genome sequencing (WGS) approach for NIPT. He will review recent clinical experience data, discuss the impact of NIPT test failures, and review quality metrics that are utilized to analyze and report NIPT results.

Prof. Yuval Yaron , Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center
Topic: Reproductive & Genetic Health
Detecting somatic mutations in neurological disorders with targeted NGS

Join Dr. Jamuar as he discusses the optimal technique for the detection of somatic mosaicism. He’ll evaluate the limitations of Sanger sequencing and highlight the advantages of targeted next-generation sequencing (NGS), sharing findings from his paper, Somatic Mutations in Cerebral Cortical Malformations, which was published in the New England Journal of Medicine.

Webinar at a glance:

  • Learn about somatic mutations and threshold of detection. 
  • Understand the prevalence of somatic mutations in neurodevelopmental disease.
  • Evaluate an optimal technique for somatic mosaicism detection
    • Limitations of Sanger sequencing
    • Advantages of targeted NGS 
Dr. Saumya Jamuar, Consultant, Genetics Service, KK Women's and Children's Hospital, Singapore
Topic: Cancer Genomics : Human Genetics & Genetic Disease : Sequencing
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: Human Genetics & Genetic Disease : Microbiology & Infectious Disease
Next-Generation Sequencing - An Introduction

Today’s complex genomic research questions demand a depth of information beyond the capabilities of traditional DNA sequencing technologies. Next-generation sequencing (NGS) has rapidly been adopted as an important research tool, enabling previously unanswered questions to be addressed. 

Illumina next-generation sequencing utilizes a fundamentally different approach from the classic Sanger chain-termination method. It leverages sequencing by synthesis (SBS) technology – tracking the addition of labelled nucleotides as the DNA chain is copied – in a massively parallel fashion.

Watch our on demand webinar to find out more on how NGS can help you gain greater insight from your studies, save time, and be more confident in your results.

Tim Watts, Sr. Marketing Specialist, Illumina, EMEA
Topic: Sequencing
RNA-Seq to impact future Colorectal Cancer (CRC) Treatment

Recent studies on colorectal cancer (CRC) have elucidated four CRC consensus molecular subtypes with potential to predict outcome and stratify patients for therapy. Oncogenomics research by Enzo Medico, MD, PhD, from Candiolo Cancer Institute in Torino, describes how his laboratory is using integrative genomic techniques in cancer research to transform the future of CRC therapy.

Enzo Medico, MD, PhD, Associate Professor, University of Torino, School of Medicine, Candiolo Cancer Institute
Topic: Cancer Genomics
Needle in a Haystack: Using targeted panels to link Phenotype to Genotype

Join Tim Watts to discover the benefits of next-generation sequencing and multi-gene targeted panels, and how they provide an efficient and cost effective workflow for analysing and interpreting research in inherited genetic diseases.

Watch this webinar to:

• Understand the benefits of targeted multi-gene panels against the traditional iterative testing and to whole exome and whole genome sequencing.
• Review of current TruSight® One and TruSight Cardio targeted sequencing panels, including new kit formats available for the MiniSeq™sequencer.

Tim Watts, Sr. Marketing Specialist, EMEA, Illumina
Topic: Reproductive & Genetic Health : Sequencing
Tips for talking to patients about NIPT: A roundtable discussion

Join Dr Martin Chavez, Dr Anupam Garg, and Kristin Dalton for a roundtable discussion as they share tips for talking to patients about noninvasive prenatal testing (NIPT). Following the discussion, Dr Chavez will address questions from the audience.

After attending, you’ll be able to:

  • Differentiate between prenatal aneuploidy screening and diagnostic testing.
  • Describe key aspects of providing pre-test and post-test counseling for NIPT based on ACOG and SMFM guidelines.
  • Understand how to talk to your patients about NIPT.
Martin Chavez, MD, Winthrop University Hospital
Topic: Reproductive & Genetic Health
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: Microbiology & Infectious Disease
A core facility case study: Transitioning from the HiSeq 2500 System to the HiSeq 4000 System

Learn how the UCSF Center for Advanced Technology transitioned from the HiSeq 2500 System to the HiSeq 4000 System. Eric Chow, PhD will highlight some of the current projects that they are running on the HiSeq 4000 System, such as the metagenomic analysis of complex samples, ATAC-seq, and CRISPR screens. Discover how the HiSeq 4000 System delivers cost-effective sequencing for a multitude of library types.

Eric Chow, PhD, Director, Center for Advanced Technology, UCSF
Topic: Sequencing
Efforts to move from Exomes to Whole Genomes in Oncology Research

Hear Prof. Christof von Kalle describe his efforts to move from exome to whole genome, challenges and successes so far and the vision of cancer care at NCT and DKFZ. Advances in high-throughput sequencing lead to increasingly accurate information about somatic alterations in cancer genomes at decreasing costs. Whole genome sequencing (WGS) provides a more complete picture considering structural variants and copy numbers and is a comprehensive way to detect non-coding mutations, including promoter enhancers. Thus, WGS may hold the key to drive precision oncology and individualized treatment decision to the next level.

Professor Christof von Kalle
Topic: Cancer Genomics
The genomic architecture of neurodegenerative diseases

Our understanding of the genetic basis of neurodegenerative diseases has grown considerably in the past decade. This was driven in large part by advances in technology that have ultimately allowed us to look at complete genomes with single base-pair resolution. A wide range of neurodegenerative diseases has benefited from these advances, with Alzheimer’s and Parkinson’s diseases being no exception. We have identified several disease causing mutations and variants that modulate risk for disease onset. These have informed us not only about genes involved in these diseases, but also about biological pathways we now know are altered in disease. Additionally, we have also been able to compare and contrast the genetic basis of these diseases. This has been tremendously informative, with diseases such as dementia with Lewy bodies showing genetic correlations with both Alzheimer’s and Parkinson’s, without these having any correlation between them.

We are now much closer to have a complete understanding of the genetic underpinnings of common forms of neurodegenerative diseases. Technology will continue to play an important role in the future as the questions we ask evolve based on the data we generate.

Jose Bras, PhD, Proleptic Lecturer and Alzheimer’s Society Research Fellow, University College London Institute of Neurology
Microbial Genomics: Analyzing Sequencing Data with One Codex

In this webinar, we will walk through the use of microbial NGS for a range of applications, such as microbiome characterization and outbreak epidemiology. We will highlight the varied functionality of the One Codex platform, from importing data from local files or BaseSpace® Sequence Hub to quantifying species in a metagenomic sample, to detecting virulence genes in individual isolates, to performing genomic epidemiology on hundreds of real-world isolates. This overview will demonstrate how a modern data platform for microbial NGS enables scientists and researchers to draw rapid, valuable insight from their microbial samples. 

Nick Greenfield, Founder & CEO, One Codex
Topic: Microbiology & Infectious Disease
Introduction to BaseSpace Variant Interpreter and an overview of the workflow

Simplifying and Expediting Genomic Workflows with Integrated Informatics.

Until now, managing, analyzing, and interpreting genomic data has been an arduous process that required disparate data systems and the need to assemble a diverse set of software applications.

In this succinct webinar, we address how BaseSpace Variant Interpreter, the newest member of the BaseSpace Informatics Suite, can help clinical research labs quickly identify, annotate, and classify disease-relevant variants and summarize significant findings in one report. Integrated with BaseSpace Sequence Hub, BaseSpace Variant Interpreter enables rapid extraction to biological insight while increasing a genomic clinical research lab’s operational efficiency with a scalable secure solution.

This webinar is part of a series exploring BaseSpace Informatics Suite. Details of additional events will be presented during the webinar.

Rebecca Hemenway, M.S. Sr. Product Manager. Donavan Cheng, Ph.D. Director, Bioinformatics., Illumina
Topic: Informatics
Insights into genetic variation driving schizophrenia

Join Steven McCarroll as he discusses his team’s work trying to find the underlying causes of schizophrenia.

This webinar covers:

  • The complex genomic interactions implicated in the development of schizophrenia
  • How cellular pruning affects adolescent brain development
  • How variation in the major histocompatibility complex (MHC) may drive pathogenic mechanisms in neural function
Steven McCarroll, PhD, Associate Professor of Genetics , Harvard University
Topic: Human Genetics & Genetic Disease
PPV of NIPT: Maximizing the value of NIPT for your patients

Join Dr Tracy Prosen to better understand the performance characteristics of noninvasive prenatal testing (NIPT), with a special focus on positive predictive value (PPV). 

After attending, you’ll be able to:

•    Describe how PPV varies for different conditions and in different testing populations
•    Calculate PPVs for effective counseling of patients with positive NIPT results

Tracy Prosen, MD, Assistant Professor, Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota
Topic: Reproductive & Genetic Health
Preparing consistent, high-quality RNA-Seq libraries with the NeoPrep™ System

Constructing libraries for sequencing is a time consuming multistep process with multiple possible failure points. The Illumina NeoPrep™ System is an automated, hands-free solution for creating libraries from fragmented genomic DNA and eukaryotic RNA with low amounts of input material. We have performed extensive testing using the NeoPrep System in our core facility, focused on its RNA-Seq capabilities. In the core setting, the NeoPrep System performs extremely well with robust metrics across many input samples, providing high complexity libraries suitable for most routine RNA-Seq analyses. rRNA levels and exon/intron ratios are comparable or better than most manual preparation methods and the run-to-run consistency addresses a key concern for most library preparations. This webinar focuses on the NeoPrep System, its capabilities and limitations, and reviews the practicalities of implementing it in your laboratory. 

Stuart Levine, PhD Director, MIT BioMicro Center
BaseSpace Suite: Overview of BaseSpace Clarity LIMS and BaseSpace Sequence Hub

Join us as we walk through two of the applications of BaseSpace Informatics Suite, the integrated informatics solution to enable genomic research and the future of precision medicine. Andrew and Jill will show you how to simplify and expedite genomic workflows with integrated informatics using both BaseSpace Clarity LIMS and BaseSpace Sequence Hub.

Webinar at a glance:

  • Description of BaseSpace Suite components
  • Demonstration of BaseSpace Clarity LIMS for wet lab management and automation
  • Demonstration of BaseSpace Sequence Hub for genomic data storage and analysis

Integration of the two applications

Andrew LeBeau and Jill Hesse, Illumina, Inc.
Next Generation IVF: How Preimplantation Genetic Screening (PGS) can improve outcomes

Join Mr Stuart Lavery in this educational webinar to hear how his network of IVF units is investigating the utility of PGS to ensure the most viable embryo is transferred. Following a review of the rationale, current clinical evidence, and potential benefits for PGS, Mr Lavery will share his experience of PGS in routine practice and his participation in STAR – a randomized clinical trial combining vitrification, single blastocyst transfer, and VeriSeq™ PGS – next generation sequencing PGS solution.

Stuart Lavery, Hammersmith and Queen Charlotte’s & Chelsea Hospitals, London
Developmental Validation of the MiSeq FGxTM Forensic Genomics System

Human DNA profiling using PCR of polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, next-generation sequencing (NGS) has matured, bringing modern advantages to forensic DNA analysis.

Dr. Cydne Holt, Associate Director, Market Development, Illumina
Topic: Forensic Genomics
HiSeq 3000/HiSeq 4000 Systems Live Demo – High-Throughput Solutions for a Broad Range of Applications
The HiSeq 3000 and 4000 Sytems have set a new standard in high-throughput genomics by extending the power of patterned flow cell technology for a broad range of applications. In a live demonstration, Dr. Godinez will provide a comprehensive overview of the exome sequencing workflow. 

  • Process more samples per run or increase coverage depth per sample
  • Complete large projects with fewer runs
  • Accelerate large-scale studies
  • Reduced price per sample for a broad of range of applications
  • Rapid, cost-effective, large-scale sequencing
  • Increased daily throughput
  • Complete Exome runs (2x75bp) in less than 2 days
Comprehensive solution:
  • Wide array of library prep solutions, including 2 new exome offerings, support a broad array of applications
  • Analysis solutions available in BaseSpace® Sequence Hub
Topic: Sequencing
Performance validation of TruSight® Tumor 15 at University Hospital Erlangen

Prof. Florian Haller will present his laboratory’s experience using TruSight Tumor 15, a gene panel for molecular analysis of solid tumor samples including the 15 most common cancer biomarkers used in laboratories today.

Attend the webinar to hear about:

• TST 15 workflow for molecular analysis of solid tumor samples

• Performance data of the panel using a set of tumor samples with known mutations.

Prof. Florian Haller, University Hospital Erlangen
Topic: Cancer Genomics
Keeping pace with immuno-oncology research breakthroughs and biomarker identification

The excitement surrounding immuno-oncology is being driven by results seen in the clinic. New treatments can potentially be made more efficacious using NGS technology that would accelerate biomarker identification and bring down costs for research subject screening and safety monitoring. Among these technologies is RNA-Seq, a flexible sequencing assay that enables multiple applications with one assay from a single sample. In this webinar, we'll summarize the clinical relevance of RNA-Seq, when and how to use expression profiling economically, some common challenges and associated remedies.

Key learning objectives
Learn how legacy RNA-Seq datasets can be revisited for new insights to keep pace with today’s rapid advance of therapeutic breakthroughs
Learn how RNA-Seq provides high-throughput, comprehensive, direct measurement of functionally relevant molecular processes
Learn more about key applications for RNA-Seq in immuno-oncology
Adrian Benjamin, PhD, Illumina and Kimberly Robasky, PhD, Q2 Solutions, Illumina and Q2 Solutions
Topic: Cancer Genomics
Gain insights into human genetics and cancer genomics with Linked-Reads and phased genome analysis.

Join Dr Hanlee Ji to learn how Linked-Reads and phased genome analysis provide insights in human genetics and oncology.

Webinar at a glance

  • Learn about generating megabase haplotypes from germline and cancer genomes and their application.
  • Discover how to resolve complex structural variation from cancer genomes using Linked-Reads and high molecular weight DNA.
  • Understand the application of megabase haplotype analysis in Mendelian disorders
Hanlee Ji, PhD , Stanford University School of Medicine
Topic: Cancer Genomics : Human Genetics & Genetic Disease
Genomes for Medicine

Join this webinar to hear Dr David Bentley, a long-time proponent of DNA sequencing and VP & Chief Scientist at Illumina, describe the value and clinical utility of whole genome sequencing (WGS) in healthcare.

From dealing with samples to data handling, interpretation and reporting, David will discuss why we focus on WGS as a tool for developing potential genetic diagnostics. Using real life cases, David will show ways in which genome sequencing has the capability to enable clinicians to provide fast diagnosis and personalised treatment. David will discuss how we envisage genome sequencing will become routine in healthcare.

Dr David Bentley, VP & Chief Scientist, Illumina
Topic: Cancer Genomics : Human Genetics & Genetic Disease
Insights into the Genetic Basis of Autoimmune Diseases

Dr Alex Marson, Sandler Faculty Fellow at the University of California, San Francisco, has developed a fine-mapping algorithm to identify candidate causal variants for autoimmune diseases from genotyping data. Join us for a live webinar as he discusses his insights into the genetic basis of autoimmune diseases.

Alex Marson, MD, PhD , University of California, San Francisco
Topic: Human Genetics & Genetic Disease : Customer
Unravelling Hematological Disorders Using Targeted NGS Panels

Prof. Torsten Haferlach, Head of MLL Munich Leukemia Laboratory, will discuss how their laboratory has implemented NGS technology for sequencing targeted gene panels.


Join in to hear about

·       Application of NGS to molecular pathology assessment of hematological malignancies

·       Integrated process for data analysis and reporting results


Join the live webinar event and participate in the Q&A session!

Prof. Dr. Dr. Torsten Haferlach, Head of Cytomorphology, MLL Munich Leukemia Laboratory
Topic: Cancer Genomics
Adopting NGS for tumor profiling: Accessible sequencing. Flexible solutions.

Next-generation sequencing (NGS) can help you avoid costly and time-consuming iterative testing while simultaneously helping to preserve precious samples. In this webinar, you will learn more about the advantages that NGS offers over traditional methods, and be introduced to the newest, cost effective solution for hematological and solid tumor profiling.

Maude Champagne, Commercial Development Manager, Oncology, Illumina
Topic: Sequencing : Cancer Genomics
The Clinical Implications of NIPT Failures

If you offer noninvasive prenatal testing (NIPT), it’s essential to understand the frequency and implications of test failures.

NIPT failures are often overlooked as a test metric.  Failure rates vary significantly based on the platform used for testing.  Recent publications suggest an increased risk of aneuploidy in pregnancies with a noninvasive prenatal test failure.

Join Professor Yuval Yaron, Director of the Prenatal Diagnosis Unit at the Tel Aviv Sourasky Medical Center, as he provides insights regarding NIPT failures. Professor Yaron will discuss publications on NIPT failures and their impact on performance statistics such as sensitivity and positive predictive value (PPV) as well as patient management.


Topic: Reproductive & Genetic Health : Customer
Introducing the MiniSeq™ System: Our simplest, most affordable sequencing solution yet.

The simple, affordable MiniSeq System empowers researchers to keep pace with sequencing technology and take control of their projects, costs, and timelines. Join Stephen Gross, PhD, and Jason Goode, PhD, as they demonstrate the push-button ease and load-and-go operation of the MiniSeq System. Learn how the integrated cluster generation, sequencing, and onboard data analysis enables diverse applications from tumor profiling to targeted expression analysis.

Stephen Gross, PhD, Scientist 2, Gene Expression and Jason Goode, PhD, Senior Product Manager, Sequencing Systems, Illumina
Topic: Sequencing
Next-Generation Sequencing (NGS) and Arrays to Profile Transcriptomic and Epigenomic Regulation in Cell Biology

Join us for a live webinar and gain a better understanding of genomic techniques used to profile the transcriptome and epigenome in complex, multifactorial disease. NGS and array platforms can allow for greater flexibility when studying gene mutations, gene expression and epigenetic regulation. Learn how NGS and arrays are advancing the study of complex disease, and in investigating various factors that can affect disease phenotype.

Fraz Syed, PhD, Marketing Manager, Britt Flaherty, PhD, Product Manager, Kevin Taylor, PhD, Sr. Manger, Market Development, Complex Disease , Illumina, Inc.
Topic: Human Genetics & Genetic Disease
Stopping the Spread of Super Bugs with NGS

Join Dr. Henrik Westh, Clinical Microbiologist for a live webinar on his work to contain the spread of super bugs. With global outbreaks becoming more common, Dr. Westh and his lab are leveraging the power of NGS platforms to understand the evolution and spread of antimicrobial-resistant Staphylococcus aureus, specifically methicillin-resistant Staphylococcus aureus (MRSA) – one of the most aggressive super bugs. Dr. Westh is working to help stop these ruthless super bugs from causing millions of illnesses and deaths worldwide.

Henrik Westh, PhD, Professor, Department of Microbiology, Copenhagen University Hospital
Topic: Microbiology & Infectious Disease : Customer
Metagenomic sequencing of skin and condylomas reveal undiscovered papillomaviruses

Human papillomavirus (HPV) is a diverse virus family with more than 200 different types known today. HPV can infect the genital tracts and cause cervical cancer as well as condylomas (genital warts). In addition, skin is also known to harbor HPV.

Join this webinar to hear Dr. Emilie Hultin from Karolinska Institutet, Stockholm (under the direction of Prof. Joakim Dillner), describe how the laboratory used next generation sequencing (NGS) to study apparently HPV-negative condyloma specimens and were able to analyze both known and novel HPV-types. The laboratory also applied NGS to a clinical research study to investigate the presence of HPV in different non-melanoma skin lesions and subsequently identified a novel HPV-type that was present in 33% of the lesions. Taken together, NGS has been instrumental in expanding our knowledge of this important family of viruses.

Topic: Microbiology & Infectious Disease : Customer
Results from using the NeoPrep System for NGS library preparation starting from DNA and RNA

In this webinar, Max Käller, PhD, Manager of Facility, Genomics Applications,
SciLifeLab, Stockholm will discuss his analysis of the NeoPrep System. Starting with DNA and RNA for multiple runs, he compares the high success rates of the NeoPrep System to other systems.

Topics will include:

• Library prep comparison of the NeoPrep System versus other automation platforms
• RNA library prep performance
• Low input RNA libraries
• DNA library prep performance and comparison with another low input kit

Max Käller, PhD, Manager of Facility, Genomics Applications, SciLifeLab
Topic: Sequencing : Customer
Use of cytogenetic arrays at the Erasmus MC

Dr. Laura van Zutven, from the Clinical Genetics Laboratory at Erasmus University Medical Center Rotterdam (Erasmus MC), describes their laboratory’s use of arrays and present case study data showing the power of arrays for clinical research studies.

Topics covered:

·      Validation of arrays for cytogenetics in their laboratory

·      Case studies showing power of array technology

Dr. Laura van Zutven, Clinical Genetics Laboratory at Erasmus University Medical Center Rotterdam (Erasmus MC)
Topic: Reproductive & Genetic Health : Customer
Insights on Gene Function in Cell Models of Brain Development

Join us for a live webinar and gain an understanding of how genes linked to intellectual disability are crucial for brain development. Lachlan Jolly, Research Fellow, School of Medicine at the University of Adelaide, will discuss the identification and characterization of x-linked intellectual disability genes using Next Generation Sequencing in patient derived cell lines. This work has led to a better understanding of relevant disease mechanisms that converge on embryonic stages of brain development.

Lachlan Jolly, Research Fellow School of Medicine at the University of Adelaide
Topic: Sequencing : Customer
Library Prep Automation-Is Microfluidics the way to go?

Ewart de Bruijn, NGS Research Facility Manager at the Utrecht Sequencing Facility in the Netherlands, shares his lab’s experience with the NeoPrep System. Don’t miss the upcoming webinar, where he will discuss their experience, and provide a hands-on perspective of the workflow results, and data.

He will also provide a perspective on the use of microfluidics technology for library preparation.

Ewart de Bruijn, NGS Research Facility Manager at the Utrecht Sequencing Facility
Topic: Sequencing : Customer
Transitioning to an RNA-Seq Workflow Solution

Join Dr. Bo Reese in a guided walkthrough of the Illumina RNA sequencing workflow. See how easy it is to make the transition to next-generation RNA sequencing with a step-by-step guide, from library prep to data analysis.

Topics will include:

  • Facilitating rapid RNA-Seq adoption and sharing success stories
  • Training methods for new-to-NGS
  • Complete workflow walkthrough from library preparation to data analysis
Bo Reese, PhD, Senior Scientist, Center for Genome Innovation, University of Connecticut
Topic: Sequencing : Customer
Paired-end amplicon sequencing uncovers new understanding of animal symbiosis.

Herbivores rely on symbiotic microbial communities to convert indigestible plant materials into accessible nutrients. Sloths are thought to be especially dependent on this symbiosis, as their mostly leaf-based diet severely limits their nutrient intake. They also engage in a complex symbiotic relationship with pyralid moths. Join us for a live webinar event to learn how Kim Dill-McFarland and her team from the University of Wisconsin-Madison used paired-end 16S amplicon sequencing on the MiSeq® System to explore the sloth's
microbe-cycling hypothesis.

Kim Dill-McFarland, PhD, University of Wisconsin
Topic: Microbiology & Infectious Disease : Customer
Quality Assurance for NGS in Molecular Pathology Diagnostics

Discover the steps that have been taken to implement next-generation sequencing (NGS) into the clinical molecular pathology diagnostic laboratory to receive an accreditation from Germany’s national accreditation body (DAkkS). Obtain unique insights that have the potential to reduce your cost and time to establish NGS in your lab.

Dr. Sabine Merkelbach-Bruse, PhD, Head of the Molecular Pathology Diagnostic Lab, University Clinic Cologne
Topic: Cancer Genomics
Advancing Pathology and Cancer Research with NGS

Dr. Platt discusses the benefits of integrating NGS into clinical oncology research. Dr. Platt will present an overview of the utility, accessibility, and ease of use of NGS in pathology and oncology applications. She’ll also share case studies that demonstrate the functionality of molecular assays and analysis options for deep sequencing of tumor samples.

Dr. Jamie Platt, PhD, Vice President, Genomic Solutions, Molecular Pathology Laboratory Network
Topic: Cancer Genomics
GEMINI (Genomic Medicine Initiative) clinical exome sequencing in practise

Cost effective tests with a standardized, efficient workflow are required for clinical laboratories with a vision to implement next generation sequencing.  In the past, a major hurdle to overcome was the significant resources required to design, test and validate multiple, evolving sequencing panels. 

Join this webinar to hear from Dr Howard Martin of Cambridge University Hospitals NHS Foundation Trust (under the direction of Prof. Steve Abbs), on how their laboratory has implemented a single test which sequences more than 4800 clinically relevant genes, while combining the benefits of both targeted gene and WES (whole exome sequencing) approaches.  At lower cost, this single sequencing test is both versatile and simple, with mutation detection rates comparable to full exome sequencing and coverage over a wide range of rare genetic diseases.

Dr Howard Martin, Cambridge University Hospitals NHS Foundation Trust
Topic: Human Genetics & Genetic Disease : Customer
NGS data storage: push-button analysis, sharing, and more

Translating the growing volume of genomic information into meaningful translational and clinical research insights is one of the biggest challenges we face. With BaseSpace®Onsite, a local cloud computing bioinformatics solution from Illumina, you can easily transfer and manage your data all on a single, secure platform.

Hear from Raymond Tecotzky, Market Manager and architect of the Informatics Ecosystem at Illumina, about the expanded capabilities of the on-premise solution, including additional applications supported. Explore the advantages of local data storage, analysis, sharing, and more.

Raymond Tecotzky, Market Manager, Illumina Informatics Ecosystem
Topic: Informatics
Leveraging Patterned Flow Cell Technology for Diverse Applications – HiSeq 3000 and HiSeq 4000

Delivering up to 1.5 Tb of data in only 3.5 days, the HiSeq 3000 and HiSeq 4000 Systems provide unparalleled speed and performance for a broad range of applications. Join Illumina Bioinformatics expert Dorothea Agius and Distinguished Scientist Gary Schroth as they discuss how you can harness the power of these systems for your high-throughput applications during this one-hour presentation.

Gary Schroth, Distinguished Scientist; Dorothea Agius, Bioinformatics Scientist, Illumina
Topic: Sequencing
Gain deeper insights with powerful bioinformatic tools.

Metagenomic studies are becoming more and more popular. From sample extraction to sequencing, our complete workflow solution is dedicated to simplifying your process. Evaluate bacterial diversity. Detect an abundance of microbes. Focus more on the biology—not the technology—with our easy-to-use metagenomics application now available on the BaseSpace® Platform. Join us to learn how to enhance your metagenomic studies. From library prep to analysis, we deliver solutions to help advance your microbiology research.

Clotilde Teiling, Microbiology Program Manager, Illumina and Poorani Subramanian, PhD, Research Scientist, CosmosID, Illumina and CosmosID
Topic: Microbiology & Infectious Disease
Beyond Gene Expression: Leveraging Next-Generation Sequencing to Study RNA Biology

In this webinar, Dr.Brenton Graveley, professor of Genetics and Genome Sciences at the University of Connecticut Health Center, will highlight the use of genomic approaches to study RNA biology. He will review the HiSeq®, NextSeq®, and MiSeq® Systems and present data demonstrating consistency. 

Topics will include:

  • Alternative splicing, circular RNAs, trans-splicing, recursive splicing, poly (A) tail length, and RNA stability studies
  • Library preparation methods and data analysis compatibility with BaseSpace® Apps.
Dr. Brenton Graveley, Professor of Genetics and Genome Sciences , University of Connecticut Health Center
Topic: Sequencing : Customer
Targeted Sequencing with the MiSeq FGx System and Data Analysis with ForenSeq Universal Analysis Software

This episode will focus on how to use the MiSeq FGx Instrument to analyze data and generate reports with ForenSeq Universal Analysis Software.

Starting with the pooled libraries from Episode 1, Brian and Steven will guide you through run set-up and sequencing using the intuitive user interface on the MiSeq FGx System, followed by streamlined and powerful data analysis and report generation using the ForenSeq Universal Analysis Software. At the conclusion of this episode, you will understand:

  • Sequencing by synthesis chemistry on this compact, all-in-one platform.
  • Load and go reagents using push-button operation.
  • Real-time run monitoring using various key metrics and color coding to measure performance and report status.
  • How to easily go from sample to highly informative results and detail-rich reports—with no need for bioinformatics expertise.
Brian Steffy, Senior Lab Manager and Steven Lee, Senior Technical Marketing Manager, Illumina
Topic: Forensic Genomics
Modeling human macrophage activation with transcriptome profiling

Increasing evidence from murine studies show that macrophages compute input signals from their tissue environment to generate specific functional programs both during homeostasis and inflammation. To translate these concepts to human macrophage biology, reductionist models have been made to study global reprogramming of human macrophages on the transcriptional level. Based on recent spectrum model of human macrophage activation (Xue et al., Immunity, 2014), the following topics will be addressed during the 1-hour presentation:

  • How specific is signal integration in macrophages?
  • What are major transcriptional hubs of macrophage activation?
  • Can such models be utilized to define in vivo macrophage biology?
Joachim L. Schultze, Director, Genomics and Immune Regulation, Life and Medical Sciences Institute (LIMES), University of Bonn
Topic: Human Genetics & Genetic Disease
Library Preparation with the ForenSeq® DNA Signature Prep Kit

In the first episode of the series, Brian and Steven will walk you through the 5 simple steps to create sequence-ready libraries. They will cover the basic protocol as well as provide unique and helpful insights for ensuring great downstream results. By the end of this episode, you will know how to:

  • Achieve high-resolution and exceptional accuracy from as little as 1 ng of DNA—even with complex mixtures or degraded DNA.
  • Perform multiplexing and straightforward sample processing.
  • Access approximately 200 genetic markers in a single test, including STRs currently utilized around the world.
Brian Steffy, Senior Lab Manager and Steven Lee, Senior Technical Marketing Manager, Illumina
Topic: Forensic Genomics
NGS applied to unravel ovarian cancer gene mutations

Watch the webinar presented by Italian cancer researchers Sergio Marchini and Luca Beltrame from the IRCCS “Mario Negri” Institute for Pharmacological Research in Milan. Using next-generation sequencing, their team carried out a retrospective study to investigate the mutational profile of ovarian cancer genes involved in pathways related to drug sensitivity in a cohort of solid tumors.

The team will discuss their results, recently published in Annals of Oncology, and the potential impact of genetic analysis to ultimately improve the clinical management of cancer therapies in the future.

Sergio Marchini and Luca Beltrame, IRCCS “Mario Negri” Institute for Pharmacological Research, Milan, Italy
Topic: Cancer Genomics : Sequencing : Customer
Transform your cytogenetics workflow

Learn how to seamlessly integrate next-generation sequencing and array applications all on a single system for your cytogenetic research. The NextSeq 550 allows laboratories to comprehensively analyze SNVs and CNVs, thereby significantly increasing the chances of detecting cytogenetic abnormalities. With the addition of BeadChip array scanning for Cytogenomics and Karyomapping applications, the NextSeq 550 System can now deliver unparalleled flexibility for your research.

Watch the webinar to discover how the new BeadChip array scanning capability will help simplify your workflow and accelerate your next breakthrough.

Rich Shippy, Director of Product Marketing , illumina
Topic: Reproductive & Genetic Health
Leading the way: Advantages of adding PGS to your IVF unit

As we explore the latest in fertility, minimizing risk of hyperstimulation, optimizing health of the embryo transferred and improving odds of singleton can be achieved with frozen single euploid embryo transfer. Providing Preimplantation Genetic Screening (PGS) requires managing patient expectations, helping the medical team understand the technology, and guiding the couple to success.

Join this educational webinar presented by Dr. Angeline Beltsos, to learn more about the advantages in PGS.

Dr. Angeline Beltsos, Fertility Centers of Illinois, Chicago, Illinois, USA
Topic: Reproductive & Genetic Health : Customer
The basics of next-generation sequencing of FFPE tumor specimens

Learn how you can get started using targeted NGS assays in your laboratory.

In this webinar, Dr. Michael Rossi from Emory University will describe how to develop and implement NGS assays for clinical research using existing technologies. Specific examples of established processes for oncology research, particularly those using FFPE tissues, will be presented

Michael R. Rossi, PhD, Assistant Professor, Emory University School of Medicine
Topic: Cancer Genomics : Sequencing : Customer
Translating NIPT into Clinical Practice: A Physician’s Perspective

Noninvasive prenatal testing (NIPT) performed with massively parallel sequencing of cell-free DNA (cfDNA testing) in maternal plasma came into use in clinical prenatal care in the US in late 2011. As a result of multiple clinical validation studies, a variety of methods/technologies have evolved with specific strengths and weaknesses. As a result, clinicians need to understand the different methodologies and know how to implement them into their clinical practice. Primary questions involve the use of NIPT as a primary or secondary screen, which patients to offer this testing to, how conventional measures, such as nuchal translucency screening and anatomy ultrasound should be used in conjunction with NIPT, and what pre- and post-test counseling is necessary. In this 45-minute webinar, Joe Leigh Simpson, MD, Senior Vice President for Research and Global Programs at the March of Dimes Foundation, will provide an overview of various approaches and discuss his recommendations on how to best implement this major advance in prenatal screening.

Joe Leigh Simpson, MD, The March of Dimes Foundation
Topic: Reproductive & Genetic Health : Customer
NGS Method Spotlight: RNA Sequencing on the NextSeq Series

The flexibility and power of the NextSeq Series supports a broad range of sequencing options—from whole genome sequencing, exomes, and targeted resequencing, to transcriptome sequencing. Join Senior Lab Manager Brian Steffy as he provides a live overview and demonstration of how the NextSeq 500 Series is part of a seamless workflow solution for RNA-Seq that takes you from sample to analyzed data.

In this webinar, you will learn how the NextSeq 500 Series makes the advantages of RNA-Seq—including broad dynamic range and the ability to discover novel features—more accessible than ever before. This presentation will feature a live demo of each step of the RNA-Seq workflow, including:

  • Selecting from a suite of library preparation options to find the best fit for your study design needs
  • Fast and easy sequencing set-up through intuitive user interface and load-and-go operation
  • Push-button data analysis through the BaseSpace Core Apps for RNA computing environment
Brian Steffy, Illumina
Topic: Sequencing
NextBio® Research in the Academic Setting

Next-generation sequencing is ushering in a new genomic era, making data integration and interpretation more critical than ever. Join us for a live webinar to learn how the NextBio Research platform can help transform your data into valuable insights quickly and easily. Learn tips from Andrew Boudreau, Sr. Market Manager of Research Informatics at Illumina on how you can best benefit from the easy-to-use platform.

The following topics will be discussed during the 1-hour presentation:

  • Providing biological context to gene expression data.
  • Leveraging curated studies from Gene Expression Omnibus, GTeX, and other sources.
  • Interpreting, aggregating, and sharing non-public data.
  • Troubleshooting RNA-Seq workflow support and integrating with the BaseSpace® Platform.
Andrew Boudreau, Sr. Market Manager, Research Informatics, Illumina
Topic: Informatics
Next-Generation Sequencing Technology Drives Discoveries in Disease Pathology

Next-generation sequencing (NGS) is playing a key role in infectious disease epidemiology for veterinary medicine—with the potential to drive breakthroughs in agriculture and genetic diversity conservation. Join us for a live webinar event and hear from Tony L. Goldberg and Sam Sibley from the University of Wisconsin-Madison about their recent research findings. Gain insights about how NGS technology is helping drive progress in disease pathology for a variety of animal species.

Tony L. Goldberg, PhD, Department of Pathobiological Sciences
Topic: Microbiology & Infectious Disease : Customer
Leveraging end-to-end RNA-Seq solutions for true discovery

While microarrays and qPCR offer flexibility in gene expression studies, neither method has the ability to enable true discovery; only the unbiased nature of RNA-Seq has the potential to identify features such as novel transcripts or splice-isoforms. At Illumina we continue to develop both the upfront library preparation and the downstream analysis options to offer end-to-end solutions for RNA-Seq projects, simplifying your workflow and the transition from the preceding methodologies.

Scott Brouilette, Ph.D, Illumina
Topic: Sequencing
New Advancements in NGS Provide Higher Data Quality and Expanded Applications

As next-generation sequencing (NGS) technology continues to advance, laboratory professionals are looking for ways to balance their need for high-quality data, high-throughput applications, and rapid turnaround times with their desire for flexible, easy-to-use technology. Join Illumina bioinformatics expert Eric Allen, MEng, and scientist Stephen Gross, PhD, as they discuss how you can harness the power of a seamless workflow solution for your lab—to improve NGS workflows and enable a full range of applications, including whole-genome sequencing, exome sequencing, targeted resequencing, and transcriptome sequencing.

During this webinar, you’ll learn how to optimize your NGS workflow with Illumina technology for a fully supported solution, from DNA/RNA to results. This presentation will review the improvements seen in version 2 chemistry as well as the complete process from library preparation to sequencing with the NextSeq Series, and automated data storage, analysis and sharing with the Illumina cloud computing environment, the BaseSpace® Platform.

Eric Allen & Stephen Gross, Illumina
Topic: Sequencing
Illumina Biobanking Webinar 3: Mid-size cohorts: International perspectives of the CHRIS study

There is an emerging understanding that deriving data from specimens stored in biobanks has the potential to drive patient care and drug development to new heights.

We invite you to learn more about how genetic and epigenetic variation can help stratify your samples for use in high-impact studies with microarray and next-generation sequencing technologies.

Mid-size cohorts: International perspectives of the CHRIS study - Dr. Cristian Pattaro, Group Leader, EURAC and Scientific Coordinator of the CHRIS Study (Italy)

Dr. Cristian Pattaro, Group Leader, EURAC and Scientific Coordinator of the CHRIS Study (Italy)
Topic: Human Genetics & Genetic Disease : Customer
Recent developments in cancer genomics

From tumor profiling to inherited risk to molecular monitoring, Illumina solutions for analysis of DNA, RNA, and epigenomics are enabling a revolution in cancer research. Gain deeper insights about how our expanding oncology portfolio is accelerating new discoveries in cancer biology and translational cancer genomics.

Join us to hear a review of recent developments in Illumina  technology and some of the latest groundbreaking discoveries from the research community. Learn how Illumina solutions for whole genome, RNA, and targeted sequencing are helping deliver high-quality results from even the most challenging samples.

Dr. Jennifer Stone, Illumina
Topic: Cancer Genomics
Application of Next-Generation Sequencing to Preimplantation Genetic Screening

With infertility rates on the rise and women waiting until later in life to have children, more patients are seeking help from assisted reproductive technologies. Although in vitro fertilization (IVF) techniques have dramatically improved, success rates remain low with only 30% to 40% of cycles resulting in live birth. Aneuploid embryos play a major role in IVF failure and miscarriages. As such, selection of euploid embryos through preimplantation genetic screening (PGS) via embryo biopsy has the potential to improve outcomes while reducing the instance of multiple gestations. For many years, the mainstay of PGS methods was fluorescence in situ hybridization (FISH) and more recently, polymerase chain reaction and DNA microarray. In 2014, a new methodology for PGS became available—next-generation sequencing (NGS). 

Learn from Kumar Duraiswamy, Associate Director, Field Medical Affairs at Illumina, during this special 45 minute presentation about how NGS technology is empowering couples to make wiser choices.

The following topics will be covered:

  • Overview of PGS methods
  • Discussion of relevant data
  • Exploration of future IVF directions
Kumar Duraiswamy, MD, MBA Associate Director, Field Medical Affairs , Illumina
Topic: Reproductive & Genetic Health
Illumina Biobanking Webinar 2 - Genomics of large cohort / population biobanks

There is an emerging understanding that deriving data from specimens stored in biobanks has the potential to drive patient care and drug development to new heights.

We invite you to learn more about how genetic and epigenetic variation can help stratify your samples for use in high-impact studies with microarray and next-generation sequencing technologies.

Genomics of large cohort / population biobanks - Kristian Hveem, professor, MD, PhD (Director of HUNT Biobank, NTNU, and the National CONOR Biobank, Norway)

Kristian Hveem, professor, MD, PhD, Director of HUNT Biobank, NTNU, and the National CONOR Biobank, Norway
Topic: Human Genetics & Genetic Disease : Customer
Forensic Genomic Workflow: Transforming your results with NGS

Learn how Illumina's Forensic Genomic Workflow can transform forensic applications. Specifically designed and validated for forensic applications, library preparation chemistry, instrument and software combine to deliver results for >200 globally recognised STR and SNP markers within a simple and easy to use workflow. Detect sequence variants within STRs, maximise information recovery from degraded samples and generate investigative leads using ancestry and phenotype informative SNPs.

Dr. David Ballard, Senior Scientist in the DNA Analysis at King's Unit, King's College London and Nicola Oldroyd, Market Development Manager for Forensic Genomics at Illumina present how this new solution can optimise results from forensic samples and broaden the scope of forensic applications.


Topic: Forensic Genomics
Discover a powerful new tool for HLA reporting and analysis

Join us for a live webinar event to learn how the TruSight® HLA Sequencing Panel can transform your research. The TruSight HLA Sequencing Panel is a comprehensive workflow solution for ultra-high-resolution human leukocyte antigen (HLA) typing, delivering unambiguous 11-locus typing all on a single assay and a single software platform. Put an end to phase ambiguities and report your results with ease and speed with one unified technology. Hear from Alex Lindell, Sr. Market Manager of HLA at Illumina, about how this new solution can optimize your productivity and maximize your HLA typing results.

Topic: HLA Typing
Illumina Biobanking Webinar 1 - Use of genotyping array for sample QC, the added advantage of stratification

There is an emerging understanding that deriving data from specimens stored in biobanks has the potential to drive patient care and drug development to new heights.

We invite you to learn more about how genetic and epigenetic variation can help stratify your samples for use in high-impact studies with microarray and next-generation sequencing technologies.

Use of genotyping array for sample QC, the added advantage of stratification - Per Hoffmann, Dr. rer. nat. (Life and Brain Research Centre, University of Bonn, Germany)

Dr. Per Hoffmann, Life and Brain Research Centre, University of Bonn, Germany
Topic: Human Genetics & Genetic Disease : Customer
Introducing the NextSeq 550: High-throughput sequencing and array scanning on a single system

Introducing the NextSeq 550 System. With the addition of BeadChip array scanning for Cytogenomics and Karyomapping applications, the NextSeq 550 System can now deliver unparalleled flexibility for your research. Discover how the new BeadChip array scanning capability will help simplify your workflow and accelerate your next breakthrough during this live webinar event. Learn how to seamlessly integrate next-generation sequencing and array applications all on a single system.

Topic: Reproductive & Genetic Health : Sequencing
Regulatory Discussion: Updates on FDA LDT and NGS Initiatives

In late 2014, the FDA released a draft guidance document outlining potential new requirements for lab-developed testing services. The updated framework will repurpose existing medical device regulations and may impose new requirements for clinical labs, hospitals, physicians, and other health care providers. In addition, the FDA released a discussion paper and announced a public meeting on regulatory oversight of next-generation sequencing tests. Find out how the changes may affect your lab in this webinar recording. Hear from Mya Thomae, Vice President of Regulatory Affairs at Illumina.

Topic: None
NIPT for all Pregnancies? A Review of the CARE (Comparison of Aneuploidy Risk Evaluations) Study

Noninvasive prenatal testing (NIPT) performed with massively parallel sequencing of cell-free DNA (cfDNA) in maternal plasma came into use in clinical prenatal care in the US in late 2011. As a result of multiple clinical validation studies, organizations such as ACOG, SMFM, and NSGC published committee opinions stating that cfDNA testing could be offered to pregnant women at high risk for fetal aneuploidy as a screening option after counseling. 

Over time, however, questions surrounding NIPT performance for low-risk pregnancies have emerged. Previous studies have been conducted in low-risk populations, and the findings are encouraging. However, the examined populations were narrowly defined, and the screening algorithms were not representative of the approaches currently used in the US. 

In contrast, the CARE study (Comparison of Aneuploidy Risk Evaluations) is a prospective, blinded multicenter observational study comparing the results of NIPT for fetal autosomal aneuploidy with the results of conventional screening for trisomies 21 and 18 in a general obstetric population. In this webinar, Lawrence D. Platt, MD, director of the Center for Fetal Medicine and Women’s Ultrasound, will review the study’s conclusion that NIPT had significantly lower false positive rates and higher PPV for T21 and T18 compared to standard screening.

Topic: Reproductive & Genetic Health
Power your next big discovery with ultra-high throughput sequencing

This recorded webinar highlights how you can complete large-scale projects in record time more cost effectively than ever with our newly expanded HiSeq and HiSeq X Series sequencing systems. Magnify your large-scale genomic research with the production power of the HiSeq 3000 and HiSeq 4000 Systems. Experience the highest throughput at the lowest price per sample across the widest range of applications. Take your population- and production-scale studies to the next level with the HiSeq X Series Systems. Reshaping the economics and scale of human whole-genome sequencing, the HiSeq X Ten and HiSeq X Five Systems deliver unprecedented throughput and the lowest cost price per human whole genome.

Learn more in this webinar given by Peter Barthmaier, Senior Product Manager of HiSeq Systems at Illumina, about how the new systems can accelerate your research.

Topic: Sequencing : Cancer Genomics : Human Genetics & Genetic Disease
Clinical Research of Complex Congenital Brain Malformations by Combined Neuroimaging and Massively Parallel Sequencing Using the TruSight One Sequencing Panel

In this webinar, we present clinical research results for an isolated index case with developmental delay and a variant of classic lissencephaly, not explained by mutations in genes currently well-established. Research was performed through trio sequencing of the child and parents using the TruSight One Sequencing Panel combined with clinical evaluation of the available cerebral MR imaging. Results were achieved within 14 working days.

Topic: Reproductive & Genetic Health
Validation of the TruSight One Sequencing Panel for Clinical Research

The clinical research application of next-generation sequencing (NGS) requires robust enrichment tests and fast protocols. While whole-exome and genome sequencing have become standard for research projects, the particularities in clinical research necessitate tests with high sensitivity for phenotype-related genes. Moreover, the risk for unsolicited findings should be low. Therefore, gene panel sequencing has been rapidly adopted in clinical research laboratories because phenotype-specific gene lists can be bundled in custom enrichment strategies. Nonetheless, the validation of these assays has amounted to impressive workloads because these gene lists undergo frequent revisions.

Topic: Reproductive & Genetic Health
Understanding Function Through Genetic Data Integration

You are invited to a practical webinar recording highlighting genetic data integration approaches featuring Dr. Tuuli Lappalainen.


Explore the power of genome and transcriptome data integration, expand your understanding of genetic variants, and map future research applications.

Topic: Human Genetics & Genetic Disease : Customer
Toward Precision Medicine in Neuropsychiatry

Dr. David Goldstein, Director of the Center for Human Genome Variation, discusses how sequencing with the HiSeq 2500 is helping advance neuropsychiatry.


Topics include:

● Progress in large-scale scale studies identifying pathogenic mutations in epilepsy, specifically de novo mutations as a cause of the epileptic encephalopathies

● How sequencing can aid diagnosis of rare, serious, unresolved genetic conditions

● Examples of how genetic diagnosis has influenced clinical management

Topic: Human Genetics & Genetic Disease : Customer
Discover a new streamlined workflow for HIV variant calling


In this webinar recording, we’ll explore an end-to-end solution for identifying mutation and predicting HIV resistance.

● Discover how ultra-deep sequencing on the MiSeq Instrument enables the identification of HIV

● Learn about the newly published HIV bioinformatics pipeline and how easy it is to use

● Optimize your HIV Variant workflow from sample preparation to discovery

Topic: None
Counting on Illumina – Application Focus: RNA-Seq

Listen to our “Counting on Illumina" webinar where the application focus is RNA-Seq.   In this session, we provide an overview of this powerful technique, including library preparation options and issues when transitioning from microarrays.

Topic: Human Genetics & Genetic Disease
Enable gene expression profiling and fusion detection in FFPE samples

Millions of archival tissue samples, particularly formalin-fixed paraffin-embedded (FFPE) derived samples, provide a large vault of information for disease research. Typically, these samples are associated with long-term phenotypic data that may yield insight in gene expression changes that occur during various disease states. Unfortunately, the fixation process and storage of FFPE samples frequently leads to high RNA degradation and generally offers limited sample material, making it difficult to perform reliable, reproducible transcriptome analysis. While it is possible to derive usable RNA from FFPE samples, the current analysis methods produce highly variable results or often require expensive deep sequencing.

Next generation RNA sequencing is an ideal platform to access FFPE tissue samples for research, as it offers extensive functional genomic information. In this webinar, learn how researchers can leverage new technology to conduct cost-effective gene expression, profiling transcriptome analysis and fusion detection studies using RNA-sequencing to analyze difficult samples.

Topic: Sequencing
On the forefront of transformation: Genomic applications in oncology

The emergence of next-generation sequencing (NGS) and extensive collaboration with the cancer community have made possible a new understanding of the genes and pathways that drive tumor growth. These advances help propel targeted pharmaceutical development and bring us closer to the realization of precision medicine. As a leader in NGS technology, Illumina is investing in the development of novel clinical oncology solutions. Join our Medical Affairs leadership team to learn about the basic principles of next-generation sequencing. Explore the applications of genomics in oncology for germline risk prediction and precision medicine, including how NGS demonstrates the importance of circulating nucleic acids for molecular monitoring.

Topic: Cancer Genomics
Lungs, Germs, and Metabolites: A Cystic Fibrosis Story

Dynamic microbial and viral communities constantly inhabit our bodies, encoding the majority of the unique genes that alter processes throughout our bodies and our lives. Persistent and unique viral and microbial communities are associated with every human, and they are powerful indicators of health and disease. Metagenomics, metabolomics, microbiology and ecological statistics can be used to answer questions about how microbes and viruses affect human health.

Next-Generation sequencing has enabled a torrent of recent discoveries about the composition and activity of human-associated microbial communities. In this webinar, we present recent work enabled by microbial DNA sequencing of human samples from healthy people and cystic fibrosis (CF) patients. Earlier and more specific diagnosis and treatment of periods of worsened symptoms known as pulmonary exacerbations in CF may be possible using paired metabolomic and metagenomic approaches to uncover biomarkers of disease state.

Topic: None
Best Practices for Obtaining RNA Sequencing Data from Formalin-fixed Paraffin-embedded (FFPE) Samples

Webinar hosted by Expression Analysis

Formalin-fixed Paraffin embedded (FFPE) tissues present many sample preparation, extraction and method development challenges. Despite these difficulties, interest in genomic analysis of FFPE samples remains high, and large collections of clinically-annotated FFPE material await analysis. The presenter will describe the methods and best practices based on the extensive work Quintiles has performed analyzing both RNA and DNA from FFPE samples.

This webinar is intended to help genomic researchers better understand technical hurdles in the analysis of FFPE-derived RNA to:

  • Learn how EA has overcome challenges inherent in FFPE samples
  • Gain insight into experimental design considerations
  • Learn how to exploit your collection of FFPE material

 By attending the webinar you will learn:

  • How RNA sequencing data derived from fresh frozen and FFPE material can be compared
  • How to design experiments that obtain meaningful data from your FFPE samples


Topic: Sequencing
The Human Virome in Health and Disease

The human virome—the collection of all the viruses within the human body—includes chronic and transient infections, endogenous retroviruses, and large bacteriophage populations that prey on human-associated bacteria. Recent studies have revealed that the human virome contains a high degree of variation. After sequencing and analyzing virome samples from healthy and diseased individuals on an Illumina HiSeq® System, researchers found that most viral contigs are novel sequences and viral communities vary greatly between individuals.

These findings provide insight into the variation between viromes, indicating that factors such as diverse viral predators, rapid viral evolution within the human body, and disease can affect the virome community. This webinar discusses the viral communities inhabiting the human body and how the virome affects human health.

Topic: None
Karyomapping—A Rapid PGD Solution for Single-Gene Disorders

Preimplantation Genetic Diagnosis (PGD) can be used where there is a risk of severe genetic disorders being inherited from parents, whether the couple has a family history of a genetic disorder or has a child affected by a genetic disease. Currently, PGD is often performed by examining the inheritance of short tandem repeats (STRs) adjacent to specific disease loci. Unfortunately, this method is complex and must be developed individually for each genetic disorder and each couple, making it time-consuming and limiting availability.

Karyomapping offers a faster, more accurate, and robust alternative to STR analysis for PGD. Using genome-wide linkage-based analysis, karyomapping detects single-gene disorders from as little as a single embryonic cell. Embryos that do not carry the defective gene can be identified and selected for transfer and subsequent implantation.

Join Professor Alan Handyside, one of the pioneers of karyomapping, and Dr. Alan Thornhill as they introduce the Illumina karyomapping solution, including the Infinium HumanKaryomap-12 BeadChip. This karyomapping assay targets ~300,000 of the most informative genomic markers resulting in comprehensive genome-wide analysis at the single-cell level.

Topic: Reproductive & Genetic Health : Customer
16S rRNA sequencing: From DNA extraction to entire microbial community analysis

Working closely with the microbial community, we’ve developed a powerful next generation sequencing solution that enables researchers to analyze an entire microbial community within a sample, including species that may not be identified otherwise. This culture-free method eliminates the time and expense involved in growing pure cultures and individually sequencing each type of bacteria.

Discover how you can leverage these next generation sequencing solutions to initiate and accelerate your own 16S rRNA studies.

Topics include:

  • An overview of the streamlined 16S rRNA metagenomics sequencing protocol
  • Discussion of analysis options with MSR and BaseSpace
  • Live demonstration of the BaseSpace 16S app
  • Case study conversation
    • A comparison of 16s metagenomic sequencing on MiSeq and 454
    • Desert tortoise conservation – disease surveillance and diagnosis
Topic: None
Somatic Variant Discovery and Translation in Cancer Genomics – Next Generation Sequencing Solutions

Next-generation sequencing (NGS)-based detection of somatic variants in tumor samples is a powerful tool to uncover the molecular drivers associated with different cancer types. This technology holds promise to enable more accurate prognoses and more effective therapy decisions – the foundation necessary to achieving precision medicine. Using whole-genome, whole-exome, and RNA-Seq, large international projects, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), have contributed greatly to the catalog of somatic driver mutations that underlie tumorigenesis and progression in many common and rare cancers. These discoveries provide basic research and drug development communities direction to focus on the targets of greatest impact in the war on cancer. In the clinical research and oncology communities, similar sequencing strategies have emerged as a powerful weapon to further understand variation in the clinical course of various cancer types. 

These strategies are now accessible to every lab with Illumina’s new NextSeq 500 system. Using a powerful combination of sample preparation, sequencing, and informatics methods, Illumina now enables researchers to perform the same groundbreaking cancer analysis pioneered by groups such as TCGA and ICGC in their labs. This experimental design is more accessible than ever before. Join us to learn how researchers are using this comprehensive approach to continue to discover the biology of cancer and translate discoveries faster than ever before.

Topic: Cancer Genomics
Creating, Expanding, and Streamlining Your Next-Generation Sequencing Portfolio using the TruSight™ One Sequencing Panel and VariantStudio


Building a comprehensive sequencing portfolio with individual panels for each condition of interest presents numerous developmental and managerial complications. To help you overcome this challenge and streamline your sequencing portfolio while maximizing assay offerings, Illumina offers the TruSight One Sequencing Panel. TruSight One is a single, large sequencing panel targeting more than 4,800 genes and covering 12 Mb of genomic content. Combining TruSight One with the VariantStudio data analysis tool creates the simplest sample-to-report workflow that can replace dozens, if not hundreds, of small, individual sequencing panels and assays. The unmatched coverage uniformity of TruSight One facilitates high levels of multiplexing, enabling sequencing of trios on a single MiSeq flow cell and 36 samples on a single HiSeq flow cell.

Topic: Sequencing : Human Genetics & Genetic Disease : Software
GenomeStudio Software for Automated Polyploid Clustering

Many plant species are polyploid organisms with multiple homologous chromosomes, which often complicates genetic analysis. Illumina has developed the GenomeStudio Polyploid Clustering Module, which features powerful DBSCAN and OPTICS algorithms, to help researchers analyze genotyping data from polyploid genomes.

This webinar, presented by Cindy Lawley, Ph.D., Global Agriculture Consortia Program Manager at Illumina, demonstrates how to use the Polyploid Clustering Module. Topics include: starting a project, optimizing cluster detection sensitivity, manually adjusting clusters, importing cluster positions, and exporting cluster data. The webinar also covers analysis of the wheat genome to demonstrate how to use the Polyploid Clustering Module to study a complex genome.

Topic: Agriculture Genomics
Molecular Pathology Reimbursement: Outcome of the 2013 Medicare Gapfilling Process

This webinar summarizes the outcome of the recently concluded Medicare gapfilling process for 114 new molecular pathology (MoPath) codes that were implemented in 2013. The presentation will address the final 2013 regional rates for these codes, as well as the implications for national payment rates in 2014. We will then look ahead to additional upcoming changes in the molecular diagnostic reimbursement landscape and the potential impact on clinical laboratories.

Topic: Diagnostics
Deep sequencing of HIV: Detection of Drug Resistance Variants and Tracking of Viral Haplotypes

HIV drug resistance testing has become an integral part of HIV clinical care. Commercially available genotypic assays identify drug resistance mutations through population sequencing of regions of the HIV protease and reverse transcriptase genes. However, these assays are insensitive to drug resistance variants when present at levels comprising less than 10 to 20 percent of the virus population.

By contrast, ultradeep sequencing allows the identification of HIV nucleotide variants and variant haplotype signatures present at <1% in patient samples. Tracking of viral haplotypes, which requires long-sequence read lengths, is particularly useful in determining whether sequentially expressed dual infections are the consequence of viral evolution, co-infection, or superinfection.

This webinar presents insight into the characterization of HIV by next-generation sequencing, including data obtained from a comparison of HIV drug-resistance variant detection in a 465-base region of HIV reverse transcriptase by the Illumina MiSeq and Roche 454 GS FLX+ platforms.

Topic: None
Implementing Informatics Solutions to Support Genomics

The Human Molecular Genetics Center at the Medical College of Wisconsin has implemented an efficient informatics solution to support genomics sequencing runs using Illumina systems. Jaime Wendt Andrae will discuss how they implemented the beta-version of Clarity Run Manager to enable sample tracking and automation of Illumina sequencing runs. Aubree Hoover will briefly introduce this new version of Clarity Run Manager, a free solution for managing projects and samples, and easily creating sample sheets for Illumina instruments.

Topic: Informatics : Customer
Ground-breaking study, identifying a causal gene mutation for two dissimilar neurological diseases

Dr. Bryan Traynor and his team participated in a ground-breaking international study, identifying a causal gene mutation responsible for two dissimilar neurological diseases, ALS and FTD. As members of a worldwide consortium, his research team used next-generation sequencing to identify a large hexanucleotide repeat that disrupts the C9ORF72 gene located on chromosome 9. The mutation accounts for approximately 40% of all familial cases of ALS and FTD in European and North American populations, and also ~1% of Alzheimer&rsquo;s disease cases. ALS, also known as Lou Gehrig&rsquo;s disease, is a fatal neurodegenerative disorder that leads to rapidly progressive paralysis and respiratory failure. Frontotemporal dementia (FTD) is the most common form of dementia in the population under the age of 65.<br /><br />This landmark discovery has impacted how these neurological disorders are diagnosed, investigated and perceived. It also provides a distinct therapeutic target for gene therapy efforts aimed at ameliorating these diseases.

Topic: Human Genetics & Genetic Disease : Customer
Real Time PCR Experimental Design and Analysis Amplified with NuPCR Reagents

Quantitative Real-Time PCR (qPCR) has been the technique of choice for gene expression analysis studies for decades. Although effective, current probe-based assays can exhibit cross-reactivity issues, require tedious design procedures, and involve expensive reagents. NuPCR reagents constitute a novel approach that uses a unique NuZyme™ complex for cost-effective, sensitive, and specific qPCR on any Real-Time PCR instrument. In addition, web-based DesignStudio™ software is available to simplify assay design and ordering. 

In this webinar, Gothami Padmabandu will discuss NuPCR chemistry and the ease of designing duplexed assays. In addition, experimental design and data analysis using NuPCR reagents in a number of different qPCR applications will be presented.

Topic: None
Identification of rare disease-causing variants using next-generation sequencing

Activating mutations in the GNAQ gene can lead to Sturge-Weber Syndrome, a rare disease affecting 1 in 20,000 people. Mutations in this same gene can also cause port-wine stain birthmarks affecting 1 in 333 individuals. In this presentation, Dr. Jonathan Pevsner of Kennedy Krieger Institute will describe his lab's research using whole-genome and targeted resequencing to identify causative variants of these somatic mosaic conditions. The presentation will also discuss the use of Illumina's TruSight Autism content set for the detection of variants associated with Autism Spectrum Disorder. 

Topic: Human Genetics & Genetic Disease : Customer
Latest Developments in Molecular Pathology (MoPath) Rate Setting

In May 2013, the Centers for Medicare and Medicaid Services (CMS) proposed new payment rates for the new MoPath codes. Many laboratories are concerned that these rates undervalue key test areas, including molecular cytogenomic, inherited disease, and cancer testing.
July 8 is the final deadline to respond to these rates and propose new values.

In this webinar, you will learn:

● About the latest developments in MoPath rate setting
● How to participate in the rate setting process to ensure appropriate reimbursement for future molecular diagnostic tests
● How and when to respond to the current rate proposal

Topic: Diagnostics
Sequencing analysis of tissue samples: Fresh frozen vs. FFPE

We'll discuss:

  • Analyzing small sample sizes of FFPE material
  • Obtaining FFPE results that are consistent with fresh-frozen results
  • Specially developed tools for comparing results
Topic: Cancer Genomics
Assembling and Analyzing Illumina Data in DNASTAR Lasergene Software

Join us to learn how to simplify your data analysis workflows for Illumina sequencing experiments. DNASTAR Lasergene software is a set of genomic assembly and analysis tools that provide a simple, yet highly flexible environment for RNA profiling, reference-guided and de novo sequence assembly, and many other workflows. During this presentation, Matthew Keyser of DNASTAR will demonstrate sequence assembly and analysis of Illumina data using Lasergene. The demonstration will include:

  • Multiple exome assembly and comparison
  • RNA-Seq alignment and analysis
  • Microbial genome assembly with gap closure
  • SeqMan NGen for de novo genome assembly on the Illumina BaseSpace® platform
Topic: Software
Exploring the Home, Hospital, and Human Microbial Interactome – The H3MP Study

Through next-generation sequencing, microbial genomic research is accelerating the pace of discovery–rapidly expanding our understanding of microbial function and interactions.

Metagenomic and microbiome studies provide researchers deep insight about the microbes that populate our surroundings, infrastructure, and built environments. In this webinar, Dr. Jack Gilbert will present initial findings from the Hospital Microbiome Project. The goal of this ongoing initiative is to characterize the taxonomic composition of surface, air, water and human-associated communities in a new hospital—starting from the introduction of patients to major surgical procedures. Please join us to see Dr. Gilbert present preliminary data and discuss what his team has discovered from this exciting endeavor.

Topic: Sequencing : Customer
Optimizing the Utility of Forensic Human Mitochondrial DNA Analysis

Our laboratory has developed a protocol designed to generate whole mitochondrial genome (mt-genome) sequencing data from robust DNA samples, such as those obtained from buccal swabs and blood stains. This approach uses a long PCR amplification technique with two overlapping primer sets, covering the entire human mt-genome. Pooled amplicons are prepared with the Nextera XT™ DNA Sample Preparation Kit and rapidly sequenced on the MiSeq system, generating high-throughput sequencing data that can be quickly analyzed using the on-board software as well as third-party software tools. Data quality is sufficient to easily determine the presence of expected polymorphisms in the samples. In addition, the deep sequencing results on carefully prepared mixtures are able to detect the presence of minor variants at the expected positions, providing a heightened level of detection of minor sequence variants. Results from single source and mixed DNA samples underscore the value and sensitivity of Illumina sequencing data, relative to Sanger sequencing, in providing increased resolution of forensic mtDNA samples.

Topic: Forensic Genomics
Genomic Sequencing in the Clinical Laboratory: Lessons Learned and Best Practices

Genome sequencing for clinical use has the potential to reduce diagnostic odysseys, refine diagnostic evaluations, increase our understanding of prognoses, and improve patient care. In order to establish whole-genome sequencing as another tool at the physician's disposal, several components must be carefully developed and evaluated. Among these are physician and patient support, informed consent, secure data management, and, critically, the analytical quality of the data generated for clinical interpretation. As we move towards an era of genomic testing and increase our knowledge of the genome, analytical validity becomes increasingly important. In this webinar we discuss the lessons and best practices learned by the CLIA-certified, CAP-accredited Illumina Clinical Services Laboratory.

Topic: Sequencing : Services
Learn How the Illumina Genome Network (IGN) Has Been Instrumental in Providing Fast, Reliable Whole Human Genome Sequencing Data

Chris Mason describes how he used the Illumina Genome Network (IGN) for low input, whole-genome sequencing of rare clinical cases with extreme phenotypes from the NIH's Undiagnosed Disease Program (UDP) and a consanguineous family with neural-tube defects (NTDs). For all sequenced samples, the IGN data provided high coverage across the genome, including regulatory regions like promoters and enhancers, allowing the research team to pinpoint likely genes for the disease phenotypes. A comparison of output data from IGN software suite (CASAVA/GROUPER) to SAMtools/GATK revealed a high overlap of SNVs and indels between software platforms. The variants specific to each software suite showed higher Ti/Tv ratio. Overall, the results highlight the ease and speed of whole-genome sequencing services for identifying disease phenotypes. The genetic data can be combined with other biological modalities (transcriptional, epigenetic, proteomic) to function as a systems biology approach for personalized medicine.

Topic: Sequencing : Services : Customer
Next-gen sequencing at the touch of a button

Explore how the MiSeq® system can empower your research. As the only fully integrated personal sequencer, MiSeq delivers a streamlined solution that takes you from rapid sample prep through automated data analysis and storage in the BaseSpace™ cloud. Sequencing doesn't get any easier than this.

In this webinar, you'll discover why Miseq is the most accurate and easiest to use benchtop sequencer. Take a tour of the system and learn about:

  • Accomplishments by researchers in your field who are using MiSeq in their labs
  • Updates to our growing applications portfolio
  • Advancements to sequencing's fastest and easiest workflow
  • Recent improvements to our sequencing-by-synthesis chemistry for faster, longer reads, and expanded capability for applications
Topic: Sequencing
Transcriptome analyses in individual cells using Smart-Seq

Methods for global gene expression analysis in individual cells have important applications in biology and medicine. This webinar describes the Smart-Seq protocol for polyA+ RNA analysis, applicable at single-cell levels. Compared to existing methods, the Smart-Seq protocol has improved read coverage across transcripts, significantly enhancing analysis of alternative transcript isoforms and improving SNP identification. The sensitivity and quantitative accuracy of the Smart-Seq method for single-cell transcriptomics have been evaluated with total RNA dilution and spike-in RNAs. This method has been proven using cancer cell lines, circulating tumor cells from melanomas, and early embryonic cells. The Smart-Seq protocol provides a robust method for addressing fundamental biological questions that require transcriptome profiling in rare or single cells.

Topic: Sequencing
Education in a Next-Gen World: Considerations for Whole-Genome Sequencing

The advent of clinically available whole-genome sequencing (WGS) offers an opportunity to educate ourselves and our colleagues about the benefits and challenges of genomic testing. In addition, we need to consider how we can best approach particular audiences, as well as the appropriate level of information to give each audience.

Topic: Sequencing
Outbreak - The Sequel: Using Next-gen Sequencing to Unravel Outbreaks of Infectious Disease

When an infectious disease outbreak occurs, public health officials attempt to identify where it started and how it spread so that they can initiate appropriate control and prevention strategies. Using a combination of field epidemiology (interviewing cases and controls) and molecular epidemiology (genotyping of bacterial or viral pathogens), they attempt to establish links between cases and develop a putative reconstruction of the outbreak. Unfortunately, the low resolution of molecular epidemiology techniques currently available to most reference microbiology laboratories cannot provide detailed information on the underlying transmission dynamics within an outbreak. However, next-generation sequencing offers exciting new possibilities for tracking disease outbreaks with high resolution. Over the course of an outbreak, a small amount of genetic variation accrues in a pathogen's genome as a result of mutations. By tracking the presence or absence of these mutations in all pathogen genomes from a given outbreak, it is possible to identify where particular variants arose and trace person-to-person transmission events. This webinar will provide an introduction to this emerging field of genomic epidemiology, highlighting the application of this approach to reconstruct outbreaks of tuberculosis in British Columbia, Canada.

Topic: Sequencing
Fast Annotation of Human Genomes on the Illumina HiSeq® 2500 System

The HiSeq 2500 System delivers incredible accuracy, throughput, and total workflow turnaround time for high-throughput applications. The simple whole-genome sequencing workflow allows you to quickly go from DNA to annotated variants for interpretation and decision-making. This webinar will highlight the latest system advances:
• New library preparation kits that enable low amounts of DNA input, including FFPE samples
• Improved sequencer performance
• The latest alignment/annotation and interpretation software

Topic: Sequencing
Evolving tools for understanding the functional genome: RNA-Seq and the ENCODE Project

RNA-Seq is a powerful tool for studying various aspects of RNA biology, including expression levels, alternative splicing, RNA editing, and gene discovery. Though RNA-Seq has long been in use, robust and easy methods for generating strand-specific libraries and libraries from total RNA samples have not been commercially available. The new Illumina Tru-Seq Strand-specific Total RNA-Seq kits facilitate the generation of high quality libraries via a simple, rapid, and familiar workflow. I will present modENCODE data generated using these new kits and compare the results to those generated from libraries prepared using previous Illumina RNA-Seq kits and the same RNA samples. Specifically, I will discuss the degree of strandedness, evenness of coverage, and discovery of transcribed regions not identified using poly(A)-selected RNA-Seq libraries.

Topic: Sequencing
Illumina IGN Webinar Series: Webinar Three - Useful Bioinformatics for Characterizing Somatic Mutations of an Oral Cancer Using a Whole-Genome Sequencing Technology

See how expert bioinformaticians have used in-house and open-source tools to re-analyze and further interrogate IGN data. The presentation will describe the computational requirements, walk you through a reanalysis pipeline, and highlight the benefits of working with universal, industry-standard file formats.

Topic: Sequencing
STAT-Seq: Rapid WGS on the HiSeq 2500 - Implications for a Neonatal Intensive Care Unit

Monogenic diseases are frequent causes of neonatal morbidity and mortality. Over 3,500 monogenic diseases have been characterized, many of which feature clinical and genetic heterogeneity. Since disease presentation at birth is often undifferentiated, there is an immense need for molecular diagnosis in infants. Disease progression in newborns is often fast and heterogeneous, so molecular diagnosis must occur rapidly for relevant clinical decision making. Here, we describe 50-hour differential diagnosis of genetic disorders by whole genome sequencing (WGS), featuring substantially automated bioinformatic analysis. This is intended to be a prototype for deployment in neonatal intensive care units.

Topic: Sequencing
How USC Leverages Bioinformatics Technologies For Epigenomics Research

Dr. Benjamin Berman
Sr. Research Associate - Bioinformatics, USC Epigenome Center
Mike Sanders
Genomics Product Manager, GenoLogics Life Sciences Software

Dr. Benjamin Berman will discuss how the USC Epigenome Center is addressing their information management challenges as they plan their transition to Illumina'€™s next generation DNA sequencing platform for The Cancer Genome Atlas project. The Center is closely integrating their Illumina array and sequencing platforms using Genologics Geneus LIMS in a unique manner. Learn how the Center is creatively employing API interfaces with software tools from both Illumina and Genologics in order to accomplish this.

Topic: Diagnostics : Customer