Current Golden Helix Webcasts

Using Clinical Reports as a part of a Gene Panel Pipeline

July 13, 2016

VarSeq Reports can be used as part of an automatic pipeline to quickly list variants with information that can be used to make actionable clinical decisions in a readable HTML format. Need to further filter the variants or add interpretation and recommendations? No problem! Clinical reports are easy to review, edit and prepare. 

This webcast will walk through preparing a template for automatic report generation, running new data through the pipeline and reviewing the generated report.

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Using WES in Distant Relationships to Identify Cardiomyopathy Genes

June 8, 2016

Using WES in distant relationships to identify cardiomyopathy genes Cardiomyopathy (DCM; MIM 115200) are myocardial diseases that are frequently hereditary, yet remain gene-elusive for 60% of affected families. Traditional gene discovery techniques dependent on multigenerational samples are difficult to apply. This is because 1. Disease is often impenetrant in the youngest generation, 2. Samples are often not available in the oldest generation and 3. Incomplete penetrance and variable expressivity are common across all generations. However, a detailed family history will often identify definitively affected but distantly related individuals. Such families are highly powered for gene discovery using whole exome sequencing (WES) and analysis in SNP and Variation Suite (SVS) software.

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Custom Family Workflows

May 11, 2016

VarSeq contains default workflows for Trio analysis which include filter chains for identifying de Novo and Compound Heterozygous variants, but what if you have data for a full Quad or even just a few siblings? How could your VarSeq workflow be adjusted to handle this custom family structure?

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Pharmacogenomic Prediction of Antracycline-induced Cardiotoxicity

April 20, 2016

The Canadian Pharmacogenomics Network for Drug Safety (CPNDS), recently discovered a novel gene (RARG) responsible for cardiomyopathy and congestive heart failure in cancer survivors and has developed clinical practice recommendations for genetic testing to reduce the incidence of anthracycline-induced cardiotoxicity in children after cancer treatment.

Join us as Dr. Folefac Aminkeng, presents the CPNDS’ important research efforts focused on understanding the role of genes in ADRs and developing drug safety solutions for cancer patients, initiatives which are critical to improving long-term survival outcomes.

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Getting Started with VSWarehouse - The User Experience

April 6, 2016

As the number of samples and associated data volume in a testing lab increases, it becomes imperative for labs to leverage state of the art warehousing technology that not only organizes data, but also aides and enables researchers and clinicians to perform further analysis, and ongoing research.

Built on the algorithms and high-performance storage technology that powers the VarSeq software, VSWarehouse offers a scalable, multi-project warehouse for NGS variant call sets, clinical reports, and a knowledge base of variant classifications.

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Cancer Workflows in VarSeq

March 2, 2016

Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go from an unfiltered variant file created by a secondary analysis pipeline to a report containing information about interesting variants.

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Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeq

February 3, 2016

As Precision Medicine is taking off, the number of samples in a testing lab and the associated data volume is increasing exponentially. In order to organize the data and build a knowledge base of cases that can be used for future analysis as well as ongoing research, labs need to leverage state of the art warehousing technology.

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A Walk Through GWAS

January 20, 2016

Genome-wide association studies (GWAS) have been providing valuable insight to the genetics of common and complex diseases for many years. In this webcast we will walk through one possible workflow for completing GWAS in Golden Helix SNP & Variation Suite (SVS) with special attention paid to adjusting analysis for population stratification.

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Two Clinical Workflows - From Unfiltered Variants to a Clinical Report

November 4, 2015

Clinical labs need to be able to process samples down to a short list of variants and publish a professional report. Two common clinical applications for genetic tests include Cancer Gene Panels and Whole Exome Trios. Using VarSeq and VSReports, we will demonstrate how easy it is to go from a variant file created by a secondary analysis pipeline containing unfiltered variants to a report containing information for variants of interest. Along the way we will discuss tips and tricks and answer frequently asked questions to help you get the most out of your data!

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SETBP1 as a novel candidate gene for neurodevelopmental disorders of speech and language

October 14, 2015

The genetic etiology of neurodevelopmental disorders has proven elusive due to the substantial phenotypic and etiological heterogeneity of their common forms. Developmental language disorders affect approximately 7% of children and are associated with negative outcomes in a multitude of domains, including social, emotional, behavioral, and academic functioning. Yet, with the exception of several reported monogenic cases, they are severely understudied with respect to their genetic bases, as the field is effectively only entering its 'GWAS era'.

One of the possible solutions is to reduce the supposed phenotypic and locus heterogeneity by studying special populations such as genetic isolates. Taking this approach, Dr. Sergey Kornilov and Dr. Elena Grigorenko's team at Yale University performed a genome-wide association and whole exome sequencing study of members of a unique geographic Russian-speaking isolate, characterized by an unusually high prevalence (i.e., around 30%) of neurodevelopmental disorders of speech and language.

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Authoring Clinical Reports in VarSeq

September 23, 2015

As labs move genetic tests into production using VarSeq, we have been looking for ways to support more of their total workflow within the same integrated expertise used to annotate, filter and interpret variants. With our upcoming release of VarSeq, we are introducing a powerful and flexible platform to author clinical reports, specialized to the needs of individual labs and tests.

This webcast shows the new VarSeq Reports add-on feature, as well as other components of the total clinical test workflow.

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Uncovering novel candidate genes for pyridoxine-responsive epilepsy in a consanguineous family

September 9, 2015

Currently, ALDH7A1 is the only gene for which mutations are known to underlie PDE. However, locus heterogeneity has been reported in some families and other genes seem to be involved. Nearly 5% of children with a typical clinical picture of PDE harbor no detectable mutation of ALDH7A1. Identifying causative genes in such families will likely lead to improved treatment for these patients and help unravel much of the unknown about pyridoxine metabolism in the human body.

In this webinar, Hilal will cover how he and his team used whole-genome SNP genotyping, genome-wide runs of homozygosity (RoH) mapping using SVS, and whole-exome sequencing to characterize the genetic defect underlying PREE in a consanguineous Omani Arab family with two affected children who have a PDE-like clinical picture but negative ATQ biomarkers.

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Pharmacological Induction of FoxO3 is a Potential Treatment for Sickle Cell Disease

August 12, 2015

Although individuals with sickle cell anemia ostensibly have a monogenetic disease, they exhibit wide variability in the degree of clinical severity. One of the most powerful and reproducible predictors of disease severity is the level of endogenous fetal hemoglobin (HbF), composed of two gamma-globin and two α-globin chains. Expression of HbF is reduced in infancy and little is known about how this regulation is accomplished. A better understanding of gamma-globin regulation could aid in the discovery and design of a specific gamma-globin inducing agent.

Taking a genomics approach to this question, Dr. Vivien Sheehan and her team investigated the natural human variation and its correlation with HbF levels to identify novel genes important for gamma-globin regulation. In this webinar, she describes how they performed whole exome sequencing (WES) and used gene-based analysis to find correlations between rare variants and endogenous HbF levels.

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Genomic Analyses for Palatability of Beef

July 8, 2015

Dr. Raluca Mateescu does research in the area of beef cattle, sheep and goat molecular genetics. Most biological traits of economic importance in domestic animals have a complex inheritance (are influenced by many genes and the environment) and the long-term research goal is to unravel the genetic basis for the phenotypic variability in this type of trait. Her research uses recent advances in the animal genomics field with the goal of improving animal production efficiency and enhancing animal products for improved human health.

In this webinar Dr. Mateescu will focus on use of SVS program to perform genome-wide association studies for individual traits describing beef palatability, identify chromosomal regions associated with these traits, estimate genomic breeding values and predict the accuracy of GEBV for palatability traits in beef.

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Using VarSeq to Improve Variant Analysis Research Workflows

June 10, 2015

Many questions must be answered when analyzing DNA sequence variants: How do I determine which variants are potentially deleterious? Is the sequencing quality sufficient? How do I prioritize the results? Which annotation sources may help answer my research question?

In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.

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Prediction and Meta-Analysis

May 13, 2015

We are excited to announce and demonstrate some new and highly requested features in this webcast, including predicting phenotypes by applying existing GBLUP or Bayesian models and meta-analysis for GWAS studies.

Recently in SVS we added additional genomic prediction tools such as Bayesian Genomic Prediction and K-Fold Cross Validation. We have continued to build out the prediction suite of tools by adding the ability to apply the results of a model to a new genomic dataset to predict the phenotype. This is designed to work hand-in-hand with the output of K-Fold cross-validation using either GBLUP or Bayes C/C-pi.

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VarSeq as a Clinical NGS Platform

April 15, 2015

The power of VarSeq's project-based repeatable workflows has already been adopted by clinical labs such as NorthShore University HealthSystem and Prevention Genetics, and we continue to build features to support the compliance and data privacy requirements of a clinical environment. This webcast highlights some of our new features for supporting gene panel screenings and rare variant diagnostics.

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The Molecular Sciences Made Personal

March 25, 2015

The premedical competencies as outlined in a recent American Association of Medical Colleges (AAMC)-HHMI report on Scientific Foundation for Future Physicians calls for stronger connections between course content and the underlying principles in health and medicine. To meet this need, I am developing chemistry courses at the University of Illinois for pre-health professionals that teach concepts and content in a personally meaningful way, thereby stimulating deep student interest and promoting curiosity-driven learning. Scientific evidence shows that people who feel curious devote more attention to an activity, process information more critically, remember information more effectively and persist on task until goals are met.

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Cancer Gene Panels

March 11, 2015

Cancer is a leading cause of death in developed countries. In this webcast Dr. Andreas Scherer will explain how personalized medicine can transform our approach to fighting this disease. He will also discuss current roadblocks and diagnostic challenges, and the pivotal role of Next Gen Sequencing to overcome these challenges.

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Getting More from GWAS

February 11, 2015

It is often possible to gain additional insights into your GWAS data by looking beyond individual SNP associations to consider more complex genetic features, such as haplotypes or homozygous segments. Some haplotypes may have stronger trait associations than are observed for the constituent SNPs. Analyzing runs of homozygosity (ROH) may reveal associations with recessive haplotypes or identify loci with multiple associated alleles.

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Population-Based DNA Variant Analysis

January 21, 2015

Many of today's researchers are generating DNA sequence data for large numbers of samples in population-based experiments. This may include whole genomes, exomes, or targeted regions. The Golden Helix SNP and Variation Suite (SVS) provides a powerful computing environment for analyzing these data and performing association tests at the gene and/or variant level.

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Genomic Prediction with Golden Helix SNP & Variation Suite

December 16, 2014

Predicting phenotypic traits from genotypes is a key focus in agrigenomics, as researchers work to increase crop yields and meat production to satisfy the needs of a growing population. Genomic prediction allows these scientists to identify the plants or animals with the best breeding potential for desirable traits without having to endure lengthy and expensive field trials.

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Getting Started with Golden Helix VarSeq: The VarSeq User Experience

November 5, 2014

Golden Helix recently announced the forthcoming public release of VarSeq, a powerful new application for interpretation of DNA sequence variants. VarSeq is designed to make variant analysis workflows fast, simple, interactive, and repeatable.

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Introducing VarSeq: Variant Discovery & Gene Panels Made Easy

October 1, 2014

We introduce to you: VarSeq! VarSeq is a next generation tool designed around a focused and intuitive user interface for analyzing Next Generation Sequencing data, powered with the same mature Golden Helix core technology for data management, annotation, and visualization.

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RNA-Seq Functionality in SVS Using Public Data

September 23, 2014

RNA-Seq analysis is the newest area of functionality in the Golden Helix SNP and Variation Suite (SVS) software. SVS offers a wide range of tools for analyzing and visualizing RNA-Seq data, with a particular focus on differential expression analysis. In this presentation, we will demonstrate some of these options using a mouse dataset downloaded from Gene Expression Omnibus (GEO) as a case study, including available functions for data summaries and quality checks, data visualization including heat maps, interactive visualization in GenomeBrowse, and statistical methods for differential expression analysis, including DESeq.

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Using Genomic Prediction for Trait Optimization

August 26, 2014

This webcast will discuss the benefits of genomic prediction for trait optimization, how to set up training and validation datasets, cover the highlights of the GBLUP method, and demonstrate genomic prediction and training/validation using GBLUP in Golden Helix's SNP and Variation Suite (SVS) software. We will use two datasets for the demonstration portion of the webcast, one plant dataset and one animal dataset.

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Tips and Tricks for Genomic Analysis

August 6, 2014

In this webcast, Ashley Hintz, Field Application Scientist, will address some common topics fielded by our support team. Topics include working with custom genomes, making collated spreadsheets, and activating/inactivating data.

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Population Structure and Genetic Improvement in Livestock

July 22, 2014

The genetic improvement of livestock has been a hot topic for almost a century, bringing together researchers, industry, and producers to work towards a common goal. Many countries currently employ extensive genetic selection programs in their cattle with pigs, sheep, and chicken close behind. In this webcast, Heather J. Huson, Ph.D. from Cornell University will focus on population dynamics and trait association in cattle and goats using high density SNP datasets.

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GWAS in a model organism: Arabidopsis thaliana

July 9, 2014

GWA studies are perhaps most often used for studying the genetic basis of human diseases, but this technology also has great utility for studying the natural variation of other organisms. In this webcast, Ashley Hintz, Field Application Scientist, will discuss the utility of SVS for analyzing plant GWA data, using publicly available SNP data for Arabidopsis thaliana as a case study. Along the way, Ashley will demonstrate how SVS can be used to manage data, analyze population structure, perform genotype QA and ultimately replicate a published genetic association in A. thaliana using EMMAX regression. She will also address the flexibility of SVS for analyzing the genomes of other plant and animal species.

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MM-KBAC – Using Mixed Models to Adjust for Population Structure in a Rare-variant Burden Test

June 10, 2014

Confounding from population structure, extended families and inbreeding can be a significant issue for burden and kernel association tests on rare variants from next generation DNA sequencing. An obvious solution is to combine the power of a mixed model regression analysis with the ability to assess the rare variant burden using methods such as KBAC or CMC. Recent approaches have adjusted burden and kernel tests using linear regression models; this method adjusts for the relatedness of samples and includes that directly into a logistic regression model.

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Examining the Genetic Underpinnings of Commonly Comorbid Language Disorders: Dyslexia and Language Impairment

May 13, 2014

Written and verbal language are vital to the development of communication skills. Unfortunately, disorders of these traits—specifically reading disability (RD) and language impairment (LI)—are common, leaving affected individuals at risk for adverse academic, socioeconomic, and psychiatric outcomes. RD and LI are complex traits that frequently co-occur, leading to the hypothesis that these disorders share genetic contributors.

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Under the Hood of Alignment Algorithms for NGS Researchers

April 16, 2014

Most NGS analysis is founded on a very simple and powerful principle: look only at the differences of your data to a reference genome of your species. Alignment algorithms are the workhorse of this approach and accounts for the vast majority of the compute time necessary in a secondary analysis workflow. In this webcast, Gabe Rudy covers the history of alignment algorithms of short read, high-throughput sequencing data and the set of tools that represent the state of the art.

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Introducing SNP & Variation Suite 8

March 11, 2014

SNP & Variation Suite (SVS) is an integrated collection of powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data. Applications include next-generation sequencing studies (DNA/RNA), genome-wide association, and copy number analysis. Golden Helix introduces a major upgrade to the product used by hundreds of organizations around the world to accelerate their research.

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Using Public Access Clinical Databases to Interpret NGS Variants

February 19, 2014

In this webcast, Gabe Rudy, Vice President of Product Development, will showcase publicly available databases and resources available for interpreting rare and novel mutations in the context of his own personal exome obtained through a limited 23andMe pilot in 2012. The last couple years have seen many changes in well-established resources such as OMIM and dbSNP, while motivating new efforts such as ClinVar and PhenoDB to bring NGS interpretation to clinical grade through a global data sharing effort.

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Maximizing Public Data Sources for Sequencing and GWAS Studies

February 4, 2014

In this webcast, Dr. Christensen will cover: options for getting GWAS and sequence information online without any associated cost, tips for working with these datasets and what you'll see in terms of data quality and usefulness, how to use public data sources in conjunction with your GWAS or sequence study (and how NOT to), and data management and manipulation features in SNP & Variation Suite to more effectively utilize online databases.

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Advancing Agrigenomic Discoveries with Sequencing and GWAS Research

January 8, 2014

In this webcast, Greta Linse Peterson will present updated workflows in SNP & Variation Suite 8 (SVS) and GenomeBrowse for agricultural genetic research. SVS includes a robust suite of analytical tools and a revolutionary genome browser in one program to support a wide-variety of species including plant, animal, and parasites. New tools make it easy to adjust for inbreeding and incomplete pedigrees, making it even easier than before to identify variants related to pest and disease resistance, increased feed efficiency, milk production, and more.

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Back to Basics: Using GWAS to Drive Discovery for Complex Diseases

December 11, 2013

Genome-wide association studies (GWAS) have been providing valuable insight to the genetics of common and complex diseases for nearly 10 years. Despite some assertions to the contrary, GWAS is not dead. GWAS is alive and well, and remains a viable technology for genetic discovery. This webcast covers: GWAS data formats, usability, and data management techniques, imputation, quality assurance, genotype association testing and statistics, and visualization. Along the way, Dr. Christensen highlights best practice approaches and common pitfalls to avoid.

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Rare Variant Analysis Workflows: Approaches to Analyzing NGS Data in Large Cohorts

November 13, 2013

Analysis of rare variants for population-level data is becoming a more common component of genomic research. Whether using exome chips, whole-exome sequencing, or even whole-genome sequencing, rare variation analysis requires a unique analytic perspective. In this presentation, we will review some of the tools available in SVS for large sequenced cohorts including summarization, visualization, and statistical analysis of rare variants using KBAC, CMC, and other methods.

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Performing Small-N Sequencing Workflows: Approaches to Analyzing Trio NGS Data

October 30, 2013

Researchers who are new to NGS data analysis will learn techniques commonly utilized in small-N sequencing workflows whereas experienced SVS users will discover more streamlined or "one-off" solutions to complement their advanced processes. The workflow for small-N trio data will cover three main aspects: data preparation, initial investigation, and variant analysis. To effectively showcase this workflow, Autumn will also highlight the online SVS Scripts Repository, which is home to several well-tested and high-quality tools that can become part of your analytic toolbox.

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Making NGS Data Analysis Clinically Practical: Repeatable and Time-Effective Workflows

Repeating a workflow that involves several different quality control, filtering, and analysis steps is burdensome and error-prone. To solve this problem, we introduce custom workflow automation in SVS, which allows you to collapse dozens of steps into a few run-specific options. This click-and-go process saves an exponential amount of time while eliminating the inevitable user error that happens with tedious repetition and ensures that the exact same protocol is followed with each run, a critical requirement for use in the clinic.

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Exploring DNA/RNA-Seq Analysis Results with Golden Helix GenomeBrowse and SVS

July 24, 2013

This webcast will demonstrate the ability of GenomeBrowse to stream sequence alignment data from the Amazon Cloud, seamlessly transitioning between whole genome views and base-pair resolution in the context of both public and custom annotation tracks. We will show how GenomeBrowse can be used in conjunction with SVS to highlight false variant calls, confirm the inheritance pattern of putative functional variants, and aid in the interpretation of a variant's impact. Examples of RNA-seq expression analysis, somatic variation in cancer, and family-based DNA-seq analysis will be included.

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Mixed Models: How to Effectively Account for Inbreeding and Population Structure in GWAS

June 5, 2013

This presentation will review four different methods of analyzing genotype data while accounting for random effects of relatedness. Methods include PCA analysis with Linear Regression, GBLUP, EMMAX, and MLMM. Comparisons will be made using data from the Sheep HapMap project and a simulated phenotype. After presenting the various methods, we will discuss how these results can be obtained using Golden Helix SNP & Variation Suite (SVS) software and how SVS can be used to compare and contrast the results.

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Knowing Your NGS Downstream: Functional Predictions

May 15, 2013

This presentation will review several of the functional prediction tools that are currently available to help researchers determine the functional consequences of genetic alterations. The biological principals underlying functional predictions will be discussed together with an overview of the methodology used by each of the predictive algorithms. Finally, we will discuss how these predictions can be accessed and used within the Golden Helix SNP & Variation Suite (SVS) software.

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Knowing Your NGS Upstream: Alignment and Variants

March 27, 2013

This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.

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Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics

March 7, 2013

Technological advances in next generation sequencing provide clinicians and researchers with more effective methods to identify pathogenic gene mutations for heritable diseases. To date, the National Eye Institute Bank lists over 450 genes associated with eye-related disorders. Analytical processing of large datasets generated can be cumbersome for all parties involved and some issues that can cause inefficiencies include learning programming languages and reliance on inconsistent freeware. In this webcast, we demonstrate the ability to maximize Golden Helix tools to find potential pathogenic variants in rare ocular diseases.

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AGBT 2013: Home Brewed Personalized Genomics - The Quest for Meaningful Analysis Results of a 23andMe Exome Pilot Trio of Myself, Wife, and Son

February 22, 2013

Personalized genomics may be moving into a new era with whole-exome and whole-genome sequencing becoming affordable and available to consumers. 23andMe recently piloted a more affordable 80x exome to their existing customers. But it remains to be seen whether this wealth of raw genomic data can be analyzed to provide meaningful results for both healthy and symptomatic individuals. By acquiring 23andMe exomes on his own family, Gabe put himself in the position of a bioinformatically inclined consumer, but non-clinician, to approach this question with his own analysis. His trio consists of a healthy father and son, and a mother with clinically-diagnosed idiopathic rheumatoid arthritis.

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New Study Identifies High-Risk Variants Associated with Autism Spectrum Disorders

January 29, 2013

Since 2002, Lineagen has been building the largest proprietary collection of ASD-related genetic variants and, in 2011, spearheaded a study to increase the clinical yield of the company's genetic diagnostic test, FirstStepDx. To find candidate variants, Linegean selected the Golden Helix services team as well as the Children's Hospital of Philadelphia Center for Applied Genomics to concurrently perform quality control, analyze the data, and interpret the results. In this webcast, Dr. Hakonarson, Dr. Leppert, Dr. Paul, and Dr. Hensel outline the study and methodology approach utilized by Lineagen to achieve a two-fold increase in detection rate of genetic variants in individuals with ASD, and Dr. Christensen shares the analytic processes Golden Helix used in this valuable research.

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@gabeinformatics: 23andMe Variant Analysis of My Personal Exome

December 5, 2012

Join Gabe Rudy as he explores his personal exome provided by the Exome Pilot project of 23andMe. Gabe will be acting as an asymptomatic consumer enthusiast as he applies the transparent techniques of high-impact variant discovery using SNP & Variation Suite (SVS) and GenomeBrowse. As he weeds out false positives and genes with low functional significance, Gabe will face the more daunting challenge of interpreting highly credible loss of function or missense variants and what if any impact that would infer to his disease risk, pharmacogenomic profile, or other annotated genomic traits.

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For additional information about webcasts, please email info@goldenhelix.com or call 1.888.589.4629.