Population Sturcture 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

September 10, 2013

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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SVS 7.7 in Action

November 20, 2012

Welcome to the seventh installment of the most powerful collection of high-performance analytic tools for managing, analyzing, and visualizing complex genomic data. SVS 7.7 includes: improved RNA-Seq Analysis Package for mRNA expression profiling, streamlined DNA-Seq workflows, and more.

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Reproducing a DNA-Seq Discovery: Finding the Causal Variant of a Novel X-Linked Disorder

October 24, 2012

In this webcast, we will analyze clinical samples to demonstrate the bioinformatic workflows and visualization techniques used to reproduce the published findings of "Ogden Syndrome" - a novel X-linked fatal genetic disorder. The analysis will be based on X chromosome exon capture and sequencing. Using SVS, we will incorporate known variant catalogs, variant classification, functional prediction, and family-based filtering to find putative causal variants. Using GenomeBrowse to investigate and confirm the analysis results, we will reproduce the single putative variant finding that was confirmed and published as the causal variant of this disorder.

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GenomeBrowse: A revolutionary visual experience for genomic data

September 12, 2012

Golden Helix GenomeBrowseTM is an evolutionary leap in genome browser technology that combines an attractive and informative visual experience with a robust, performance-driven backend. The marriage of these two equally important components results in a product that makes other genome browsers look like 1980s DOS programs.

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Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data

August 8, 2012

Personalized genomics, using a trio study design (father, mother, and affected child) allows the identification of candidate novel and rare polymorphisms that have the potential to cause disease. In this presentation, Dr. Kenneth Kaufman will demonstrate the analysis of whole-exome DNA sequencing data from a family trio study. Typically, these studies generate ~100,000 variations per trio. In an advanced workflow, a combination of functional and sequence quality control measurements will be used to filter the DNA sequence data to obtain a small number of candidate de Novo, rare-recessively inherited, and compound heterozygous mutations.

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Raise Your Expectations of Agrigenomic Genetic Research Software

July 26, 2012

Improving the value of crops and livestock in today's world requires an in-depth understanding of genetic variation and how it relates to traits of interest. Such understanding starts with high quality data. But it's made possible through powerful analytics. You paid good money for your data. Now you can take advantage of all it has to offer.In this webcast, Dr. Bryce Christensen will introduce SNP & Variation Suite 7 for agricultural genetic research. SVS 7 delivers world-class analytic tools in a user-friendly, yet extraordinarily powerful interface. No more struggling to coerce command-line software – designed exclusively for human genetics – to work for the plant or animal species you're studying. SVS 7 supports a wide-variety of species enabling you to quickly and easily identify variants related to pest and disease resistance, increased feed efficiency, milk production, and more.

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Leveraging Annotation Databases and Bioinformatic Filtering to Effectively Analyze NGS Data

June 26, 2012
Bioinformatics filtering and rare variant analysis are some of the most relevant approaches to taking advantage of the latest in high-throughput sequencing technologies. The capacity to generate data long ago eclipsed the ability to make sense of that data. In this presentation, Daniel Frost, Golden Helix's Field Application Scientist, will leverage the most prevalent annotation databases and the latest Golden Helix technology to demonstrate a straightforward way to visually and statistically understand your data.

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Learning From Our GWAS Mistakes: From experimental design to scientific method

April 19, 2012
Why is bad or non-existent experimental design so prevalent in our field? In this webcast, Dr. Lambert expounds upon the deep systemic problems that plague our field stepping back to look at them from a broader paradigmatic perspective. He discusses real examples of poorly designed experiments showing what should not be done and concludes with practical advice on how to avoid common and costly mistakes in your own research.

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Speeding Up the Hunt for Casual Trait Mutations in Cattle and Other Agrigenomic Species

December 7, 2011
As a Research Geneticist at the USDA-ARS, Dr. Matthew McClure has published several papers on feed efficiency, beef tenderness, and genetic differentiation between breeds using SNP and GWAS studies. His latest work also incorporates next-generation sequencing technologies with an increased focus on the genetic cause of disease in cattle and other animals, including Weaver Syndrome. In this webcast, Dr. McClure will describe his current research in agrigenomics, the technologies and methods he is using to identify causal mutations for Mendelian and complex traits, and how Golden Helix's SNP & Variation Suite has sped up the pace of discovery.

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ASHG Ancillary Event: Effectively Deriving Meaning from DNA Resequencing Variant Analysis

October 13, 2011
In this ancillary event recording, Dr. Christensen demonstrates next-generation DNA sequencing variant analysis including:

  • Starting with sequence variant sites in a family trio and identifying a single gene exhibiting compound heterozygosity of rare damaging variants
  • Filtering large-scale NGS data to damaging rare variants
  • Using collapsing methods to explore associations between rare variants and phenotypes.

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ASHG Ancillary Event: Optimization of Illumina mRNA-Seq Experimental Results and Conversion to a User Friendly Analysis Solution

October 13, 2011
RNA-Seq is becoming the tool of choice for gene expression studies, as it can facilitate the investigation of phenomena beyond the reach of traditional microarrays, such as novel transcripts and isoforms, alternative splice sites, and allele-specific expression. Additionally, it provides greater coverage and higher quality genetic data than microarrays. Golden Helix and Expression Analysis have built an analysis solution in which RNA-seq bioinformatic processes will be performed in a service-based cloud compute environment. This offering will address the obstacles of sequence data by providing cloud-based and integrated desktop analysis tools that are scalable, affordable, and simplified.

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Sequence Variant Analysis with Golden Helix SNP & Variation Suite

September 28, 2011
In this presentation, Dr. Bryce Christensen explores tertiary methods - the "sense-making" part - of next-gen sequencing analysis including: starting with 5.2 M sequence variant sites in a family trio and systematically identifying a single gene exhibiting compound heterozygosity of rare damaging variants; practical workflows for filtering large-scale NGS data to damaging rare variants; and using collapsing methods to explore associations between rare variants and phenotypes.

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Next-Gen Sequencing Workshop: How to Effectively Derive Meaning from DNA Variant Data

August 11, 2011
Learn more about Golden Helix's SNP & Variation Suite (SVS) – a powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale sequence and array-based data. Applications of SVS include candidate gene analysis, genome-wide association, copy number analysis, and next-generation sequencing. This webinar will focus primarily on rare variant analysis for DNA-sequencing.

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First Look at SVS 7.5

August 3, 2011
The fifth installment of SNP & Variation Suite (SVS) 7 fills out the Sequence Analysis Module premiered in version 7.4, giving you more ways to explore and analyze your NGS data to identify variants that matter. The Genome Browser has also received a lot of attention, including two new features for greater plotting control.

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First Look at SVS 7.4

February 2, 2011
With over 30 new features, the fourth installment of SNP & Variation Suite 7 will empower you to explore your data as never before. Analyze rare variants with a new sequence analysis module. Improve your GWAS and CNV results with state-of-the-art workflows. Dramatically increase your productivity. And gain greater insights with the most advanced genome browser. This is just a taste of what you'll discover on your way to more impactful research.

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ASHG 2010: Improving the Power of Your Study with Advanced Genotype Calling, Imputation, and Next-Generation Sequencing

November 4, 2010
The volume of GWAS data is constantly growing. The content of SNP arrays is increasing, consortium efforts are accelerating, public databases are expanding, and we are at the threshold of the sequencing revolution. The increasing amount of data, and especially the increasing ability to identify rare sequence variants, presents a variety of complex problems for statistical analysis and identification of disease susceptibility loci.

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Common Genetic Variants Modulate Nicotinic Alpha5 Receptor mRNA Expression and Risk for Nicotine Dependence

October 27, 2010
CHRNA5, encoding the nicotinic alpha5 subunit, is implicated in nicotine addiction, lung cancer, and chronic obstructive pulmonary disease. Expression of this gene is significantly associated with promoter polymorphisms, but the responsible sequence variants remain uncertain. In this webcast, Ryan Smith and Audrey Papp of Ohio State University will discuss their search for cis-regulatory variants, by measuring allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanning the CHRNA5 locus for regulatory variants.

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IGES 2010: Combining Next-Gen Sequencing and SNP Microarray Data Using Imputation

October 10, 2010
As new sequencing technologies become available, a question has risen: how can we bridge all of the microarray work with next generation sequencing? Dr. Lambert discusses using imputation from the dense genotype calls of the 1,000 Genomes Project to fill that gap and an alternative approach to marry the two.

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CSCDA 2010: Design and Analysis of GWAS using CNVs

August 25, 2010
Incorporating CNVs into genome-wide association studies promises to explain more of the heritability of disease than that accounted for by SNPs alone. This potential goldmine however, has been plagued by myriad of technical and experimental challenges. We examine the most persistent issues in CNV-based GWAS, including: study design, sample quality control, correcting for batch effects and genomics wave, inherited and de novo copy number detection, CNV-based association testing, and rare variant analysis.

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CSCDA 2010: Genotype Calling and Imputation with BEAGLE and BEAGLECALL

August 24, 2010
In this webcast, Dr. Lambert discusses the tools BEAGLECALL (to re-call genotypes) and BEAGLE (for imputation) including their advantages, limitations, when to utilize each, and comparisons to other methods.

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Introducing SVS 7.3

July 28, 2010
The third installment of SVS 7 extends our dedication to a rich, multi-dimensional analytic approach to genetic research, empowering more people than ever to uncover the genetic cause of disease, drug response, and other conditions.

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Achieving Genome-Wide Success Part III: Quality Assurance and Data Prep for SNP and CNV Studies

December 9, 2009
The following recording is from the Golden Helix ancillary event hosted in conjunction with the 2009 American Society of Human Genetics annual meeting. Dr. Lambert examines best practices, pitfalls, and analytic methods learned from over 30 genome-wide SNP, CNV, and eQTL association studies.

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ASHG 2009 Ancillary Event: Achieving Genome-Wide Success from SNPs to CNVs to eQTL

October 22, 2009
The following recording is from the Golden Helix ancillary event hosted in conjunction with the 2009 American Society of Human Genetics annual meeting. Dr. Lambert examines best practices, pitfalls, and analytic methods learned from over 30 genome-wide SNP, CNV, and eQTL association studies.

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Achieving Genome-Wide Success Part II: Study Design in SNP and CNV Studies

October 7, 2009
Part 2 of the Achieving Genome-Wide Success, Dr. Christophe Lambert examines the effects of poor study design in genetic association studies. Strategies and techniques for good study design will also be discussed.

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IGES 2009: Overcoming Data Quality and Copy Number Detection Issues in Genome-Wide CNV Association Studies

October 19, 2009
The following is a recording of Dr. Christophe Lambert's invited talk at the International Genetic Epidemiology Society 2009 Annual Meeting.

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Joint Statistical Meeting 2009 Talk

August 5, 2009
Overcoming data quality and copy number detection issues in genome-wide CNV association studies,

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Achieving Genome-Wide Success Part I

February 18, 2009
Dr. Christophe Lambert examines some of the more persistent challenges he's experienced in SNP and CNV genome-wide association studies, and the novel methods used to overcome them.

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Genome-Wide Association Analysis Reveals Putative Alzheimer's Disease Susceptibility Loci in Addition to APOE

December 2, 2008
Dr. Christoph Lange presents an overview of his most recent research on Alzheimer's Disease with PBAT.

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Introduction to SNP & Variation Suite 7

Dr. Christophe Lambert and John Nord of Golden Helix introduce the new features and capabilities released in SNP & Variation Suite v7.

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Genome Wide SNP and CNV Association Studies Identify Genetic Factors for Lung Cancer

October 28, 2008
Dr. Amos describes the approaches he and his team at The University of Texas have taken in identifying genetic factors influencing the risk for lung cancer development.

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IGES 2008 Talk: Methods and Discoveries Drawn from 20 Whole Genome Copy Number Variation Studies

September 16, 2008
Includes discussion of Wellcome Trust copy number variation association results.

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Emerging Methods in Whole Genome CNV Association

July 23, 2008
Discussion of key strategies, methods and workflows used on over twenty whole genome copy number variation (CNV) association studies.

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On the Replication of Genetic Associations: Timing Can Be Everything

April 15, 2008
Dr. Jessica Lasky Su presents discusses her research and the PBAT methods used to find a whole genome age-dependent association that was replicated in five of eight studies.

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On the Analysis of Copy-Number Variations in Genome-Wide Association Studies: A Translation of the Family-Based Association Test

March 18, 2008
Dr. Christoph Lange presents an overview of his recent work with Dr. Juliana Ionita-Laza on analyzing copy number variations in family-based association studies using PBAT.

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SNP, ROH and CNV Association Analysis Overview with Affymetrix SNP Arrays 5.0 and 6.0

February 7, 2008
An overview of various whole genome methods and workflows for analyzing Affymetrix SNP and copy number data with the SNP & Variation Suite.

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Using Runs of Homozygosity to Identify Recessive Loci

January 24, 2008
Dr. Todd Lencz address the theoretical and statistical underpinnings of whole genome homozygosity association (WGHA) and its potential utility in studies of complex disease.

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Whole Genome Copy Number Association Analysis with Golden Helix

November 14, 2007
A first look at the CNV segmentation and association methods implemented in the Copy Number Analysis Module (CNAM).

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Whole Genome Association Study of Schizophrenia

May 9, 2007
Dr. Todd Lencz presents the analysis and results of his whole genome association study of Schizophrenia.

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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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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

September 10, 2013

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

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.

Access Webcast »

SVS 7.7 in Action

November 20, 2012

Welcome to the seventh installment of the most powerful collection of high-performance analytic tools for managing, analyzing, and visualizing complex genomic data. SVS 7.7 includes: improved RNA-Seq Analysis Package for mRNA expression profiling, streamlined DNA-Seq workflows, and more.

Access Webcast »

Reproducing a DNA-Seq Discovery: Finding the Causal Variant of a Novel X-Linked Disorder

October 24, 2012

In this webcast, we will analyze clinical samples to demonstrate the bioinformatic workflows and visualization techniques used to reproduce the published findings of "Ogden Syndrome" - a novel X-linked fatal genetic disorder. The analysis will be based on X chromosome exon capture and sequencing. Using SVS, we will incorporate known variant catalogs, variant classification, functional prediction, and family-based filtering to find putative causal variants. Using GenomeBrowse to investigate and confirm the analysis results, we will reproduce the single putative variant finding that was confirmed and published as the causal variant of this disorder.

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Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data

August 8, 2012

Personalized genomics, using a trio study design (father, mother, and affected child) allows the identification of candidate novel and rare polymorphisms that have the potential to cause disease. In this presentation, Dr. Kenneth Kaufman will demonstrate the analysis of whole-exome DNA sequencing data from a family trio study. Typically, these studies generate ~100,000 variations per trio. In an advanced workflow, a combination of functional and sequence quality control measurements will be used to filter the DNA sequence data to obtain a small number of candidate de Novo, rare-recessively inherited, and compound heterozygous mutations.

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Raise Your Expectations of Agrigenomic Genetic Research Software

July 26, 2012

Improving the value of crops and livestock in today's world requires an in-depth understanding of genetic variation and how it relates to traits of interest. Such understanding starts with high quality data. But it's made possible through powerful analytics. You paid good money for your data. Now you can take advantage of all it has to offer.In this webcast, Dr. Bryce Christensen will introduce SNP & Variation Suite 7 for agricultural genetic research. SVS 7 delivers world-class analytic tools in a user-friendly, yet extraordinarily powerful interface. No more struggling to coerce command-line software – designed exclusively for human genetics – to work for the plant or animal species you're studying. SVS 7 supports a wide-variety of species enabling you to quickly and easily identify variants related to pest and disease resistance, increased feed efficiency, milk production, and more.

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Leveraging Annotation Databases and Bioinformatic Filtering to Effectively Analyze NGS Data

June 26, 2012
Bioinformatics filtering and rare variant analysis are some of the most relevant approaches to taking advantage of the latest in high-throughput sequencing technologies. The capacity to generate data long ago eclipsed the ability to make sense of that data. In this presentation, Daniel Frost, Golden Helix's Field Application Scientist, will leverage the most prevalent annotation databases and the latest Golden Helix technology to demonstrate a straightforward way to visually and statistically understand your data.

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Learning From Our GWAS Mistakes: From experimental design to scientific method

April 19, 2012
Why is bad or non-existent experimental design so prevalent in our field? In this webcast, Dr. Lambert expounds upon the deep systemic problems that plague our field stepping back to look at them from a broader paradigmatic perspective. He discusses real examples of poorly designed experiments showing what should not be done and concludes with practical advice on how to avoid common and costly mistakes in your own research.

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ASHG Ancillary Event: Effectively Deriving Meaning from DNA Resequencing Variant Analysis

October 13, 2011
In this ancillary event recording, Dr. Christensen demonstrates next-generation DNA sequencing variant analysis including:

  • Starting with sequence variant sites in a family trio and identifying a single gene exhibiting compound heterozygosity of rare damaging variants
  • Filtering large-scale NGS data to damaging rare variants
  • Using collapsing methods to explore associations between rare variants and phenotypes.

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Sequence Variant Analysis with Golden Helix SNP & Variation Suite

September 28, 2011
In this presentation, Dr. Bryce Christensen explores tertiary methods - the "sense-making" part - of next-gen sequencing analysis including: starting with 5.2 M sequence variant sites in a family trio and systematically identifying a single gene exhibiting compound heterozygosity of rare damaging variants; practical workflows for filtering large-scale NGS data to damaging rare variants; and using collapsing methods to explore associations between rare variants and phenotypes.

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Next-Gen Sequencing Workshop: How to Effectively Derive Meaning from DNA Variant Data

August 11, 2011
Learn more about Golden Helix's SNP & Variation Suite (SVS) – a powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale sequence and array-based data. Applications of SVS include candidate gene analysis, genome-wide association, copy number analysis, and next-generation sequencing. This webinar will focus primarily on rare variant analysis for DNA-sequencing.

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First Look at SVS 7.5

August 3, 2011
The fifth installment of SNP & Variation Suite (SVS) 7 fills out the Sequence Analysis Module premiered in version 7.4, giving you more ways to explore and analyze your NGS data to identify variants that matter. The Genome Browser has also received a lot of attention, including two new features for greater plotting control.

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First Look at SVS 7.4

February 2, 2011
With over 30 new features, the fourth installment of SNP & Variation Suite 7 will empower you to explore your data as never before. Analyze rare variants with a new sequence analysis module. Improve your GWAS and CNV results with state-of-the-art workflows. Dramatically increase your productivity. And gain greater insights with the most advanced genome browser. This is just a taste of what you'll discover on your way to more impactful research.

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ASHG 2010: Improving the Power of Your Study with Advanced Genotype Calling, Imputation, and Next-Generation Sequencing

November 4, 2010
The volume of GWAS data is constantly growing. The content of SNP arrays is increasing, consortium efforts are accelerating, public databases are expanding, and we are at the threshold of the sequencing revolution. The increasing amount of data, and especially the increasing ability to identify rare sequence variants, presents a variety of complex problems for statistical analysis and identification of disease susceptibility loci.

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IGES 2010: Combining Next-Gen Sequencing and SNP Microarray Data Using Imputation

October 10, 2010
As new sequencing technologies become available, a question has risen: how can we bridge all of the microarray work with next generation sequencing? Dr. Lambert discusses using imputation from the dense genotype calls of the 1,000 Genomes Project to fill that gap and an alternative approach to marry the two.

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CSCDA 2010: Design and Analysis of GWAS using CNVs

August 25, 2010
Incorporating CNVs into genome-wide association studies promises to explain more of the heritability of disease than that accounted for by SNPs alone. This potential goldmine however, has been plagued by myriad of technical and experimental challenges. We examine the most persistent issues in CNV-based GWAS, including: study design, sample quality control, correcting for batch effects and genomics wave, inherited and de novo copy number detection, CNV-based association testing, and rare variant analysis.

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CSCDA 2010: Genotype Calling and Imputation with BEAGLE and BEAGLECALL

August 24, 2010
In this webcast, Dr. Lambert discusses the tools BEAGLECALL (to re-call genotypes) and BEAGLE (for imputation) including their advantages, limitations, when to utilize each, and comparisons to other methods.

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Introducing SVS 7.3

July 28, 2010
The third installment of SVS 7 extends our dedication to a rich, multi-dimensional analytic approach to genetic research, empowering more people than ever to uncover the genetic cause of disease, drug response, and other conditions.

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Achieving Genome-Wide Success Part III: Quality Assurance and Data Prep for SNP and CNV Studies

December 9, 2009
The following recording is from the Golden Helix ancillary event hosted in conjunction with the 2009 American Society of Human Genetics annual meeting. Dr. Lambert examines best practices, pitfalls, and analytic methods learned from over 30 genome-wide SNP, CNV, and eQTL association studies.

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ASHG 2009 Ancillary Event: Achieving Genome-Wide Success from SNPs to CNVs to eQTL

October 22, 2009
The following recording is from the Golden Helix ancillary event hosted in conjunction with the 2009 American Society of Human Genetics annual meeting. Dr. Lambert examines best practices, pitfalls, and analytic methods learned from over 30 genome-wide SNP, CNV, and eQTL association studies.

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Achieving Genome-Wide Success Part II: Study Design in SNP and CNV Studies

October 7, 2009
Part 2 of the Achieving Genome-Wide Success, Dr. Christophe Lambert examines the effects of poor study design in genetic association studies. Strategies and techniques for good study design will also be discussed.

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IGES 2009: Overcoming Data Quality and Copy Number Detection Issues in Genome-Wide CNV Association Studies

October 19, 2009
The following is a recording of Dr. Christophe Lambert's invited talk at the International Genetic Epidemiology Society 2009 Annual Meeting.

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Joint Statistical Meeting 2009 Talk

August 5, 2009
Overcoming data quality and copy number detection issues in genome-wide CNV association studies,

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Achieving Genome-Wide Success Part I

February 18, 2009
Dr. Christophe Lambert examines some of the more persistent challenges he's experienced in SNP and CNV genome-wide association studies, and the novel methods used to overcome them.

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Introduction to SNP & Variation Suite 7

Dr. Christophe Lambert and John Nord of Golden Helix introduce the new features and capabilities released in SNP & Variation Suite v7.

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IGES 2008 Talk: Methods and Discoveries Drawn from 20 Whole Genome Copy Number Variation Studies

September 16, 2008
Includes discussion of Wellcome Trust copy number variation association results.

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Emerging Methods in Whole Genome CNV Association

July 23, 2008
Discussion of key strategies, methods and workflows used on over twenty whole genome copy number variation (CNV) association studies.

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SNP, ROH and CNV Association Analysis Overview with Affymetrix SNP Arrays 5.0 and 6.0

February 7, 2008
An overview of various whole genome methods and workflows for analyzing Affymetrix SNP and copy number data with the SNP & Variation Suite.

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Whole Genome Copy Number Association Analysis with Golden Helix

November 14, 2007
A first look at the CNV segmentation and association methods implemented in the Copy Number Analysis Module (CNAM).

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Population Sturcture 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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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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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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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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Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data

August 8, 2012

Personalized genomics, using a trio study design (father, mother, and affected child) allows the identification of candidate novel and rare polymorphisms that have the potential to cause disease. In this presentation, Dr. Kenneth Kaufman will demonstrate the analysis of whole-exome DNA sequencing data from a family trio study. Typically, these studies generate ~100,000 variations per trio. In an advanced workflow, a combination of functional and sequence quality control measurements will be used to filter the DNA sequence data to obtain a small number of candidate de Novo, rare-recessively inherited, and compound heterozygous mutations.

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Speeding Up the Hunt for Casual Trait Mutations in Cattle and Other Agrigenomic Species

December 7, 2011
As a Research Geneticist at the USDA-ARS, Dr. Matthew McClure has published several papers on feed efficiency, beef tenderness, and genetic differentiation between breeds using SNP and GWAS studies. His latest work also incorporates next-generation sequencing technologies with an increased focus on the genetic cause of disease in cattle and other animals, including Weaver Syndrome. In this webcast, Dr. McClure will describe his current research in agrigenomics, the technologies and methods he is using to identify causal mutations for Mendelian and complex traits, and how Golden Helix's SNP & Variation Suite has sped up the pace of discovery.

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Common Genetic Variants Modulate Nicotinic Alpha5 Receptor mRNA Expression and Risk for Nicotine Dependence

October 27, 2010
CHRNA5, encoding the nicotinic alpha5 subunit, is implicated in nicotine addiction, lung cancer, and chronic obstructive pulmonary disease. Expression of this gene is significantly associated with promoter polymorphisms, but the responsible sequence variants remain uncertain. In this webcast, Ryan Smith and Audrey Papp of Ohio State University will discuss their search for cis-regulatory variants, by measuring allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanning the CHRNA5 locus for regulatory variants.

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Genome-Wide Association Analysis Reveals Putative Alzheimer's Disease Susceptibility Loci in Addition to APOE

December 2, 2008
Dr. Christoph Lange presents an overview of his most recent research on Alzheimer's Disease with PBAT.

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Genome Wide SNP and CNV Association Studies Identify Genetic Factors for Lung Cancer

October 28, 2008
Dr. Amos describes the approaches he and his team at The University of Texas have taken in identifying genetic factors influencing the risk for lung cancer development.

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On the Analysis of Copy-Number Variations in Genome-Wide Association Studies: A Translation of the Family-Based Association Test

March 18, 2008
Dr. Christoph Lange presents an overview of his recent work with Dr. Juliana Ionita-Laza on analyzing copy number variations in family-based association studies using PBAT.

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On the Replication of Genetic Associations: Timing Can Be Everything

April 15, 2008
Dr. Jessica Lasky Su presents discusses her research and the PBAT methods used to find a whole genome age-dependent association that was replicated in five of eight studies.

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Using Runs of Homozygosity to Identify Recessive Loci

January 24, 2008
Dr. Todd Lencz address the theoretical and statistical underpinnings of whole genome homozygosity association (WGHA) and its potential utility in studies of complex disease.

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Whole Genome Association Study of Schizophrenia

May 9, 2007
Dr. Todd Lencz presents the analysis and results of his whole genome association study of Schizophrenia.

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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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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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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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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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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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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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@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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Reproducing a DNA-Seq Discovery: Finding the Causal Variant of a Novel X-Linked Disorder

October 24, 2012

In this webcast, we will analyze clinical samples to demonstrate the bioinformatic workflows and visualization techniques used to reproduce the published findings of "Ogden Syndrome" - a novel X-linked fatal genetic disorder. The analysis will be based on X chromosome exon capture and sequencing. Using SVS, we will incorporate known variant catalogs, variant classification, functional prediction, and family-based filtering to find putative causal variants. Using GenomeBrowse to investigate and confirm the analysis results, we will reproduce the single putative variant finding that was confirmed and published as the causal variant of this disorder.

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GenomeBrowse: A revolutionary visual experience for genomic data

September 12, 2012

Golden Helix GenomeBrowseTM is an evolutionary leap in genome browser technology that combines an attractive and informative visual experience with a robust, performance-driven backend. The marriage of these two equally important components results in a product that makes other genome browsers look like 1980s DOS programs.

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Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data

August 8, 2012

Personalized genomics, using a trio study design (father, mother, and affected child) allows the identification of candidate novel and rare polymorphisms that have the potential to cause disease. In this presentation, Dr. Kenneth Kaufman will demonstrate the analysis of whole-exome DNA sequencing data from a family trio study. Typically, these studies generate ~100,000 variations per trio. In an advanced workflow, a combination of functional and sequence quality control measurements will be used to filter the DNA sequence data to obtain a small number of candidate de Novo, rare-recessively inherited, and compound heterozygous mutations. In addition, Dr. Kaufman will demonstrate how to use Golden Helix's latest tool, GenomeBrowse and sequencing BAM files to decrease the number of false positive candidate polymorphisms.

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ASHG Ancillary Event: Optimization of Illumina mRNA-Seq Experimental Results and Conversion to a User Friendly Analysis Solution

October 13, 2011
RNA-Seq is becoming the tool of choice for gene expression studies, as it can facilitate the investigation of phenomena beyond the reach of traditional microarrays, such as novel transcripts and isoforms, alternative splice sites, and allele-specific expression. Additionally, it provides greater coverage and higher quality genetic data than microarrays. Golden Helix and Expression Analysis have built an analysis solution in which RNA-seq bioinformatic processes will be performed in a service-based cloud compute environment. This offering will address the obstacles of sequence data by providing cloud-based and integrated desktop analysis tools that are scalable, affordable, and simplified.

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