VS-CNV Annotations from the User's Perspective
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Next-generation sequencing has enabled clinicians and researchers alike to identify novel genetic variants associated with rare Mendelian Diseases across the human genome. To help enable researchers and clinicians understand the role of CNVs in human health and disease, Golden Helix has a fully integrated CNV annotations to provide clinicians and researchers with more effective methods to identify pathogenic CNVs for heritable diseases. In this webcast, we will present our comprehensive clinical workflows that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
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CRISPR-Cas9 is a powerful gene editing tool that has promising applications in public health. It allows targeted editing of genes and could help treat diseases like HIV/AIDS, cancer, and antibiotic resistance. However, there are also ethical concerns about its use, such as off-target effects and questions around human enhancement. Going forward, CRISPR holds potential for developing new therapies and improving agriculture, but its applications will require addressing safety, consent, and access issues.
How giab fits in the rest of the world seqc2 tumor normal
This document describes a bioinformatics workflow to annotate somatic mutations with four confidence levels. It involved analyzing variants called from 63 pairs of tumor-normal BAM files from 21 replicates across 6 institutions. Variants were classified using SomaticSeq and classifications were consistent across sequencing replicates and aligners. The confidence levels and variant allele frequencies were broken down, and VAF peaks corresponded to copy number states while shifts corresponded to copy number changes. A subset of calls were validated using AmpliSeq and Ion Torrent sequencing, and limitations included unmappable regions, very low VAF variants, and complex variants. The workflow resulted in a comprehensive somatic mutation call set across the genome down to ~5% VAF.
CRISPR/Cas9 Platform
As a leading provider of gene editing service, Creative Biogene has launched a powerful CRISPR/Cas9 Platform. Our platform performs gene knockout/knockin programme with CRISPR/Cas9 system, from designing gRNA constructs to transfection and single clone generation of a wide range of cells, including difficult-to-transfect and tumor cell lines, as well as plants, mouse and other animal models.
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Analyzing Fusion Genes Using Next-Generation Sequencing
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How giab fits in the rest of the world seqc2 tumor normal
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Similar to VS-CNV Annotations from the User's Perspective
Golden Helix's End-to-End Solution for Clinical Labs
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
Comprehensive Clinical Workflows for Copy Number Variants in VarSeq
While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
Golden Helix has developed and validated with our clinical partners a specialized NGS-based CNV caller capable of detecting deletion and duplication events as small as single-exons and as large as whole chromosome aneuploidy events.
As this capability is applied to large panels and exomes with many putative CNVs per sample, it is important to distinguish between rare and common CNV regions as well as pull in clinical assessments done on similar CNVs that match the clinical phenotype under test.
Enjoy this webcast recording where we review the expanded capabilities of CNV analysis in VarSeq including how to:
Annotate CNV against genes, population catalogs, and clinical sources
Automate the prioritizing of CNVs in your test-specific workflows with customized annotation and filtering steps
Interpret CNVs in your samples in conjunction with NGS variants with both visual and algorithm support
Capture the expert curation of variants in your labs in a CNV based Assessment Catalog
Expand your clinical reports with annotated and interpreted CNVs alongside your existing NGS variants
Centralize your knowledge-base in VSWarehouse for both variants and CNVs
We hope you enjoy this as we review and demonstrate the comprehensive support for CNVs in VarSeq and how these concepts apply to your clinical genetic tests.
Cancer Workflows in VarSeq
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.
Cancer Workflows in VarSeq
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.
This webcast will highlight VarSeq's support for Cancer Gene Panels and Tumor-Normal workflows by demonstrating:
• Variant, Region and Sample Quality Assurance
• Filtering to variants in targeted cancer genes relevant to the tumor type
• Summarizing variants in a clinical report
Annotating and Cataloging CNVs in VarSeq
Golden Helix offers software solutions for analyzing copy number variations (CNVs) detected from next-generation sequencing (NGS) data. Their VarSeq software uses normalization, reference samples, and probabilistic modeling to call CNVs from gene panels, exomes, and whole genomes. It flags low quality CNV calls and samples based on coverage and variability. VarSeq annotates CNVs by comparing to public databases and applying the Jaccard index metric to determine similarity between regions. Golden Helix will demonstrate VarSeq at the AMP conference in November 2018.
An Exploration of Clinical Workflows in VarSeq
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
Performing a Trio Analysis in VSClinical
We recently have exposed the powerful application of our newly released product, VSClinical and the included ACMG Guidelines. Our previous webcasts covered some basics on new algorithms and annotations behind the variant scoring and classification. Taking a step back for a moment, there are many long-time VarSeq users are familiar with our Trio template that comes packaged with the software. But, how does the Trio analysis fit into VSClinical?
In this webcast, we are going to explore some modifications to our baseline trio template showing how to incorporate the ACMG classification results into the various workflows. This will include capturing de novo, compound heterozygous, and dominant heterozygous variants. We will score criteria related to variant frequency, gene impact, and available study information. Additionally, we will also investigate the clinical section of the ACMG guideline tool to see how to leverage the inheritance and allelic state of each variant. After this webcast, the user will discover new avenues of examining trio data by utilizing the ACMG classifier to improve upon one of our classic templates.
Annotation capabilities
VarSeq provides powerful annotation capabilities for variant analysis including gene tracks, assemblies, variant functions, frequency tracks, functional predictions, and transcript annotations. It integrates information from over 20 public databases and sources and updates annotations monthly to provide the most current clinically relevant information for researchers. By centralizing variant annotations from disparate sources, VarSeq saves customers significant time and resources compared to manual curation of this data.
Clinical Reporting Made Easy
This webcast will walk through preparing a template for report generation, reviewing the generated report and performing some report customizations.
Clinical Reporting Made Easy
Clinical labs need to be able to process samples down to a shortlist of variants and publish a professional report. VSReports helps scientists and clinicians alike create timely, actionable reports that can improve clinical decision making and streamline patient care by seamlessly incorporating the results of tertiary analysis into a customizable clinical report.
Reports are fully customizable, containing focused and actionable data. Additionally, reports can be branded and styled to match the documents that your lab typically produces. With tight integration to your analysis results, you can also pull in additional annotation sources relevant to the sample being tested.
This webcast will walk through preparing a template for report generation, reviewing the generated report and performing some report customizations.
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analyses. However, standard commercial exome kits are limited to targeting exon coding regions, leaving significant gaps in coverage between genes which could hinder comprehensive CNV detection.
Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Twist Exome 2.0 Plus Comprehensive Exome Spike-in capture panel with added "backbone" probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25kb, 50kb, and 100kb intervals. In this webcast, we discuss the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV in identifying known CNVs using the Coriell CNVPANEL01 reference set.
This webcast reviews:
-The sensitivity rate for the detection of known CNV events at all three probe densities.
-The impact of best-practice quality metrics and filters on sensitivity.
-How VarSeq’s CNV annotation capabilities can be leveraged to identify likely pathogenic CNVs.
-The interpretation of clinically relevant CNVs using VSClinical.
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
In the rapidly evolving field of genomic analysis, staying current with the latest research, data sources, and test advancements is crucial. In this webinar, we review how VarSeq addresses the needs to stay on top of the latest with the release of VarSeq 2.6.0.
This release features an exome-optimized workflow for LOH and CNV calling as well as the introduction of VSPGx to produce pharmacogenomic reports for gene panels as well as exomes and genomes. With the recent release of gnomAD v4, we have had many requests for the integration of this large update to the most population frequency source. With VarSeq 2.6.0, the latest version of gnomAD has been integrated into VSClinical and the updated tracks spans beyond variants to cover CNVs and gene scores to update all your workflows to the latest data.
In this webcast, we will cover.
Improved VS-CNV performance and updated exome analysis workflows.
Pharmacogenomics in action: Utilizing VSPGx for exome and genome assessments.
gnomAD v4 in practice: Updated automated and manual variant interpretation workflows.
Join us for an insightful session on the latest VarSeq 2.6.0 features, bringing you the most up-to-date data and workflows for your genomic analysis.
Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeq
1) The document discusses a genetic data warehousing solution called VSWarehouse from Golden Helix that allows users to store, query, and analyze large genomic datasets.
2) VSWarehouse uses a column-based storage approach that is more scalable than traditional row-based databases and allows efficient querying and joining of variant call and sample data.
3) Golden Helix is launching an early adopter program for VSWarehouse, offering interested customers the chance to influence the product roadmap in exchange for a discounted license and commitment through March 2016.
Using VarSeq to Improve Variant Analysis Research Workflows
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.
The presentation will include interactive demonstrations using VarSeq to analyze variants found by exome sequencing of an extended family with a complex disease. We will review strategies for assessing variant quality, applying genomic annotations, incorporating custom annotation sources, and creating variant filters in VarSeq. We will also demonstrate the PhoRank gene ranking algorithm and its application for prioritizing variants.
Using VarSeq to Improve Variant Analysis Research Workflows
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.
Two Clinical Workflows
This document discusses two clinical workflows for analyzing genetic variants from raw data to a clinical report. It describes using VarSeq software to filter variants from gene panel or exome/genome sequencing data, review and annotate variants of interest, and generate a customized report. It also covers using repeatable VarSeq workflows and the VSPipeline tool to automate high-throughput analysis and generate standardized deliverables for each sample.
Two Clinical Workflows - From Unfiltered Variants to a Clinical Report
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!
Processing Hereditary Cancer Panels in VarSeq
Processing variants related to cancer is an incredibly critical process and a primary goal is to not only assess the variants rapidly but also accurately. A major improvement to cancer panel workflow efficiency is to utilize VarSeq for variant filtering, annotating, and interpretation. In this webcast we’ll cover some important quality assurance capabilities VarSeq provides, multiple approaches to build targeted panels, how to access/utilize numerous cancer annotations, and finally work through the ACMG guideline process on the selected germline cancer variants. The overall goal is to cover the basics of building the cancer gene panel project template so that it can be used routinely in high throughput environments.
2012 10-24 - ngs webinar
This document discusses GeneRead DNAseq Targeted Exon Enrichment and the GeneRead Library Quantification System for next generation sequencing. It begins with an introduction and agenda, then discusses targeted enrichment including the workflow, principles, data analysis, pathway content, performance data, and an application example. It also discusses library quantification including the workflow and an application example. In summary, the document presents Qiagen's GeneRead DNAseq and Library Quant systems as targeted enrichment and library quantification solutions for next generation sequencing applications.
Fine-tuning CNV Analysis for the Clinical Analysis of NGS Samples
Copy number variations (CNVs) are associated with a variety of genetic disorders including autoimmune diseases, autism, and cancer. VS-CNV gives clinicians and researchers the ability to detect both large and small CNV events, annotate them against a wide array of useful data sources, and perform filtering to obtain a small set of clinically relevant variations. In this webcast, we will discuss methods for adjusting algorithm sensitivity, leveraging CNV assessment catalogs, and excluding problematic CNV calls.
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Golden Helix's End-to-End Solution for Clinical Labs
Golden Helix's End-to-End Solution for Clinical Labs
Comprehensive Clinical Workflows for Copy Number Variants in VarSeq
Comprehensive Clinical Workflows for Copy Number Variants in VarSeq
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeq
Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeq
Using VarSeq to Improve Variant Analysis Research Workflows
Using VarSeq to Improve Variant Analysis Research Workflows
Using VarSeq to Improve Variant Analysis Research Workflows
Using VarSeq to Improve Variant Analysis Research Workflows
Two Clinical Workflows - From Unfiltered Variants to a Clinical Report
Two Clinical Workflows - From Unfiltered Variants to a Clinical Report
Fine-tuning CNV Analysis for the Clinical Analysis of NGS Samples
Fine-tuning CNV Analysis for the Clinical Analysis of NGS Samples
More from Golden Helix
Introducing VarSeq Dx as a Medical Device in the European Union
A transition period regarding in vitro medical device (IVD) regulation in the European Union (EU) is upon us. The former IVDD regulations are phasing out and IVDR 2017/746 has already taken its place as the acting regulation for IVD manufacturers but also lab developed tests (LDTs) and health institutions. In our upcoming webcast we will talk about the roles and significance of IVDR and ISO 13485 certification for clinical labs and for Golden Helix as a medical device manufacturer.
Join us as we will introduce VarSeq 2.6.1 complete with Dx Mode, which offers the use of VarSeq as CE marked medical device. Even more we will also present strategies to facilitate the transition of Golden Helix customers to operate in accordance with IVDR.
Introducing VSPGx: Pharmacogenomics Testing in VarSeq
Inter-individual variability in drug response poses a significant challenge for clinicians, with much of this variability resulting from inherited genetic differences. While the field of pharmacogenomics (PGx) can provide powerful insights into how genomic factors affect drug response, the implementation of PGx testing in the clinic is hampered by the difficulty of translating genetic test results into actionable recommendations. In this webcast, we will discuss VarSeq’s new PGx testing capabilities, including the ability to identify actionable pharmacogenomic diplotypes and generate clinical reports.
In this webcast you will learn:
-How to identify pharmacogenomic diplotypes and drug recommendations from NGS data.
-How to incorporate externally called CNVs and SVs into your PGx annotations.
-How to generate customizable PGx reports from these annotations.
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
From gene panels to whole genome, from short to long-read sequencing, the VarSeq suite is the solution for NGS analysis and reporting in a modern clinical lab. VarSeq handles the spectrum of variant types (SNV, Indel, CNV, Fusions) and provides automated classification and reporting capabilities following the ACMG and AMP guidelines. With our new PacBio partnership, we are more adaptable than ever with creating a spectrum of custom workflows to suit our unique user needs.
This webcast will review:
-Data analysis scaling from Gene Panel to Genome analysis with VarSeq and VSWarehouse.
-Analysis and annotation of SNVs, Indels, CNVs, and fusions.
-A close look at a PacBio long-read trio analysis.
Come join us for this showcase in modern VarSeq analysis capabilities.
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. The latest SVS release introduces a significant leap in capabilities, with a focus on advanced Polygenic Risk Score (PRS) calculations. PRS has become a fundamental tool in genomic research, enabling the identification of correlations between genotypic variants and phenotypes across large populations.
This enhancement is particularly relevant for researchers working on large cohorts and meta-analysis. Please join us as we explore:
-SVS Workflow Review: A review of the extensive capabilities of SVS to meaningful insights from large cohorts and association test result datasets
-Computing Polygenic Risk Scores: An overview of the PRS capabilities in SVS, including Clumping and Thresholding and creation of multiple PRS models
-Evaluating and Applying PRS: Evaluating PRS models in-sample and out-of-sample and applying PRS models to perform trait prediction
-Future Implications: Brief exploration of how these advancements in SVS could influence future genomic research.
This webcast will explore how SVS facilitates the creation of multiple PRS models from large-scale genomic data, such as those obtained from extensive cohort studies or comprehensive meta-analyses. Join us to discover how these latest updates in SVS are supporting large-scale genomic research.
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
With our recent launch of VarSeq 2.5.0, our ability to expedite somatic analysis for NGS labs is more accessible than ever before. Our recent webcasts have shown our range of updates, including our new oncogenicity classifier and carrier status workflows:
Identifying Oncogenic Variants in VarSeq
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
In this user perspective webcast, we will highlight how the combination of our new oncogenicity classifier and the updates to our CancerKB database streamline the interpretation of oncogenic variants. In addition, as NGS labs progress from gene panels to WES analysis for ideal genomic signature generation, we will demonstrate how a VarSeq somatic workflow can scale with these increased scopes of data analysis with ease.
Our user perspective webcast will cover:
Application of virtual panels to WES tumor/normal workflows.
Use of the oncogenicity classifier to streamline filter chains.
Updates to our CancerKB database to include the CancerKB gene track.
Including parallel germline secondary findings for the whole NGS workflow.
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
Golden Helix introduced new capabilities in VarSeq 2.5.0 to support carrier screening analysis through NGS data. Key features include the ability to import partnered samples, detect shared carrier variants between samples at the gene level using a couples carrier screening workflow, and generate clinical reports that calculate reproductive risks and include variant interpretations. The software is designed to scale from gene panels to whole exomes/genomes. A demo showed how these new features streamline the carrier screening analysis process from data import and filtering to clinical reporting.
Identifying Oncogenic Variants in VarSeq
The interpretation of somatic variants can be a challenging process. While AMP Guidelines provide detailed rules for accessing the clinical evidence associated with a specific variation, they do not specify criteria for determining if a variant is likely to be a driver mutation, which generates functional changes that enhance tumor cell proliferation. In this webcast, we will discuss a new VarSeq algorithm for estimating the oncogenicity of a variant. This will include a deep dive into our oncogenicity scoring system and a discussion of the various criteria used to distinguish driver mutations from benign variations and variants of uncertain significance.
What you will learn in this webcast:
-How to use the scoring algorithm to identify variants with evidence of oncogenicity
-Which criteria are used to assess a variant's oncogenicity
-How to evaluate the oncogenicity of a variant in VSClinical
Best Practices for Validating a Next-Gen Sequencing Workflow
Validating an NGS workflow is an iterative process that begins with collaboration with personnel and planning protocols for the entire workflow from sample preparation, sequencing and variant calling, all the way to data analysis and reporting. At Golden Helix, while we do not provide pre-validated black-box workflows, we provide our customers with support to validate workflows in a transparent manner, and assist them in reaching production deadlines. This webcast will be led by members of our Field Application Scientist team, and we will explore some of the best practices for NGS workflow validation that we have observed and helped to implement based on real-world examples from our customer base. Key topics for discussion will include:
Sample preparation and collection of adequate case/control data
Designing a robust workflow with special considerations for single versus family analyses and phenotypic considerations
Generating the desired output for clinical or other reports
Real world NGS workflow validation strategies
Tune in for tips and strategies that you can deploy when designing and validating your NGS workflow.
2023 Innovation Awards Winner, Dr. Muthukumaran
Expanded carrier screening in an infertile/affected Couple for determining carrier status for genetic mutations - VarSeq Couple Carrier Workflow
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
The document provides information about Golden Helix's VarSeq 2.4.0 software and its VSClinical ACMG workflow module. It summarizes a presentation given on the topic, including details about Golden Helix as a company, the content covered in the presentation, and examples that will be demonstrated including analysis of variants, copy number variants, and structural variants from PacBio long read sequencing data using VSClinical.
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
Mendelian disorders can be caused by various classes of genetic mutations, from small variants to CNVs and even Structural Variants. With the introduction of VarSeq 2.4.0, we are excited to unveil the latest advancements in VSClinical ACMG, focusing on the integration of Structural Variants and the enhanced automation capabilities that streamline your analysis process.
Join us in this webcast as we dive into the following topics:
Integration of Structural Variants: Learn how VarSeq 2.4.0 enables you to import and incorporate Structural Variants into your VSClinical ACMG evaluations and reports, providing a comprehensive understanding of the genetic landscape.
Advanced Automation in the ACMG Interface: Discover how evaluation scripts can be employed to automate the VSClinical ACMG interface, allowing you to perform custom actions or eliminate manual steps, thus increasing efficiency and reducing the risk of errors.
End-to-End Automation: Explore how VSPipeline can fully automate your analysis process, from raw VCF to report, ensuring a streamlined and consistent workflow that saves time and resources.
Harnessing the Power of VSClinical: Gain insights into how VarSeq 2.4.0 empowers you to tackle complex genomic data, enabling faster and more accurate identification of Mendelian disorders and facilitating personalized patient care.
With the advanced capabilities of VarSeq 2.4.0 and VSClinical, you can now unlock a new level of precision and efficiency in diagnosing Mendelian disorders. This webcast will showcase the latest innovations in variant interpretation and automation, exemplifying why the VarSeq Clinical Suite is the premier NGS analysis platform for germline and cancer testing.
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
There is a strong motivation for labs to bring most, if not all, of their next-gen sequencing pipeline in-house. This is especially relevant for clinical applications where there is a need to validate any routine diagnostics when seeking to provide genetic results to patients. The entirety of the NGS pipeline is highly automatable and comprised of multiple stages but from the geneticist's point of view, the tertiary stage requires the lengthiest review. This stage is where the geneticist sifts through the massive collection of genetic variants to find and report on those most relevant to the patient or population. Unfortunately, the tertiary stage can be a fairly sophisticated process and there aren’t many tools on the market that handle it comprehensively and simply. Many of the tools that are available may have severe limitations on the scale of genomic data they can process or limitations on the types of NGS assays that can be designed. Moreover, their license model may be on an individual sample basis and present cost-benefit hurdles for the user, especially when sample load will inevitably increase. Fortunately, none of these assay or cost-based issues are relevant with Golden Helix products.
The goal of this webcast is to expose our viewers to the versatility that GHI VarSeq provides when constructing your dream NGS assay. This demonstration will provide examples of germline and somatic workflows for both single and multi-sample analysis for a variety of different disorders. Please join us and learn more about the analytical possibilities you can achieve when using the VarSeq software.
Prenatal Genetic Screening with VarSeq
Our past webcast explored the current approaches for screening and diagnosis of genetic disorders in prenatal testing. While the methods available at the time were robust, they were severely limited, creating a need for a higher diagnostic yield and more efficient analysis for a wider range of genetic tests. The solution proposed was to improve and simplify prenatal screening and diagnosis with whole exome sequencing (WES).
During that webcast, we highlighted the advantages of WES over traditional methods such as karyotyping and chromosomal microarray, including improved accuracy, granularity, and cost-effectiveness. We also emphasized the potential of WES to expand diagnosis for many other adverse maternal-fetal complications beyond the large aneuploidy events previously covered. However, there was still an intimidation factor when it came to the massive data output from the exome. Fortunately, Golden Helix provided the necessary tools to build and standardize these genetic assays, simplifying the analytical process while leveraging increased diagnostic output. We explored our VarSeq software to demonstrate some example workflows of cases positive for Trisomy 21, an exon loss in DMD related to Duchenne Muscular Dystrophy, and detection of a single base change resulting in a LOF variant in RUNX1 relevant to hereditary leukemia.
Our goal was to expose our viewers to the methods of conquering this vast NGS-based data and play a role in dissolving any feeling of intimidation. Overall, exome sequencing has the potential to vastly improve diagnostic outcomes and widen discoveries in the research related to prenatal testing, and Golden Helix products are designed to facilitate this process.
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
NGS tests in the clinic cover more use cases than ever and are increasingly complex to implement. This leads to an increase in time to validate and bring tests to production, impacting a lab’s ability to be economically viable and serve the needs of patients. Core to the complexity is the expansion of tests to include multiple types of biomarkers and variants, including CNVs, gene fusions, and genomic signatures. The bioinformatics demands of these pipelines require powerful tools with built-in capabilities to handle the diverse needs of modern NGS tests and to integrate and automate the disparate steps leading to clinical insight.
Join us in this webinar as we explore the VarSeq suites’ capabilities as a fast, modular, and highly configurable solution for variant analysis and interpretation. We will cover:
The bioinformatic diversity of comprehensive genetic tests with NGS
Automation of FASTQ to clinical reports without losing control over the results of a test
Leverage built-in and custom automation capabilities in the VSClinical cancer guideline workflow to reduce work and improve accuracy
Reporting the relevant diagnostic and therapeutic findings for a patient based on the raw genomic data of modern NGS tests requires both human experience and advanced analysis software. We hope you can join us as we unpack how automation is a critical part of implementing NGS tests and furthering the application of precision medicine.
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
Comprehensive genomic testing via next generation sequencing (NGS) is being increasingly adapted as part of cancer care in conjunction with molecular and immunohistochemical tests. Comprehensive genomic profiling potentially expands the number of targeted therapies that are available to patients, improves patient diagnosis and prognosis, and increases the number of clinical trials that are relevant to patients. However, with these advancements come challenges such as gaps in expertise resulting in inadequate efforts to interpret genomic data accurately and efficiently, poorly coordinated efforts to implement precision care, patients being diagnosed and treated despite inadequate access to relevant information and subsequent lack of patient exposure to all available treatment options.
Golden Helix CancerKB v2.0 provides a means of closing the gap, whether you're a beginner who is trying to capture the vast amount of knowledge in the cancer field or an expert who has high sample volume AND needs to keep up with the ever-evolving knowledge of Tier II and III variants. In this webcast, we will discuss and apply Golden Helix CancerKB in the context of cancer precision medicine. Golden Helix CancerKB is systematically curated and reviewed by experts in the field and contains information about cancer genes, biomarkers, and treatments generated from several trusted cancer resources. With VarSeq 2.3.0’s added support for comprehensive cancer genomic profiling tests, Golden Helix CancerKB has expanded to include interpretations for genomic signatures, combination biomarkers, and more investigational (tier II) biomarkers, among several other additions that will be discussed. With the Golden Helix CancerKB database, users will experience a streamlined automatic matching of biomarkers to available drugs and trials which ultimately saves users massive amounts of time and effort while reducing the possibility for errors.
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
VarSeq 2.3.0 facilitates the evaluation of a multitude of somatic genomic variations with a more refined user interface to streamline variant evaluation. Our recent webcasts have shown the full range of these newly developed upgrades:
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Now, we are showing it all in action from the user’s perspective. This webcast will provide a comprehensive demonstration of performing somatic variation analysis and reporting. We will review how to use workflow automation to expedite the NGS project creation process and report rendering. We will also demonstrate the streamlined capture of knowledge during variant evaluation by leveraging our clinical expert-curated interpretations with the Golden Helix Cancer Knowledge Base (CancerKB).
We hope you will join us to see VarSeq 2.3.0 from a user’s perspective, covering:
-Somatic variant workflows: necessary algorithms and filtering strategies
-Import of all relevant biomarker and genomic signatures data from TSO-500
-Review content and value of clinically curated interpretations and treatments with CancerKB
-Interpretation of structural variants in the VSClinical AMP Guidelines workflow
-Workflow automation with VSPipeline
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
Next Generation Sequencing allows for the detection of a wide variety of genomic alterations. This includes small mutations, copy number variants and complex rearrangements. However, it can be difficult to annotate, filter, and interpret these alterations.
As part of our VarSeq 2.3.0 release, we have greatly simplified this process by allowing you to import, annotate, and filter mutations across all spectrums of genomic variation. This supports concurrent importation of small variants and CNVs as well as complex rearrangements. This release also includes strong support for structural variant annotation, filtering, and interpretation, including structural variant effect prediction. After filtering is complete, any clinically relevant structural variants can be interpreted with the VSClinical AMP Guidelines workflow and included in the final clinical report.
Come join us for this webcast to discuss VarSeq’s enhanced import and annotation capabilities, including:
Concurrent importation of variants CNVs and complex rearrangements
Improved multi-threaded import which dramatically speeds up the importation of large VCFs
Annotation of structural variants and prediction of effect
Interpretation of structural variants in the VSClinical AMP Guidelines workflow
Support for visualization and use of CRAM files as input for computing coverage statistics
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Precision medicine for cancer is rapidly accelerating because of the development and approval of targeted molecular therapies. These therapies require new genomic biomarkers as an indication for use, and require evaluating additional mutation types that are available in comprehensive genomic profiling assays as well as the small variants detected by Next-Generation Sequencing gene panels.
We are excited to announce VarSeq 2.3.0 which will update the VSClinical AMP workflow to meet the growing needs of labs conducting comprehensive genomic profiling (CGP) of tumors. This includes built-in support for the Illumina TruSight Oncology 500 (TSO-500) kit as well as similar kits from other vendors. The VSClinical AMP workflow has also gained native support for the bioinformatic outputs of CGP kits. Join us to learn about comprehensive genomic profiling in cancer, specifically:
Evaluation and clinical reporting of genomic signatures such as Microsatellite (MSI), Tumor mutation burden (TMB), PD-L1, Homologous recombination deficiency (HRD) statuses, and more.
Built-in TSO-500 import and expandable import capabilities for new genomic data types through the new advanced workflow scripting system.
Golden Helix CancerKB updates with report-ready genomic-signature interpretations written for approved therapies as well as gene interpretations for all 500 genes of the TSO-500 panel. In addition, CancerKB scopes have been extended to reference multiple relevant biomarkers in a single interpretation, capture approved therapies at the tumor type level, and include interpretations for clinically relevant negative findings.
Expanded clinical trial support to include international trials and the ability to search within proximity of European postal codes. VSClinical is accessing all active studies in AACT/ClinicalTrials.gov wherein users can search and select trials based on relevant drugs, biomarkers, and the geographic distance to the patient or testing site.
VarSeq 2.3.0 will deliver powerful capabilities for genomic profiling in cancer, enabling a new level of personalized and effective care for your patients. We look forward to demonstrating these updates and Golden Helix’s continued innovation making the VarSeq Clinical Suite the NGS analysis platform of choice for germline and cancer testing.
Single Sample and Family Based Genome Analysis With VarSeq
One major hurdle facing medicine is the need to quickly identify and assess the genetic components contributing to rare diseases. It has been estimated that nearly 350 million people suffer from rare diseases, 140 million of which are children, of whom ~30% do not live past their fifth birthday1,2. The specific issue to overcome is reducing morbidity by facilitating rapid diagnosis and treatment. Fortunately, the cost of whole genome sequencing has dropped below the $1000 mark, which not only makes the NGS approach more affordable but has become the status quo method of comprehensive diagnosis for these rare disorders. Currently, there are limited options in the market when it comes to quality software that can scale to this size of data and handle variant processing and evaluation in a timely fashion. Fortunately, Golden Helix has sought to set the market standard for top-quality NGS analysis with our bioinformatic software VarSeq. The focus of this webcast will be to explore example workflows tailored for rare disorders and elaborate on how best to expedite the NGS pipeline process with our command-line tool VSPipeline.
During the webcast, we will address the following:
Customizing clinically validated NGS workflows with VarSeq for both single sample and trios
Demonstrating the automation of ACMG-based guideline review in the VSClinical variant interpretation hub and rendering of customized clinical reports
Expediting the NGS workflow via Golden Helix command-line tool VSPipeline
We look forward to you joining us for our presentation, where we can demonstrate the value of our products when building your next-gen workflows. Ultimately, we wish to diminish the intimidation of genome workflow design and leave our future customers feeling confident that there is capable software to suit their needs.
Bick D, Jones M, Taylor SL, et al. Case for genome sequencing in infants and children with rare, undiagnosed or genetic disease. J Med Genet 2019; 56:783-791.
Owen M, Lefebvre S, Hansen C, et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13: 4057. https://doi.org/10.1038/s41467-022-31446-6
User perspective for somatic variant analysis in VSClinical AMP
Somatic analysis is a complex and precise process that is constantly evolving. As the volume of available data and the accessibility of sequencing technology increase, so too does the value of a versatile, well-vetted, and efficient workflow solution. In this webcast, we will take a deep dive into the current state of our AMP interpretation software and explore various ways to optimize workflows. For anyone from grizzled VarSeq veterans to those seeing our software for the first time and labs of any size, we will provide a practical overview of our somatic analysis capabilities and how those capabilities scale with improving technology.
Throughout this webcast we will be discussing the following:
- Universal principles of somatic workflows, providing baseline recommendations
- Specific tumor-normal and somatic-only use cases
- VSClinical AMP interpretation hub and some variants of interest
- Opportunities for automation and how to decrease time to report for increased throughput
Join us as we show off the versatility and scalability of our AMP interpretation capabilities!
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VS-CNV Annotations from the User's Perspective
- 1. Workflows for Copy Number Variants in VarSeq A Users Perspective Steve Hystad – Field Application Scientist 20 most promising Biotech Technology Providers Top 10 Analytics Solution Providers Hype Cycle for Life sciences
- 2. Use the Questions pane in your GoToWebinar window Questions during the presentation
- 3. Golden Helix – Who We Are Golden Helix is a global bioinformatics company founded in 1998. GWAS Genomic Prediction Large-N-Population Studies RNA-Seq Large-N CNV-Analysis Variant Warehouse Centralized Annotations Hosted Reports Sharing and Integration Variant Calling Filtering and Annotation Clinical Reports CNV Analysis Pipeline: Run Workflows
- 4. Cited in over 1100 peer-reviewed publications
- 5. Over 350 customers globally
- 6. Golden Helix – Who We Are When you choose a Golden Helix solution, you get more than just software REPUTATION TRUST EXPERIENCE INDUSTRY FOCUS THOUGHT LEADERSHIP COMMUNITY TRAINING SUPPORT RESPONSIVENESS INNOVATION and SPEED CUSTOMIZATIONS
- 7. VarSeq Clinical Workflows Stack
- 8. VarSeq CNV Gene Panels Exomes Genomes Annotate and Filter VS-CNV - Call CNVs from Gene Panels VS-CNV 2.0 - Call large and small CNVs & LOH on Exome datasets Whole Genome Sequence CNV Caller - Call CNVs from low and ultra low read depth datsets. - Call CNVs from the command line CNV annotations - Quickly examine clinically relevant CNVs - Reduce false positives and filter out common CNVs - Capture and store clinical CNV assessments VarSeq
- 9. CNV Detection Chromosomal microarray - Current best practice - Slow - Additional expense - Only detects large events CNV calling from NGS data - Calls from existing coverage data - Detects small single-exon events - Provides faster results, simplified clinical workflow
- 10. CNV Detection via NGS CNVs are called from coverage data Challenges - Coverage varies between samples - Coverage fluctuates between targets - Systematic biases impact coverage Solutions - Data Normalization - Reference Sample Comparison
- 11. CNV calling in VarSeq Reference samples used for normalization Metrics - Z-score: number of standard deviations from reference sample mean - Ratio: sample coverage divided by reference sample mean - VAF: Variant Allele Frequency For Gene Panels and Exomes - Probabilistic model used to call CNVs - Segmentation identifies large cytogenetic events For Whole Genome Data - Targets segmented using Z-scores - Events called based on Z-score and Ratio thresholds
- 12. Annotations RefSeq • Genes • Clinical Assessments • Population Frequencies • Cancer • CNV Genomic Superdups low Complexity Regions ExAC CNV
- 13. Sample Data for Single Exome Analysis Four Single Exome Samples BAM files from 1000 Genomes Phase 3 Illumina Exome Alignment Used Sentieon tools for variant calling. Sample CRExome-18 has chronic history of stomach ulcers and reported hearing impairment phenotype.
- 15. Lets Review Gene Panels Exomes Genomes Annotate and Filter VS-CNV - Call CNVs from Gene Panels, Exomes, and WGS CNV annotations - Quickly examine clinically relevant CNVs - Reduce false positives and filter out common CNVs CNV algorithms - Complete control over annotations - Match Gene linked to Phenotype - CNV Phorank! CNV Assessment Catalogs - Build knowledge base - Plot, Annotate, and Repeat VarSeq
- 16. Webcasts - CNV Analysis in VarSeq – December 7th 2016 - Calling Large LOH and CNV Events with NGS Exomes – March 8th 2017 - CNV Analysis in VarSeq – A User’s Perspective – April 19th 2017 - Comprehensive Clinical Workflows for CNVs in VarSeq – Sept 27th 2017 Tutorials - VarSeq CNV Caller Tutorial Support from Field Application Scientists - Support@Goldenhelix.com CNV Resources
- 17. Additional Information Secondary Analysis ebook - Calling SNVs & CNVs from NGS data Golden Helix at ASHG 2017! - Booth 902 - Come see demos and ask us questions! VarSeq CNV Powerpack (end Oct) - VarSeq + VSCNV + Sentieon + VSReports - $ 15,995 SVS & VarSeq Bundle - CADD & OMIM included - $7,995 Small Lab Warehouse + VS-CNV - 2 users $36,00
- 18. Questions or more info: Email info@goldenhelix.com Request an evaluation of the software at www.goldenhelix.com