Golden Helix's End-to-End Solution for Clinical Labs
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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!
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Creating & Managing Reusable Gene Lists with VSClinical
Golden Helix supports performing repeatable clinical workflows designed to meet the needs of your lab's clinical genetic tests. A critical component of any genetic test is the reporting of clinically significant genes and the ability to limit interpretations to a predefined set of test-specific genes. This webinar will cover the upcoming “Managed Gene List” feature of VarSeq and VSClinical which enables the defining and re-use of gene lists outside of individual product templates.
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Genetic testing labs deal with personal data in categories with the highest level of security requirements: personal identity and medical records. Given the liability and risk associated with a breach of this secure information, it is not surprising that many labs and institutes that aggregate genomic data prefer if not require on-premise analysis and storage solutions.
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VSWarehouse: Tracking Changing Variant Evidence and Classifications
Over the years, VarSeq has evolved into a powerfully efficient next-gen sequencing variant analysis platform. Some of the recent advances Golden Helix has made to this software have been to implement the standard ACMG and AMP guidelines for variant classification and interpretation. The guidelines are composed of many criteria impacting any variant final classification. These criteria consider topics such as frequency of the variant among the population, functional predictions, hotspot pathogenic rich regions in the gene, as well as known clinical submissions from other labs. The reality with this guideline review is that variant evidence can changeover time. Among the long list of databases needed to automate this guideline process, many databases have massive updates or are frequently updated perhaps on a month-to-month basis. So, it follows that any classification can be altered once discoveries for these variants are made. A problem that arises is, how to manage changing classifications, retroactively review previous patient outcomes and updatevariant classifications accordingly. Fortunately, Golden Helix has solved this dilemma with the use of our VSWarehouse genomic repository.
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An Exploration of Clinical Workflows in VarSeq
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Utility of gene ranking in genetic testing
Scenarios that warrant the use of PhoRank 2.0
New ranking strategies provided by recent papers
Benchmarks of PhoRank 2.0 on published datasets
Golden Helix provides a comprehensive solution for NGS testing labs to perform best practice guidelines such as ACMG and AMP. Our gene ranking methods provide a vital role in scaling tests to large gene panels and exomes. Please join us as we review the testing workflow and how this significant update to our gene ranking algorithm fits into the testing workflow.
An Exploration of Clinical Workflows in VarSeq
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AMP-Based Variant Classification with VSClinical
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Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
For the past year, Golden Helix has been preparing a VarSeq release that includes ACMG Guidelines scoring and classification for not only single nucleotide variants but also copy number variants. In the past few months, our webcasts have introduced these guidelines and explored example CNVs that demonstrated the automated scoring of CNVs according to the new ACMG CNV Guidelines. However, there are many other new features and upgrades that have been incorporated into this VarSeq release. These upgrades have largely been driven by input from VarSeq users! That’s why I am very excited to explore these features together in the upcoming webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”. In this webcast, we will walk through a workflow with SNVs and CNVs highlighting many of the new features and upgrades that will improve and streamline your ACMG workflow. Notably, we will see how these new features can also be incorporated into clinical reports.
Specifically, we will cover the following features:
New and improved ACMG Classifier algorithms
New and improved assessment catalogs for saving classifications and interpretations
New Project Options interface for creating patient evaluations
Now offering three new word-based clinical report templates
Inclusion of additional sections and features to the clinical reports
Enhanced report customization capability
Efficient Application of NGS Family-Based Analysis
Golden Helix is committed to providing next-gen sequencing solutions that are comprehensive and efficient. A significant portion of our user base processes pediatric cases or requires the ability to run family-based analyses that can be applied to all inheritance models in order to identify rare variants in Mendelian disorders and cancer. To increase diagnostic yield and reduce time to clinical results, these models and workflows must be easy to set up and used efficiently. Optimization can involve all the steps, including data import, workflow design (variant filtering), a detailed evaluation of variant impact and clinical relevance via ACMG guidelines and AMP guidelines, as well as providing a full clinical report.
VarSeq is the best tool to accomplish this task. VarSeq, our tertiary analytics platform, is designed to process all sizes of genomic data. It can filter through all variants in order to identify clinically relevant variants. The results are evaluated using automated and standardized guidelines. This webcast will demonstrate workflows tailored to different pedigree scenarios. It will also demonstrate VarSeq features designed to speed up analysis time while maintaining consistency with outcomes.
In this webcast, we will cover the following topics:
Explore various family-based project designs (includes trio and duo & extended families)
Discuss various inheritance models (compound het, de novo, dominant inherited, etc)
Briefly examine the ACMG guidelines relevant to inheritance and review an example trio clinical report
Demonstrate how VSPipeline can automate the creation of projects
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
We have seen the widespread adoption of VarSeq in the clinic. It is chosen for its versatility and flexibility as well as the extensive catalog of annotations provided by Golden Helix. In a genetic testing scenario, VarSeq provides the annotated and filtered list of high-quality variants to that are ready for the user to classify and interpret.
In this webcast, we introduce a new product VSClinical that enables the interpretation of variants following the ACMG Guidelines. By incorporating new algorithms and annotation sources, detailed variant scoring and classification can occur right within VarSeq and without the need for additional external tools or resources.
Join us to see these upcoming capabilities:
Streamline the ACMG scoring guidelines with supportive recommendation and incorporated historical precedence
See the new algorithms behind the automated recommendation algorithm, and how they provide various levels of evidence
Drill down to an unprecedented level of supporting evidence for mutation hot spots, splice site predictions, and related clinical assertions
Build your own lab practices around new capabilities of blinded interpretations, collaborative interpretation review and detailed audit logs for CLIA compliance
Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation
In combination, this can be a game-changer for any clinical lab looking to improve their efficiency and reproducibility of the most complex step in the genetic testing workflow.
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...
This document summarizes a presentation given by Gabe Rudy, VP of Product & Engineering at Golden Helix, on updated strategies and expanded capabilities for exome analysis with VS-CNV and VSClinical. The presentation demonstrates new features for enhanced variant analysis, including analyzing splice site, non-coding RNA, and mitochondrial variants. It also reviews improvements to Golden Helix's exome CNV calling in VarSeq, including a new low-quality target filter strategy that reduces the number of CNVs called while maintaining sensitivity and precision. Additional capabilities discussed include generating synchronized clinical reports and incorporating virtual gene panels.
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.
Family-Based Workflows in VarSeq and VSClinical
Golden Helix is a single testing paradigm that allows users to start with next-generation sequencing data and finish with a clinical report. Our solutions are comprehensive as they are all performed in one software suite, which can save time and money as they prevent the need to outsource to different companies. Furthermore, our software is fully transparent in that you have full control over the steps performed in your analysis. Golden Helix is also on the forefront in the clinical workspace as we have implemented the ACMG and AMP guidelines to evaluate single nucleotide variants, insertions and deletions, as well as structural variants.
Beyond these functionalities, Golden Helix provides the ability to perform family-based analysis. Our ACMG and Exome trio templates give users a starting point to understand the different inheritance models ranging from transmitted to de novo variants, but we also have features that can provide additional evidence for both traditional and nontraditional family-based workflows. Specifically, we have algorithms that can be implemented to look at extended pedigree information and sample relatedness as well as options for examining whether a given variant such as a CNV segregates among similarly affected family members. In this webcast, we would like to demonstrate these features and show some solutions for the analysis of different family structures.
As an overview, this webcast will cover:
- Implementing filter logics for different family structures
- Algorithms that can be used for establishing clinical significance in family-based workflows
- Visualization capabilities for further understanding of inheritance models
- Confirming and evaluating transmitted CNVs
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Annotation sources are constantly evolving, sometimes quite literally overnight. This is especially true in the case of cancer databases. These ever-evolving annotation sources, coupled with increasing research publications, make it difficult to do variant analysis with up-to-date scientific knowledge. With the resources available to an individual clinician or single lab, this may even prove impossible. Fortunately, VSClinical provides access to the most current clinical annotation sources - automating scoring and interpreting variants according to the most recent ACMP and AMPO guidelines. This includes many fast-changing sources such as ClinVar and COSMIC, as well as expert-curated reviews of literature and the latest drug-labeling from regulatory bodies.
In this webcast, we demonstrate the automation of a cancer workflow with enhanced cancer annotations for somatic and germline cancer variants:
- Golden Helix’s own CancerKB database has been updated to include new interpretations for genes and biomarkers with AMP Tier Level I evidence for drug sensitivity, resistance, diagnostic, and prognostic information.
- We feature a new Golden Helix curated annotation source that automates the scoring of TP53 variants with the special rule specifications by ClinGen’s TP53 Expert Panel.
- The ClinGen Expert Curated Interpretation of Variants has always been available as an annotation source for VarSeq projects, but now the expert comments and interpretations can automatically be pulled into VSClinical and used for clinical reports.
This webcast walks through a hematological-focused cancer workflow that shows off the enhanced cancer annotations and CancerKB updates!
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
The document describes funding that supported research conducted by Golden Helix. It lists several National Institute of General Medical Sciences grant numbers that supported the work. The principal investigator for the grants is named as Dr. Andreas Scherer, CEO of Golden Helix. It is noted that the content of any research supported by this funding is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.
Introducing Drugs & Trials for Cancer Diagnostics
When interpreting a variant using the AMP/ASCO guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials, FDA approved therapies and peer-reviewed studies. Unfortunately, strong evidence linking specific genetic biomarkers to FDA-approved therapies only exists for a small number of cancers. Thus, most variants require an exploration of clinical practice guidelines, peer-reviewed literature, and large-scale cancer mutation databases to effectively assess the clinical significance of a given mutation.
This webcast explores this new incorporation of Drugs & Trials Annotations in VSClinical's AMP Workflow covering:
Identification of relevant clinical evidence for drug sensitivity and resistance based on patient biomarkers and tumor type
Review of clinical trial information including inclusion criteria, trial status, and contact information
Management of citations associated with relevant, targeted therapies
Evaluation of a biomarkers clinical evidence tier based on available evidence for drug sensitivity and resistance
CNV Annotations: a crucial step in your variant analysis
Since the development of our NGS-based CNV solutions for VarSeq and SVS, we've generated a long list of content demonstrating simple workflows to help isolate clinically relevant events for a given sample. However, it's just as important to talk about the exclusionary filters that help remove any extraneous CNVs from the analysis.
Golden Helix stands alone in our delivery of multiple methods for filtering down to top-quality, rare, and clinically relevant variants. This webcast will focus on the application of the various CNV annotations, discussing their purpose and usability in quickly removing CNVs with high-population frequency, duplicated regions inherent to the human genome, benign events, and events known in healthy individuals.
Please join us in an exploration of VarSeq's unique CNV annotation capabilities to see how users can overcome the challenges of NGS-based CNV detection.
What will you learn in this webcast?
Initial assessment of sample and CNV event quality
General review and understanding of various CNV annotations in VarSeq
The application of CNV annotations to eliminate common and benign CNVs
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Guidelines
Golden Helix is announcing an upgrade to their VSWarehouse and VarSeq software. The upgrade includes new features that allow somatic variant analysis and interpretation using American College of Medical Genetics and Genomics and Association for Molecular Pathology guidelines. Variants can be stored and annotated in the centralized VSWarehouse database and shared across projects and collaborators. Clinical reports generated in VarSeq can also be stored in the VSWarehouse for integration with electronic medical records. The software aims to help researchers and clinicians efficiently analyze biomarkers and classify variants according to established clinical evidence tiers.
Whole Genome Trait Association 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. As Next-Generation Sequencing of whole genomes becomes more affordable, large cohorts of Whole Genome Sequencing (WGS) samples are available to search for additional trait association signals that were not found in array-based testing. In fact, recent papers have shown that WGS analysis using advanced GREML (Genomic Relatedness Restricted Maximum Likelihood) techniques is able to outperform micro-array based GWAS methods in the analysis of complex traits and proportion of the trait heritability explained.
Our latest update release of SVS has expanded the exiting maximum likelihood and GRM methods to support these new techniques. We have also enhanced various other association testing and prediction methodologies. This webcast showcases:
- Newly supported analysis workflow for whole genome variants using LD binning and enhanced GBLUP analysis
- Enhanced gender correction using REML
- Additional capabilities for genomic prediction and phenotype prediction
We are continually improving our products based on our customer’s feedback. We hope you enjoy this recording highlighting the exciting new features and select enhancements we have made.
Advanced VSClinical Reports with Scripting and Custom Integrations
Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines for the evaluation of variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since VSClinical was introduced, we have provided a powerful Word-based templating system that allows labs to customize reports to include their specific content and branding.
Although powerful, this capability has been limited to customizing the contents of a Word file. Sometimes, the next logical step for the VSClinical analysis result is not a Word file, but some other file or target system: A database, LIMS, EMR, or even just a custom structured text file.
Join us in this webinar, as we discuss the next version of VarSeq, which will introduce a powerful scripting and custom integration engine built into VSClinical Reports. We will cover:
Capabilities and outputs of the workflows of VSClinical ACMG and Cancer
Content of VSClinical reports, including sample-QC, coverage statistics, custom gene panels, and data providence
The shipped report templates that range from gene panels to exome trios and comprehensive cancer testing
The new custom script-based reports and example workflows it enables
The tools enabling a powerful developer experience when building custom outputs and integrations
The VarSeq Suite holds customization and extendibility as core values, allowing the powerful capabilities of variant analysis to be truly customized to the needs of a specific laboratory and NGS test. The new scripting and integration capabilities build on this tradition for the VSClinical workflows. We hope you can join us as we explore this topic in-depth in this webinar.
Evaluating Oncogenicity in VSClinical
Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses a variety of metrics to classify a given somatic mutation into one of the following categories: oncogenic, likely oncogenic, benign, likely benign, or uncertain significance. This scoring system is heavily inspired by the ACMG Guidelines for the interpretation of germline mutations but has several important differences to make it more applicable in the context of somatic variant interpretation.
Our oncogenicity scoring system relies on an additive point system in which points are assigned to a given variant based on several criteria. Many of the criteria are shared by the ACMG Guidelines for germline variant interpretation, such as population frequency information, variant effect on protein function, and nearby pathogenic variants in catalogs such as ClinVar. However, other criteria are specific to the world of somatic variant interpretation. These include the variant’s presence in somatic catalogs such as COSMIC, the effect of other known oncogenic variants in the same gene, and the variant’s presence in known cancer hotspots or active binding sites. These criteria are combined by summing over the scores for all applicable scoring criteria. Scores exceeding 3 indicate an oncogenic or likely oncogenic classification, while scores falling below -3 indicate a benign or likely benign classification.
In this webcast, we discuss how each of these scoring criteria are combined to obtain an oncogenicity classification. This includes a discussion of the considerations taken into account during the development of this scoring system and a detailed analysis of several example mutations to illustrate the system in practice.
Next-Generation Sequencing Analysis in VSClinical
VarSeq is a tertiary analysis platform that allows users to filter and annotate NGS sequencing data to identify clinically relevant variants. Following this workflow, VSClinical can then be used to automate both germline and somatic variant analysis in accordance with the ACMG and AMP guidelines by using a variety of functional prediction models and clinical and reviewer-based annotations. Once variant or biomarker interpretations are completed, they can be rendered in a customizable clinical report and stored in an internal assessment catalog as an internal variant database repository. Together, implementation of VSClinical will promote increased lab throughput as well as accuracy and compliance with the ACMG and AMP guidelines, which in turn can save time and money. To show the capabilities of our software, this webcast will provide a demonstration of how to use VarSeq and VSClinical for the evaluation of both germline and somatic variants in accordance with the ACMG and AMP Guidelines.
In this webcast, we will cover:
- Filter logics for germline and somatic variants and selecting them into the VSClinical interface
- Capabilities of functional prediction and splice site algorithms for edge case variants
- The functionality of changing the clinically relevant transcript on variant interpretation
- Rendering a clinical report with germline and somatic variants with the inclusion of clinical trials
Advanced Report Customization via VSClinical
This document provides a summary of a presentation about advanced customization capabilities for clinical reports using VSClinical software:
- VSClinical allows customization of clinical reports through custom HTML, XML, JSON templates and scripts to enhance Word reports and integrate with REST APIs.
- Templates are provided for germline and somatic variant analysis that include ACMG/AMP guidelines and can be further customized.
- Reports can include additional data such as gene impact analysis, drug/trial information, and machine-readable outputs like JSON can be generated.
- A product demo was given to showcase report customization features.
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Interpreting somatic variants for the clinical genetic testing of tumors requires hands-on time of the most skilled clinical lab personnel. Various clinical and genomic sources must be queried, papers and guidelines referenced, and an evaluation of the clinical actionability of the mutation determined by the following the AMP guidelines. Yet, there is tremendous potential for reuse of this time consuming and valuable work!
Earlier this summer we launched our VSClinical AMP Guidelines workflow which integrates a lab-specific knowledgebase that saves every biomarkers interpretation in up to seven different snippets that ar reusable across various genomic and clinical contexts. Furthermore, our cancer workflow is bundled with the Golden Helix CancerKB, our expert-curated interpretations of the most common biomarkers for the most common cancer types, reducing the time to your first precision medicine report.
Follow along as we cover:
The interpretation of clinically actionable biomarkers for targeted molecular therapy and diagnostic/prognostic clinical reports for cancer
The different levels and scopes of re-use of the interpretation for each biomarker
Saving, re-using and updating these interpretations over time by multiple users within a clinical lab with an integrated lab-specific knowledgebase
The built in Golden Helix CancerKB that provides default interpretations for most cancer genes, biomarkers and many clinically actionable Tier I/II drug sensitivity and resistance interpretations.
In the world of genomics shaping precision medicine in oncology, the limiting factor is the time-to-sign-off on fully interpreted molecular profile reports.
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Golden Helix is a bioinformatics company that has developed software tools like CancerKB to help accelerate next-generation sequencing (NGS) cancer testing. CancerKB is a curated knowledgebase that provides clinically relevant information and interpretations of cancer variants to help generate standardized clinical reports. It is updated based on current guidelines, literature, and customer feedback to integrate the most relevant cancer data and help clinicians evaluate NGS results more efficiently. Golden Helix also acknowledges funding support from the National Institutes of Health.
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.
Automating the ACMG Guidelines with VSClinical
Clinical Genetic testing requires a complex analysis using the totality of our knowledge about the clinical relevance of a variant and a gene. This includes bioinformatic evidence as well as clinical evidence. The ACMG Guidelines provided a framework in which to score variants based on this evidence, and while some of those scoring criteria require close consultation of the clinical context for a given patient, much of it can be automated.
In this webcast, we review how VSClinical automates the ACMG scoring guidelines while integrating the collective lab expertise from previously classified variants and preferences about genes. We will cover:
Using the ACMG Auto Classifier as part the filtering strategy for gene panels and trio workflows
How gene preferences such as the default transcript, inheritance model, and disorder are updated and saved from VSClinical and used in all future analysis
How the per-variant recommendation engine builds on the auto-classification with descriptive reasons for answering each criterion yes or no
Using the auto-interpretation to present the evidence for all scored criteria in a human-readable paragraph
Working with VSClinical’s self-learning knowledgebase that incorporates previously classified variants and genes inform the interpretation of new variants!
VS-CNV Annotations from the User's Perspective
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.
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.
More Related Content
What's hot
Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
For the past year, Golden Helix has been preparing a VarSeq release that includes ACMG Guidelines scoring and classification for not only single nucleotide variants but also copy number variants. In the past few months, our webcasts have introduced these guidelines and explored example CNVs that demonstrated the automated scoring of CNVs according to the new ACMG CNV Guidelines. However, there are many other new features and upgrades that have been incorporated into this VarSeq release. These upgrades have largely been driven by input from VarSeq users! That’s why I am very excited to explore these features together in the upcoming webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”. In this webcast, we will walk through a workflow with SNVs and CNVs highlighting many of the new features and upgrades that will improve and streamline your ACMG workflow. Notably, we will see how these new features can also be incorporated into clinical reports.
Specifically, we will cover the following features:
New and improved ACMG Classifier algorithms
New and improved assessment catalogs for saving classifications and interpretations
New Project Options interface for creating patient evaluations
Now offering three new word-based clinical report templates
Inclusion of additional sections and features to the clinical reports
Enhanced report customization capability
Efficient Application of NGS Family-Based Analysis
Golden Helix is committed to providing next-gen sequencing solutions that are comprehensive and efficient. A significant portion of our user base processes pediatric cases or requires the ability to run family-based analyses that can be applied to all inheritance models in order to identify rare variants in Mendelian disorders and cancer. To increase diagnostic yield and reduce time to clinical results, these models and workflows must be easy to set up and used efficiently. Optimization can involve all the steps, including data import, workflow design (variant filtering), a detailed evaluation of variant impact and clinical relevance via ACMG guidelines and AMP guidelines, as well as providing a full clinical report.
VarSeq is the best tool to accomplish this task. VarSeq, our tertiary analytics platform, is designed to process all sizes of genomic data. It can filter through all variants in order to identify clinically relevant variants. The results are evaluated using automated and standardized guidelines. This webcast will demonstrate workflows tailored to different pedigree scenarios. It will also demonstrate VarSeq features designed to speed up analysis time while maintaining consistency with outcomes.
In this webcast, we will cover the following topics:
Explore various family-based project designs (includes trio and duo & extended families)
Discuss various inheritance models (compound het, de novo, dominant inherited, etc)
Briefly examine the ACMG guidelines relevant to inheritance and review an example trio clinical report
Demonstrate how VSPipeline can automate the creation of projects
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
We have seen the widespread adoption of VarSeq in the clinic. It is chosen for its versatility and flexibility as well as the extensive catalog of annotations provided by Golden Helix. In a genetic testing scenario, VarSeq provides the annotated and filtered list of high-quality variants to that are ready for the user to classify and interpret.
In this webcast, we introduce a new product VSClinical that enables the interpretation of variants following the ACMG Guidelines. By incorporating new algorithms and annotation sources, detailed variant scoring and classification can occur right within VarSeq and without the need for additional external tools or resources.
Join us to see these upcoming capabilities:
Streamline the ACMG scoring guidelines with supportive recommendation and incorporated historical precedence
See the new algorithms behind the automated recommendation algorithm, and how they provide various levels of evidence
Drill down to an unprecedented level of supporting evidence for mutation hot spots, splice site predictions, and related clinical assertions
Build your own lab practices around new capabilities of blinded interpretations, collaborative interpretation review and detailed audit logs for CLIA compliance
Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation
In combination, this can be a game-changer for any clinical lab looking to improve their efficiency and reproducibility of the most complex step in the genetic testing workflow.
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...
This document summarizes a presentation given by Gabe Rudy, VP of Product & Engineering at Golden Helix, on updated strategies and expanded capabilities for exome analysis with VS-CNV and VSClinical. The presentation demonstrates new features for enhanced variant analysis, including analyzing splice site, non-coding RNA, and mitochondrial variants. It also reviews improvements to Golden Helix's exome CNV calling in VarSeq, including a new low-quality target filter strategy that reduces the number of CNVs called while maintaining sensitivity and precision. Additional capabilities discussed include generating synchronized clinical reports and incorporating virtual gene panels.
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.
Family-Based Workflows in VarSeq and VSClinical
Golden Helix is a single testing paradigm that allows users to start with next-generation sequencing data and finish with a clinical report. Our solutions are comprehensive as they are all performed in one software suite, which can save time and money as they prevent the need to outsource to different companies. Furthermore, our software is fully transparent in that you have full control over the steps performed in your analysis. Golden Helix is also on the forefront in the clinical workspace as we have implemented the ACMG and AMP guidelines to evaluate single nucleotide variants, insertions and deletions, as well as structural variants.
Beyond these functionalities, Golden Helix provides the ability to perform family-based analysis. Our ACMG and Exome trio templates give users a starting point to understand the different inheritance models ranging from transmitted to de novo variants, but we also have features that can provide additional evidence for both traditional and nontraditional family-based workflows. Specifically, we have algorithms that can be implemented to look at extended pedigree information and sample relatedness as well as options for examining whether a given variant such as a CNV segregates among similarly affected family members. In this webcast, we would like to demonstrate these features and show some solutions for the analysis of different family structures.
As an overview, this webcast will cover:
- Implementing filter logics for different family structures
- Algorithms that can be used for establishing clinical significance in family-based workflows
- Visualization capabilities for further understanding of inheritance models
- Confirming and evaluating transmitted CNVs
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Annotation sources are constantly evolving, sometimes quite literally overnight. This is especially true in the case of cancer databases. These ever-evolving annotation sources, coupled with increasing research publications, make it difficult to do variant analysis with up-to-date scientific knowledge. With the resources available to an individual clinician or single lab, this may even prove impossible. Fortunately, VSClinical provides access to the most current clinical annotation sources - automating scoring and interpreting variants according to the most recent ACMP and AMPO guidelines. This includes many fast-changing sources such as ClinVar and COSMIC, as well as expert-curated reviews of literature and the latest drug-labeling from regulatory bodies.
In this webcast, we demonstrate the automation of a cancer workflow with enhanced cancer annotations for somatic and germline cancer variants:
- Golden Helix’s own CancerKB database has been updated to include new interpretations for genes and biomarkers with AMP Tier Level I evidence for drug sensitivity, resistance, diagnostic, and prognostic information.
- We feature a new Golden Helix curated annotation source that automates the scoring of TP53 variants with the special rule specifications by ClinGen’s TP53 Expert Panel.
- The ClinGen Expert Curated Interpretation of Variants has always been available as an annotation source for VarSeq projects, but now the expert comments and interpretations can automatically be pulled into VSClinical and used for clinical reports.
This webcast walks through a hematological-focused cancer workflow that shows off the enhanced cancer annotations and CancerKB updates!
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
The document describes funding that supported research conducted by Golden Helix. It lists several National Institute of General Medical Sciences grant numbers that supported the work. The principal investigator for the grants is named as Dr. Andreas Scherer, CEO of Golden Helix. It is noted that the content of any research supported by this funding is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.
Introducing Drugs & Trials for Cancer Diagnostics
When interpreting a variant using the AMP/ASCO guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials, FDA approved therapies and peer-reviewed studies. Unfortunately, strong evidence linking specific genetic biomarkers to FDA-approved therapies only exists for a small number of cancers. Thus, most variants require an exploration of clinical practice guidelines, peer-reviewed literature, and large-scale cancer mutation databases to effectively assess the clinical significance of a given mutation.
This webcast explores this new incorporation of Drugs & Trials Annotations in VSClinical's AMP Workflow covering:
Identification of relevant clinical evidence for drug sensitivity and resistance based on patient biomarkers and tumor type
Review of clinical trial information including inclusion criteria, trial status, and contact information
Management of citations associated with relevant, targeted therapies
Evaluation of a biomarkers clinical evidence tier based on available evidence for drug sensitivity and resistance
CNV Annotations: a crucial step in your variant analysis
Since the development of our NGS-based CNV solutions for VarSeq and SVS, we've generated a long list of content demonstrating simple workflows to help isolate clinically relevant events for a given sample. However, it's just as important to talk about the exclusionary filters that help remove any extraneous CNVs from the analysis.
Golden Helix stands alone in our delivery of multiple methods for filtering down to top-quality, rare, and clinically relevant variants. This webcast will focus on the application of the various CNV annotations, discussing their purpose and usability in quickly removing CNVs with high-population frequency, duplicated regions inherent to the human genome, benign events, and events known in healthy individuals.
Please join us in an exploration of VarSeq's unique CNV annotation capabilities to see how users can overcome the challenges of NGS-based CNV detection.
What will you learn in this webcast?
Initial assessment of sample and CNV event quality
General review and understanding of various CNV annotations in VarSeq
The application of CNV annotations to eliminate common and benign CNVs
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Guidelines
Golden Helix is announcing an upgrade to their VSWarehouse and VarSeq software. The upgrade includes new features that allow somatic variant analysis and interpretation using American College of Medical Genetics and Genomics and Association for Molecular Pathology guidelines. Variants can be stored and annotated in the centralized VSWarehouse database and shared across projects and collaborators. Clinical reports generated in VarSeq can also be stored in the VSWarehouse for integration with electronic medical records. The software aims to help researchers and clinicians efficiently analyze biomarkers and classify variants according to established clinical evidence tiers.
Whole Genome Trait Association 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. As Next-Generation Sequencing of whole genomes becomes more affordable, large cohorts of Whole Genome Sequencing (WGS) samples are available to search for additional trait association signals that were not found in array-based testing. In fact, recent papers have shown that WGS analysis using advanced GREML (Genomic Relatedness Restricted Maximum Likelihood) techniques is able to outperform micro-array based GWAS methods in the analysis of complex traits and proportion of the trait heritability explained.
Our latest update release of SVS has expanded the exiting maximum likelihood and GRM methods to support these new techniques. We have also enhanced various other association testing and prediction methodologies. This webcast showcases:
- Newly supported analysis workflow for whole genome variants using LD binning and enhanced GBLUP analysis
- Enhanced gender correction using REML
- Additional capabilities for genomic prediction and phenotype prediction
We are continually improving our products based on our customer’s feedback. We hope you enjoy this recording highlighting the exciting new features and select enhancements we have made.
Advanced VSClinical Reports with Scripting and Custom Integrations
Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines for the evaluation of variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since VSClinical was introduced, we have provided a powerful Word-based templating system that allows labs to customize reports to include their specific content and branding.
Although powerful, this capability has been limited to customizing the contents of a Word file. Sometimes, the next logical step for the VSClinical analysis result is not a Word file, but some other file or target system: A database, LIMS, EMR, or even just a custom structured text file.
Join us in this webinar, as we discuss the next version of VarSeq, which will introduce a powerful scripting and custom integration engine built into VSClinical Reports. We will cover:
Capabilities and outputs of the workflows of VSClinical ACMG and Cancer
Content of VSClinical reports, including sample-QC, coverage statistics, custom gene panels, and data providence
The shipped report templates that range from gene panels to exome trios and comprehensive cancer testing
The new custom script-based reports and example workflows it enables
The tools enabling a powerful developer experience when building custom outputs and integrations
The VarSeq Suite holds customization and extendibility as core values, allowing the powerful capabilities of variant analysis to be truly customized to the needs of a specific laboratory and NGS test. The new scripting and integration capabilities build on this tradition for the VSClinical workflows. We hope you can join us as we explore this topic in-depth in this webinar.
Evaluating Oncogenicity in VSClinical
Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses a variety of metrics to classify a given somatic mutation into one of the following categories: oncogenic, likely oncogenic, benign, likely benign, or uncertain significance. This scoring system is heavily inspired by the ACMG Guidelines for the interpretation of germline mutations but has several important differences to make it more applicable in the context of somatic variant interpretation.
Our oncogenicity scoring system relies on an additive point system in which points are assigned to a given variant based on several criteria. Many of the criteria are shared by the ACMG Guidelines for germline variant interpretation, such as population frequency information, variant effect on protein function, and nearby pathogenic variants in catalogs such as ClinVar. However, other criteria are specific to the world of somatic variant interpretation. These include the variant’s presence in somatic catalogs such as COSMIC, the effect of other known oncogenic variants in the same gene, and the variant’s presence in known cancer hotspots or active binding sites. These criteria are combined by summing over the scores for all applicable scoring criteria. Scores exceeding 3 indicate an oncogenic or likely oncogenic classification, while scores falling below -3 indicate a benign or likely benign classification.
In this webcast, we discuss how each of these scoring criteria are combined to obtain an oncogenicity classification. This includes a discussion of the considerations taken into account during the development of this scoring system and a detailed analysis of several example mutations to illustrate the system in practice.
Next-Generation Sequencing Analysis in VSClinical
VarSeq is a tertiary analysis platform that allows users to filter and annotate NGS sequencing data to identify clinically relevant variants. Following this workflow, VSClinical can then be used to automate both germline and somatic variant analysis in accordance with the ACMG and AMP guidelines by using a variety of functional prediction models and clinical and reviewer-based annotations. Once variant or biomarker interpretations are completed, they can be rendered in a customizable clinical report and stored in an internal assessment catalog as an internal variant database repository. Together, implementation of VSClinical will promote increased lab throughput as well as accuracy and compliance with the ACMG and AMP guidelines, which in turn can save time and money. To show the capabilities of our software, this webcast will provide a demonstration of how to use VarSeq and VSClinical for the evaluation of both germline and somatic variants in accordance with the ACMG and AMP Guidelines.
In this webcast, we will cover:
- Filter logics for germline and somatic variants and selecting them into the VSClinical interface
- Capabilities of functional prediction and splice site algorithms for edge case variants
- The functionality of changing the clinically relevant transcript on variant interpretation
- Rendering a clinical report with germline and somatic variants with the inclusion of clinical trials
Advanced Report Customization via VSClinical
This document provides a summary of a presentation about advanced customization capabilities for clinical reports using VSClinical software:
- VSClinical allows customization of clinical reports through custom HTML, XML, JSON templates and scripts to enhance Word reports and integrate with REST APIs.
- Templates are provided for germline and somatic variant analysis that include ACMG/AMP guidelines and can be further customized.
- Reports can include additional data such as gene impact analysis, drug/trial information, and machine-readable outputs like JSON can be generated.
- A product demo was given to showcase report customization features.
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Interpreting somatic variants for the clinical genetic testing of tumors requires hands-on time of the most skilled clinical lab personnel. Various clinical and genomic sources must be queried, papers and guidelines referenced, and an evaluation of the clinical actionability of the mutation determined by the following the AMP guidelines. Yet, there is tremendous potential for reuse of this time consuming and valuable work!
Earlier this summer we launched our VSClinical AMP Guidelines workflow which integrates a lab-specific knowledgebase that saves every biomarkers interpretation in up to seven different snippets that ar reusable across various genomic and clinical contexts. Furthermore, our cancer workflow is bundled with the Golden Helix CancerKB, our expert-curated interpretations of the most common biomarkers for the most common cancer types, reducing the time to your first precision medicine report.
Follow along as we cover:
The interpretation of clinically actionable biomarkers for targeted molecular therapy and diagnostic/prognostic clinical reports for cancer
The different levels and scopes of re-use of the interpretation for each biomarker
Saving, re-using and updating these interpretations over time by multiple users within a clinical lab with an integrated lab-specific knowledgebase
The built in Golden Helix CancerKB that provides default interpretations for most cancer genes, biomarkers and many clinically actionable Tier I/II drug sensitivity and resistance interpretations.
In the world of genomics shaping precision medicine in oncology, the limiting factor is the time-to-sign-off on fully interpreted molecular profile reports.
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Golden Helix is a bioinformatics company that has developed software tools like CancerKB to help accelerate next-generation sequencing (NGS) cancer testing. CancerKB is a curated knowledgebase that provides clinically relevant information and interpretations of cancer variants to help generate standardized clinical reports. It is updated based on current guidelines, literature, and customer feedback to integrate the most relevant cancer data and help clinicians evaluate NGS results more efficiently. Golden Helix also acknowledges funding support from the National Institutes of Health.
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.
Automating the ACMG Guidelines with VSClinical
Clinical Genetic testing requires a complex analysis using the totality of our knowledge about the clinical relevance of a variant and a gene. This includes bioinformatic evidence as well as clinical evidence. The ACMG Guidelines provided a framework in which to score variants based on this evidence, and while some of those scoring criteria require close consultation of the clinical context for a given patient, much of it can be automated.
In this webcast, we review how VSClinical automates the ACMG scoring guidelines while integrating the collective lab expertise from previously classified variants and preferences about genes. We will cover:
Using the ACMG Auto Classifier as part the filtering strategy for gene panels and trio workflows
How gene preferences such as the default transcript, inheritance model, and disorder are updated and saved from VSClinical and used in all future analysis
How the per-variant recommendation engine builds on the auto-classification with descriptive reasons for answering each criterion yes or no
Using the auto-interpretation to present the evidence for all scored criteria in a human-readable paragraph
Working with VSClinical’s self-learning knowledgebase that incorporates previously classified variants and genes inform the interpretation of new variants!
What's hot (20)
Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
Efficient Application of NGS Family-Based Analysis
Efficient Application of NGS Family-Based Analysis
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
CNV Annotations: a crucial step in your variant analysis
CNV Annotations: a crucial step in your variant analysis
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Guidelines
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Guidelines
Advanced VSClinical Reports with Scripting and Custom Integrations
Advanced VSClinical Reports with Scripting and Custom Integrations
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Similar to Golden Helix's End-to-End Solution for Clinical Labs
VS-CNV Annotations from the User's Perspective
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.
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.
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.
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
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.
2015 functional genomics variant annotation and interpretation- tools and p...
Presented at the 2015 Functional Genomics Symposium in Doha, Qatar: http://events.sidra.org/event/functional-genomics-symposium/
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.
Getting Started with VSWarehouse - The User Experience
Built on the algorithms and high-performance storage technology that powers the VarSeq software, VSWarehouse offers a scalable, multi-project warehouse for NGS variant call sets, clinical reports, and a knowledge base of variant classifications.
Getting Started with VSWarehouse
As the number of samples and associated data volume in a testing lab increases, it becomes imperative for labs to leverage state of the art warehousing technology that not only organizes data, but also aides and enables researchers and clinicians to perform further analysis, and ongoing research.
Built on the algorithms and high-performance storage technology that powers the VarSeq software, VSWarehouse offers a scalable, multi-project warehouse for NGS variant call sets, clinical reports, and a knowledge base of variant classifications.
In this webinar, we will discuss 4 topics:
1. How to use VSWarehouse as an annotation source. We will explore questions like:
Have I ever seen this variant before?
At what frequency? (How many heterozygous and homozygous genotypes?)
Have I used this variant in a clinical report for any previous samples?
2. Using VSWarehouse to alert for changes in public annotations that warrant a review of previously reported decisions. We can use this to answer questions such as:
What has changed in public databases like ClinVar since I last accessed this variant?
3. How researchers with lots of data can use VSWarehouse to create a single repository of clinical samples that allows for retrospective cohort research studies.
4. Using the VSWarehouse API to query for information such as:
How many samples have been added to the warehouse in the past day/week/month/year?
How many tests did I conduct in the past day/week/month/year?
These questions and many more are answered by our integrated variant warehousing solution. VSWarehouse retains data from sample VCFs or their genomic annotations, even as new samples and updated annotations are added. VSWarehouse creates a single annotated matrix of all unique variants for all uploaded samples and can be accessed through multiple interfaces.
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: 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.
Apac distributor training series 3 swift product for cancer study
This document provides an overview of Swift Biosciences' product training series for their APAC distributors on using Swift products for cancer studies. It summarizes different Swift library preparation and sequencing kits that can be used for various cancer applications, including genomic sequencing, RNA sequencing, amplicon panels, hybridization capture, and DNA methylation. The document also reviews types of mutations found in cancer, considerations for cancer clinical workflows, and provides an example of using Swift's 2S Turbo kit for targeted sequencing of formalin-fixed, paraffin-embedded tissue samples.
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.
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.
Tools for Using NIST Reference Materials
This document discusses the Genome in a Bottle Consortium's efforts to develop reference materials and standards to validate next generation sequencing assays. It provides an overview of the consortium's goals to generate reference genomes with highly confident variant calls and accompanying data to allow labs to compare results and assess false positives and false negatives. The document describes some examples of how labs are using the consortium's data on the NA12878 genome to benchmark sequencing platforms and bioinformatics workflows.
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.
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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
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: 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!
Maximizing Profitability in your NGS Testing Lab
The automation of clinical NGS workflows provides a number of important benefits for labs. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In turn, these benefits create higher profitability from a P&L perspective.
Golden Helix software is designed to meet these needs by automating the full analysis workflow from sequencer to clinical report on a fixed annual subscription model. We are looking forward to discussing the best practices of maximizing profitability in your NGS testing lab and how Golden Helix supports these efforts.
Join us in this webinar as we cover how to develop repeatable cancer and germline interpretation workflows that scale from panels to whole exomes and genomes.
Handling a Variety of CNV Caller Inputs with VarSeq
Golden Helix is presenting on their software VarSeq, which can handle a variety of CNV caller inputs. VarSeq uses normalization and reference sample comparison to call CNVs from NGS coverage data. It can detect small, medium, and large CNVs from gene panels, whole exomes, and whole genomes. Previous customers have validated VarSeq for these applications. The presentation demonstrates VarSeq's CNV detection approach and ability to import calls from external callers. It also discusses using VarSeq with their guidelines software to evaluate CNV impact according to ACMG/AMP standards.
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Introducing VarSeq Dx as a Medical Device in the European Union
Introducing VarSeq Dx as a Medical Device in the European Union
Introducing VSPGx: Pharmacogenomics Testing in VarSeq
Introducing VSPGx: Pharmacogenomics Testing in VarSeq
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
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
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Single Sample and Family Based Genome Analysis With VarSeq
Single Sample and Family Based Genome Analysis With VarSeq
User perspective for somatic variant analysis in VSClinical AMP
User perspective for somatic variant analysis in VSClinical AMP
Handling a Variety of CNV Caller Inputs with VarSeq
Handling a Variety of CNV Caller Inputs with VarSeq
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Pediatric Emergency Care for Children | Apollo HospitalApollo 24/7 Adult & Paediatric Emergency Services
At Apollo Hospital, Lucknow, U.P., we provide specialized care for children experiencing dehydration and other symptoms. We also offer NICU & PICU Ambulance Facility Services. Consult our expert today for the best pediatric emergency care.
For More Details:
Map: https://cutt.ly/BwCeflYo
Name: Apollo Hospital
Address: Singar Nagar, LDA Colony, Lucknow, Uttar Pradesh 226012
Phone: 08429021957
Opening Hours: 24X7R3 Stem Cell Therapy: A New Hope for Women with Ovarian Failure
Discover the groundbreaking advancements in stem cell therapy by R3 Stem Cell, offering new hope for women with ovarian failure. This innovative treatment aims to restore ovarian function, improve fertility, and enhance overall well-being, revolutionizing reproductive health for women worldwide.
COPD Treatment in Ghatkopar,Mumbai. Dr Kumar Doshi
Are you or a loved one affected by Chronic Obstructive Pulmonary Disease (COPD)? Discover comprehensive and advanced treatment options with Dr. Kumar Doshi, a preeminent COPD specialist based in Ghatkopar, Mumbai.
Dr. Kumar Doshi is dedicated to delivering the highest standard of care for COPD patients. Whether you are seeking a diagnosis, a second opinion, or exploring new treatment avenues, this presentation will guide you through the exceptional services available at his practice in Ghatkopar, Mumbai.
Friendly Massage in Ajman - Malayali Kerala Spa Ajman
At Malayali Kerala Spa Ajman, Full Service includes individualized care for every client. We specifically design each massage session for the individual needs of the client. Our therapists are always willing to adjust the treatments based on the client's instruction and feedback. This guarantees that every client receives the treatment they expect.
By offering a variety of massage services, our Ajman Spa Massage Center can tackle physical, mental, and emotional illnesses. In addition, efficient identification of specific health conditions and designing treatment plans accordingly can significantly enhance the quality of massaging.
At Malayali Kerala Spa Ajman, we firmly believe that everyone should have the option to experience top-quality massage services regularly. To achieve that goal we offer cheap massage services in Ajman.
If you are interested in experiencing transformative massage treatment at Malayali Kerala Spa Ajman, you can use our Ajman Massage Center WhatsApp Number to schedule your next massage session.
Contact @ +971 529818279
Visit @ https://malayalikeralaspaajman.com/
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The "Comprehensive Rainy Season Advisory: Safety and Preparedness Tips" offers essential guidance for navigating rainy weather conditions. It covers strategies for staying safe during storms, flood prevention measures, and advice on preparing for inclement weather. This advisory aims to ensure individuals are equipped with the knowledge and resources to handle the challenges of the rainy season effectively, emphasizing safety, preparedness, and resilience.
The Power of Superfoods and Exercise.pdf
Healthy Eating Habits:
Understanding Nutrition Labels: Teaches how to read and interpret food labels, focusing on serving sizes, calorie intake, and nutrients to limit or include.
Tips for Healthy Eating: Offers practical advice such as incorporating a variety of foods, practicing moderation, staying hydrated, and eating mindfully.
Benefits of Regular Exercise:
Physical Benefits: Discusses how exercise aids in weight management, muscle and bone health, cardiovascular health, and flexibility.
Mental Benefits: Explains the psychological advantages, including stress reduction, improved mood, and better sleep.
Tips for Staying Active:
Encourages consistency, variety in exercises, setting realistic goals, and finding enjoyable activities to maintain motivation.
Maintaining a Balanced Lifestyle:
Integrating Nutrition and Exercise: Suggests meal planning and incorporating physical activity into daily routines.
Monitoring Progress: Recommends tracking food intake and exercise, regular health check-ups, and provides tips for achieving balance, such as getting sufficient sleep, managing stress, and staying socially active.
Surface guided deep inspiration breath hold (SG-DIBH) in ultra-hypofractionat...
Cynthia Aristei
Professor
University of Perugia and Perugia General Hospital
Italy
Gemma Wean- Nutritional solution for Artemia
GEMMA Wean is a high end larval co-feeding and weaning diet aimed at Artemia optimisation and is fortified with a high level of proteins and phospholipids. GEMMA Wean provides the early weaned juveniles with dedicated fish nutrition and is an ideal follow on from GEMMA Micro or Artemia.
GEMMA Wean has an optimised nutritional balance and physical quality so that it flows more freely and spreads readily on the water surface. The balance of phospholipid classes to- gether with the production technology based on a low temperature extrusion process improve the physical aspect of the pellets while still retaining the high phospholipid content.
GEMMA Wean is available in 0.1mm, 0.2mm and 0.3mm. There is also a 0.5mm micro-pellet, GEMMA Wean Diamond, which covers the early nursery stage from post-weaning to pre-growing.
Top massage center in ajman chandrima Spa
We are one of the top Massage Spa Ajman Our highly skilled, experienced, and certified massage therapists from different corners of the world are committed to serving you with a soothing and relaxing experience. Luxuriate yourself at our spas in Sharjah and Ajman, which are indeed enriched with an ambiance of relaxation and tranquility. We could confidently claim that we are one of the most affordable Spa Ajman and Sharjah as well, where you can book the massage session of your choice for just 99 AED at any time as we are open 24 hours a day, 7 days a week.
Visit : https://massagespaajman.com/
Call : 052 987 1315
MBC Support Group for Black Women – Insights in Genetic Testing.pdf
Christina Spears, breast cancer genetic counselor at the Ohio State University Comprehensive Cancer Center, joined us for the MBC Support Group for Black Women to discuss the importance of genetic testing in communities of color and answer pressing questions.
TEST BANK FOR Health Assessment in Nursing 7th Edition by Weber Chapters 1 - ...
TEST BANK FOR Health Assessment in Nursing 7th Edition by Weber Chapters 1 - ...rightmanforbloodline
TEST BANK FOR Health Assessment in Nursing 7th Edition by Weber Chapters 1 - 34.
TEST BANK FOR Health Assessment in Nursing 7th Edition by Weber Chapters 1 - 34.
TEST BANK FOR Health Assessment in Nursing 7th Edition by Weber Chapters 1 - 34.一比一原版(USF毕业证)旧金山大学毕业证如何办理
USF毕业证offer【微信95270640】《旧金山大学毕业证购买》《如何办理USF毕业证旧金山大学文凭学历》Q微信95270640实体公司，专业可靠，办理毕业证办美国成绩单,做加拿大文凭学历认证,办新西兰学位证，学位证书是什么?《制作旧金山大学毕业证多少钱》《USF学历证书丢了怎么办理》办澳洲文凭认证，办留信网认证（网上可查，实体公司，专业可靠）
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如果你回国在学历认证方面有以下难题请联系我们我们将竭诚为你解决认证瓶颈
1所有材料真实但资料不全无法提供完全齐整的原件。【如：成绩单丶毕业证丶回国证明等材料中有遗失的。】
2获得真实的国外最终学历学位但国外本科学历就读经历存在问题或缺陷。【如：国外本科是教育部不承认的或者是联合办学项目教育部没有备案的或者外本科没有正常毕业的。】
3学分转移联合办学等情况复杂不知道怎么整理材料的。时间紧迫自己不清楚递交流程的。
如果你是以上情况之一请联系我们我们将在第一时间内给你免费咨询相关信息。我们将帮助你整理认证所需的各种材料.帮你解决国外学历认证难题。
国外旧金山大学旧金山大学硕士学位证成绩单办理方法：
1客户提供办理信息：姓名生日专业学位毕业时间等（如信息不确定可以咨询顾问：我们有专业老师帮你查询旧金山大学旧金山大学硕士学位证成绩单）；
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6快递给客户（国内顺丰国外DHLUPS等快读邮寄）。头贼脑的倒也逗人喜爱日上三竿时山娃总爱窜进自家瓜棚里跟小伙伴们坐着聊天聊着聊着便忍不住往瓜田里逡巡一番抱起一只硕大的西瓜用石刀劈开抑或用拳头砸开每人抱起一大块就啃啃得满嘴满脸猴屁股般的红艳大家一个劲地指着对方吃吃地笑瓜裂得古怪奇形怪状却丝毫不影响瓜味甜丝丝的满嘴生津遍地都是瓜横七竖八的活像掷满了一地的大石块摘走二三只爷爷是断然发现不了的即便发现爷爷也不恼反而教山娃辨认孰熟孰嫩孰甜孰淡名义上是护瓜吃
CANSA support - Caring for Cancer Patients' Caregivers
International Cancer Survivors Day is celebrated during June, placing the spotlight not only on cancer survivors, but also their caregivers.
CANSA has compiled a list of tips and guidelines of support:
https://cansa.org.za/who-cares-for-cancer-patients-caregivers/
Hypertension and it's role of physiotherapy in it.
This particular slides consist of- what is hypertension,what are it's causes and it's effect on body, risk factors, symptoms,complications, diagnosis and role of physiotherapy in it.
This slide is very helpful for physiotherapy students and also for other medical and healthcare students.
Here is summary of hypertension -
Hypertension, also known as high blood pressure, is a serious medical condition that occurs when blood pressure in the body's arteries is consistently too high. Blood pressure is the force of blood pushing against the walls of blood vessels as the heart pumps it. Hypertension can increase the risk of heart disease, brain disease, kidney disease, and premature death.
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Golden Helix's End-to-End Solution for Clinical Labs
- 1. Golden Helix’s End-to-End Solution for Clinical Labs Steven Hystad - Field Application Scientist Nathan Fortier – Senior Software Engineer 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 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 1,100 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
- 9. Why Sentieon? – Pipeline Improvements Why Improve Broad’s GATK Haplotype Caller? GATK Haplotype Caller is the most accurate DNA analysis tool Problem: GATK Haplotype Caller is too Slow Solution Consistent: No down-sampling or thread dependency = no run-to-run differences = More accurate No Javascript: low level C More Robust: Can handle joint genotyping on over 100K samples simultaneously without needing a gVCF Software-only Solution: Easily deployable, easily scalable, and easily upgraded. Two Product Lines DNAseq – BWA-GATK Haplotype Caller Tnseq – MuTect and MuTec2
- 10. Performance: Sentieon vs Broad DNAseq TNseq
- 11. Proven Accuracy – Precision FDA Consistency Challenge - Processed single sample consistency - Single biological sample x two library preps - Top overall performance - Highest reproducibility Truth Challenge - Determine accuracy in Truth Set - Highest indel precision - Highest SNP recall
- 12. Proven Accuracy - ICGC-TCGA DREAM Mutation Calling Challenge Evaluates Somatic Variant Call Accuracy SNV INDEL Structural Variants Sentieon 98.57% Sentieon 98.14% Sentieon 100% Bina/Roche 97.57% Bina/Roche 97.01% Genowis 99.82% Genowis 96.92% OICR‐GSI 86.99% Gridss 99.63% Sentieon leads in all categories
- 13. Customizable secondary pipeline Sequencer Sentieon Linux CNV caller FASTQ BAM VCF -Annotate & filter -Clinical reports
- 14. CNV and LoH Detection VarSeq Calls CNVs on - Gene Panel Data - Exome Data - Whole Genome Data Faster than CMA and MLPA Utilizes existing coverage data Calls CNVs of every size - Small Single Exon Events - Large Cytogenetic Events
- 15. 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
- 16. 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
- 17. VarSeq Full Clinical Stack
- 18. VarSeq Suite Variant annotation, filtering, and interpretation Rich visualizations with GenomeBrowse built-in Powerful GUI and command-line interfaces Repeatable workflows VarSeq Simple Flexible Scalable
- 19. Example Workflows Illumina TruSight Cancer Sequencing Panel - Oncogenes & Tumor Suppressor Genes - Drug Targeting Information & Ongoing Clinical Trials Exome Trio Workflow - Casual Variants Associated with Phenotype - Incidental Findings Hereditary Risk Sequencing Panel - Comprehensive coverage of 175 genes with known associations to inherited cardiac conditions, cancers, and other inherited diseases.
- 20. Sample Data for Cancer Gene Panels Illumina TruSight Cancer Sequencing Panel - Comprehensive coverage of 154 genes designed to target exons of key tumor suppressor genes and frequently cited oncogenes. - BAM and VCF files for each replicate are available VSReports
- 22. Sample Data for Exome Trio Workflows NA1278 17-year old Caucasian Women - Admitted for Symptoms of Acute Gastroenteritis. - Serum testing revealed elevated pancreatic enzymes. - Genetic testing revealed Heterozygosity for CFTR gene mutation Δ F508 Incidental Findings NA12891NA12892 NA12878
- 24. VSWarehouse – Variant Warehouse Server A place to archive full VCFs of every sequenced sample Centralized genomic data hosting, integration with other systems Ask the Variant Warehouse: - Have I ever seen this variant in my previous test samples? - At what frequency? (counts as well) - Does this gene contain other rare variants in my cohort? - Did I provide a pathogenicity assessment for this variant? Has that changed? - Has ClinVar changed since that assessment was initially made? - Have I put this variant into a clinical report for any previous samples?
- 25. Integration with VarSeq VarSeq can “Export to Warehouse” - Create a new Project - Current project template is used - Add Variants to Existing (data only) Annotate with Warehouse Counts - Allele / Genotype counts computed on warehouse variants (or other sources in template). Remote Assessment Catalogs - Customize databases of variant classifications or internal flags like false-positives. Remote Reports - Central versioning of report - Queryable database of all saved reports, with all data in form ready for EMR/LIMS integration
- 26. VSWarehouse – Centralized Collaboration Project A Project B VSWarehouse Server Group A Group B Collaborators
- 27. VSWarehouse – Centralized Collaboration
- 28. VarSeq Full Clinical Stack
- 29. Questions or more info: Email info@goldenhelix.com Request an evaluation of the software at www.goldenhelix.com