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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.
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An Exploration of Clinical Workflows in VarSeq
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
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.
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.
AMP-Based Variant Classification with VSClinical
The document discusses Golden Helix's VSClinical software and its capabilities for analyzing biomarkers and variants according to AMP and ACMG guidelines. VSClinical provides a four-phased workflow to 1) filter variants, 2) assess evidence, 3) develop classifications, and 4) include interpretations in clinical reports. It leverages Golden Helix's CancerKB knowledgebase to accelerate variant interpretation and standardized reporting. The document demonstrates VSClinical's analysis and reporting of variants from a myeloid gene panel according to AMP guidelines.
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
Golden Helix's End-to-End Solution for Clinical Labs
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
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!
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
Recommended
An Exploration of Clinical Workflows in VarSeq
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
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.
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.
AMP-Based Variant Classification with VSClinical
The document discusses Golden Helix's VSClinical software and its capabilities for analyzing biomarkers and variants according to AMP and ACMG guidelines. VSClinical provides a four-phased workflow to 1) filter variants, 2) assess evidence, 3) develop classifications, and 4) include interpretations in clinical reports. It leverages Golden Helix's CancerKB knowledgebase to accelerate variant interpretation and standardized reporting. The document demonstrates VSClinical's analysis and reporting of variants from a myeloid gene panel according to AMP guidelines.
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
Golden Helix's End-to-End Solution for Clinical Labs
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
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!
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
Building Secure Analysis and Storage Systems with Golden Helix
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.
Golden Helix is in a unique position to provide completely on-premise analysis solutions with a history of building analysis software from the ground-up on first principles and a focus on providing integrated, turn-key solutions. This allows for a licensing model based on training and supporting users, not tracking per-sample usage of cloud resources. As the regulatory environment around the world strengthens the privacy rights of individuals and the outcry around data breaches raises the stakes for building a secure system, we have developed a number of best practices for building secure, offline genomic analysis pipelines. Watch as we cover:
- Building a FASTQ to clinical reports pipeline behind a firewall
- On-premise analysis, warehouse and data servers independent of the internet
- Single sign-on based on local credential systems and without internet access
- Storage and network considerations for the analysis of patient-linked data
- Choose when to update and validate new pipelines, data sources and software versions
We hope you enjoy as we review the capabilities and best practices in building the most secure environment for hosting the analytics behind your precision medicine tests.
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.
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.
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.
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.
In this webcast, we are going to explore the value and application of VSWarehouse. Our example variants will showcase a situation where variants of uncertain significance ultimately reach a pathogenic classification based on updates to ClinVar. This change will be presented not only in VarSeq with listings of previous samples but also shown directly from the VSWarehouse browser in a ClinVar classification tracker. We will also look at an alternative situation where the classification may change to benign for some previously reported variants which would require follow-up with the patient. The importance of a tool like the ClinVar tracker in VSWarehouse cannot be understated as it is a simple way to comprehensively review the backlog of changing variant classifications when users must update their locked down validated NGS pipeline. Please join us in the upcoming webcast to explore how these features in VarSeq and VSWarehouse work to allow users thorough accountability in updating historical patient results with new variant evidence
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
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.
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
When performing variant analysis on whole exome or large gene panels, clinicians must sort through thousands of variants to determine which variants are most likely to be associated with the patient’s phenotypes. To assist with this process, we have implemented the PhoRank algorithm, which incorporates phenotypic associations to highlight the most relevant genes with potentially damaging variants. PhoRank 1.0 supports researchers leveraging all possible gene-disease associations by traversing multiple gene and pathway ontologies. Recent papers have demonstrated new techniques that have improved ranking performance in a clinical context. We have incorporated these new strategies into PhoRank 2.0: providing better ranking and improved computational performance for most clinically diagnostic and testing scenarios. Join us in this webinar as we cover:
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.
Clinical Reporting Made Easy
This webcast will walk through preparing a template for report generation, reviewing the generated report and performing some report customizations.
Introducing VSClinical AMP Guidelines: A Comprehensive Workflow for NGS Testi...
Golden Helix is introducing new guidelines for next-generation sequencing (NGS) testing of cancer samples using their VSClinical software. The AMP guidelines provide a comprehensive workflow for variant filtering, annotation, classification evidence levels, and integrated clinical reporting of somatic and germline variants. The software utilizes various data sources to aid in cancer interpretation and allows users to save and reuse interpretations. An upcoming webinar will demonstrate how to score somatic variants for oncogenicity using VSClinical.
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.
BIO 2010 Partnering with Patients
The document discusses various ways that nonprofit organizations partner with patients and the medical research community to advance research and drug development. It provides examples of how organizations fund research, develop tools and resources, facilitate clinical trials, advocate for policy changes, and build communities to accelerate the development of new treatments. Specific organizations highlighted include the Alzheimer's Drug Discovery Foundation, Juvenile Diabetes Research Foundation, Multiple Myeloma Research Foundation, ALS Therapy Development Institute, and Genetic Alliance.
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!
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
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.
The community has stepped up to provide disease-specific gene lists that are validated and well-researched for specific genetic disorders. In this webinar, we will discuss how these gene lists can be incorporated into your VSClinical workflows and we will demonstrate how these gene lists can be modified to meet the specific needs of your lab.
Things you will learn:
How to manage gene lists in a single location and use them for filtering, annotation, and reporting
How to use the recently released ACMG Secondary Findings v3.0 list for reporting incidental findings
How to leverage the well-researched PanelApp knowledgebase to construct your gene lists based on different levels of evidence for a specific disease
How to define gene lists based on the specific phenotypes and disorders you are targeting with your tests
A Walk Through GWAS
Genome-wide association studies (GWAS) have been providing valuable insight to the genetics of common and complex diseases for many years. In this webcast we will walk through one possible workflow for completing GWAS in Golden Helix SNP & Variation Suite (SVS) with special attention paid to adjusting analysis for population stratification.
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.
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
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.
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.
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.
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/
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Building Secure Analysis and Storage Systems with Golden Helix
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.
Golden Helix is in a unique position to provide completely on-premise analysis solutions with a history of building analysis software from the ground-up on first principles and a focus on providing integrated, turn-key solutions. This allows for a licensing model based on training and supporting users, not tracking per-sample usage of cloud resources. As the regulatory environment around the world strengthens the privacy rights of individuals and the outcry around data breaches raises the stakes for building a secure system, we have developed a number of best practices for building secure, offline genomic analysis pipelines. Watch as we cover:
- Building a FASTQ to clinical reports pipeline behind a firewall
- On-premise analysis, warehouse and data servers independent of the internet
- Single sign-on based on local credential systems and without internet access
- Storage and network considerations for the analysis of patient-linked data
- Choose when to update and validate new pipelines, data sources and software versions
We hope you enjoy as we review the capabilities and best practices in building the most secure environment for hosting the analytics behind your precision medicine tests.
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.
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.
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.
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.
In this webcast, we are going to explore the value and application of VSWarehouse. Our example variants will showcase a situation where variants of uncertain significance ultimately reach a pathogenic classification based on updates to ClinVar. This change will be presented not only in VarSeq with listings of previous samples but also shown directly from the VSWarehouse browser in a ClinVar classification tracker. We will also look at an alternative situation where the classification may change to benign for some previously reported variants which would require follow-up with the patient. The importance of a tool like the ClinVar tracker in VSWarehouse cannot be understated as it is a simple way to comprehensively review the backlog of changing variant classifications when users must update their locked down validated NGS pipeline. Please join us in the upcoming webcast to explore how these features in VarSeq and VSWarehouse work to allow users thorough accountability in updating historical patient results with new variant evidence
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
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.
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
When performing variant analysis on whole exome or large gene panels, clinicians must sort through thousands of variants to determine which variants are most likely to be associated with the patient’s phenotypes. To assist with this process, we have implemented the PhoRank algorithm, which incorporates phenotypic associations to highlight the most relevant genes with potentially damaging variants. PhoRank 1.0 supports researchers leveraging all possible gene-disease associations by traversing multiple gene and pathway ontologies. Recent papers have demonstrated new techniques that have improved ranking performance in a clinical context. We have incorporated these new strategies into PhoRank 2.0: providing better ranking and improved computational performance for most clinically diagnostic and testing scenarios. Join us in this webinar as we cover:
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.
Clinical Reporting Made Easy
This webcast will walk through preparing a template for report generation, reviewing the generated report and performing some report customizations.
Introducing VSClinical AMP Guidelines: A Comprehensive Workflow for NGS Testi...
Golden Helix is introducing new guidelines for next-generation sequencing (NGS) testing of cancer samples using their VSClinical software. The AMP guidelines provide a comprehensive workflow for variant filtering, annotation, classification evidence levels, and integrated clinical reporting of somatic and germline variants. The software utilizes various data sources to aid in cancer interpretation and allows users to save and reuse interpretations. An upcoming webinar will demonstrate how to score somatic variants for oncogenicity using VSClinical.
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.
BIO 2010 Partnering with Patients
The document discusses various ways that nonprofit organizations partner with patients and the medical research community to advance research and drug development. It provides examples of how organizations fund research, develop tools and resources, facilitate clinical trials, advocate for policy changes, and build communities to accelerate the development of new treatments. Specific organizations highlighted include the Alzheimer's Drug Discovery Foundation, Juvenile Diabetes Research Foundation, Multiple Myeloma Research Foundation, ALS Therapy Development Institute, and Genetic Alliance.
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!
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
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.
The community has stepped up to provide disease-specific gene lists that are validated and well-researched for specific genetic disorders. In this webinar, we will discuss how these gene lists can be incorporated into your VSClinical workflows and we will demonstrate how these gene lists can be modified to meet the specific needs of your lab.
Things you will learn:
How to manage gene lists in a single location and use them for filtering, annotation, and reporting
How to use the recently released ACMG Secondary Findings v3.0 list for reporting incidental findings
How to leverage the well-researched PanelApp knowledgebase to construct your gene lists based on different levels of evidence for a specific disease
How to define gene lists based on the specific phenotypes and disorders you are targeting with your tests
A Walk Through GWAS
Genome-wide association studies (GWAS) have been providing valuable insight to the genetics of common and complex diseases for many years. In this webcast we will walk through one possible workflow for completing GWAS in Golden Helix SNP & Variation Suite (SVS) with special attention paid to adjusting analysis for population stratification.
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.
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
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.
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.
What's hot (20)
Building Secure Analysis and Storage Systems with Golden Helix
Building Secure Analysis and Storage Systems with Golden Helix
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...
VSWarehouse: Tracking Changing Variant Evidence and Classifications
VSWarehouse: Tracking Changing Variant Evidence and Classifications
CNV Annotations: a crucial step in your variant analysis
CNV Annotations: a crucial step in your variant analysis
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
Introducing VSClinical AMP Guidelines: A Comprehensive Workflow for NGS Testi...
Introducing VSClinical AMP Guidelines: A Comprehensive Workflow for NGS Testi...
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Guidelines
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Guidelines
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Efficient Application of NGS Family-Based Analysis
Efficient Application of NGS Family-Based Analysis
Creating & Managing Reusable Gene Lists with VSClinical
Creating & Managing Reusable Gene Lists with VSClinical
Advanced VSClinical Reports with Scripting and Custom Integrations
Advanced VSClinical Reports with Scripting and Custom Integrations
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
Similar to Annotation capabilities
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.
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/
Axt microarrays
This document discusses clinical and consumer applications of microarrays and genotyping technologies. It provides an overview of genotyping and different technologies like PCR microarrays and SNP microarrays. It describes how microarrays are still useful despite the rise of sequencing due to their low cost, high throughput, and ability to test millions of markers. The document outlines several applications of microarrays like direct-to-consumer testing, pharmacogenetics, and clinical sequencing. It also discusses challenges and trends in these areas like global initiatives to increase genomic data sharing.
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.
2015 TriCon - Clinical Grade Annotations - Public Data Resources for Interpre...
The availability and details of using public genomic annotation sources to do clinical grade genomic diagnosis, using the exomes of myself, wife and son as the case study.
Using the GRCh38 reference assembly for clinical interpretation in VSClinical
Although the latest reference genome (build 38) was released in 2009, it has taken quite a while to come into its own as a baseline for the clinical interpretation of variants in human disease. A lot of this was momentum, while some of it was concerns about compatibility with other labs and published literature. Yet the largest hindrance was the lack of support of the bioinformatic tools and requisite databases required to analyze variants. When we released VSClinical, we wanted those concerns to be removed from the choice of what reference genome a lab may choose to use.
In this webcast, we will:
Review the cost and benefits of using the new GRCh38 reference genome in the context of clinical genetics.
Look at the public data resources that have native support, and Golden Helix’s effort to lift over the ones that do not.
Provide examples of situations where changing reference genomes introduces or negates artifacts caused by errors in the reference sequence.
Demonstrate VarSeq’s new ability to lift over to the new reference genome while importing your VCFs into a project.
Go through VSClinical using the new human reference genome, with full annotation support and downstream use of assessment catalogs and writing of reports.
Whether you have already made the switch or considering the possibility, this webcast will provide you with what you need to know about using the new reference genome for clinical genetic testing as well as human disease research using VarSeq. We hope to see you there!
CNV, GWAS & Clinical Analysis Advancements in SVS
Copy number variation (CNV) can be drivers in many genetic diseases and can be called using our clinical and research application platforms: VarSeq and SVS, respectively. Using these platforms, CNV are called using the existing coverage data stored in your BAM files and are detected using a targeted or binned region approach. As the targeted approach has been demonstrated in previous webcasts, we wanted to focus on the binned region approach that is implemented for detecting CNV from shallow-coverage whole-genome sequencing (WGS) data. In this webinar we will cover:
-Providing an overview of how the binned region approach on whole genomes can be used to call large copy number events in both VarSeq and SVS
Additional analysis in SVS following the CNV calling steps that takes advantage of the rich research platform SVS provides
-Other updates in the latest version of SVS to improve GWAS workflows
The addition of the Clinical Variant Scoring module to SVS to provide advanced variant annotations for functional predictions and conservation scores
SVS continues to be an industry-leading platform for genomic researchers studying humans as well as plant and animal species. Enjoy this webcast on whole-genome CNV calling and the latest capabilities of SVS!
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.
Using Public Access Clinical Databases to Interpret NGS Variants
In this webcast on February 19th, Gabe Rudy, Vice President of Product Development, will showcase publicly available databases and resources available for interpreting rare and novel mutations in the context of his own personal exome obtained through a limited 23andMe pilot in 2012.
The last couple years have seen many changes in well-established resources such as OMIM and dbSNP, while motivating new efforts such as ClinVar and PhenoDB to bring NGS interpretation to clinical grade through a global data sharing effort.
In this webcast, Gabe will cover:
The changing landscape of public annotations: Then, Now, and Soon.
Will the new human reference (GRCh38) released in December be a game changer?
Specific examples of improvements in annotation and algorithms that result in more accurate analysis of his own exome.
The utility and progress of NGS to different clinical applications in terms of public resources: carrier screening, hereditary cancer risk, pharmacogenomics, oncology care, and genetic disorder diagnosis.
Sharing of new clinical data: How both variation and phenotype level data is currently being shared and what will be the way forward to match rare and undiagnosed cases at a global scale.
Processing Hereditary Cancer Panels in VarSeq
Processing variants related to cancer is an incredibly critical process and a primary goal is to not only assess the variants rapidly but also accurately. A major improvement to cancer panel workflow efficiency is to utilize VarSeq for variant filtering, annotating, and interpretation. In this webcast we’ll cover some important quality assurance capabilities VarSeq provides, multiple approaches to build targeted panels, how to access/utilize numerous cancer annotations, and finally work through the ACMG guideline process on the selected germline cancer variants. The overall goal is to cover the basics of building the cancer gene panel project template so that it can be used routinely in high throughput environments.
140128 use cases of giab RMs
The document discusses various use cases of the Genome in a Bottle (GIAB) Reference Materials from the NIST. It provides examples of how several organizations, including NIST, HSPH, MoCha lab at NCI, Personalis, Mount Sinai, Qiagen, and others are using the GIAB reference materials and consensus variant lists to evaluate sequencing platforms and variant calling pipelines, tune variant calling parameters, assess specificity of targeted sequencing assays, and characterize regions of the exome. The GIAB materials are serving as a useful community resource and gold standard for benchmarking sequencing and analysis methods.
Functional Predictions and Conservation Scores in VSClinical
Computational evidence plays a vital role in the interpretation of variants using the ACMG guidelines. This includes functional prediction scores like SIFT and PolyPhen2, as well as conservation metrics such as GERP++ and PhyloP. In this webcast, we review the conservation scores and functional prediction algorithms available in VSClinical. This includes a discussion of our own implementation of these algorithms, along with a comparison to more recent variant prediction methods.
Big Data at Golden Helix: Scaling to Meet the Demand of Clinical and Research...
This document summarizes Golden Helix's capabilities for handling big data in genomics. It discusses how Golden Helix's software tools like VarSeq and the Variant Storage Warehouse can scale to handle large volumes of genomic and clinical data from whole genome sequencing, exome sequencing, and large population studies. It provides examples of how these tools have been used for clinical and research applications like variant filtering, annotation, and analysis of rare variants. The presentation concludes with a demonstration of the software.
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.
Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation Sources
Earlier this year we launched our latest product VSClinical featuring workflow support for the ACMG guidelines with advanced automation capabilities and per-criteria recommendations. It has been amazing to watch the adoption of this product in labs doing both germline and in some cases cancer variant interpretation. Our latest VarSeq 2.1 release demonstrates our approach to iterative product improvements based on our engaged relationship with our customers and includes numerous improvements to VSClinical.
In this webcast, we cover the new and updated capabilities that can add value to your genetic testing workflows as well as review the VarSeq workflow support somatic variant interpretation in tumors by leveraging our cancer-specific annotations sources. In this webcast, we:
Demonstrate the new “Consortium Classification” support in VSClinical to have an additional ClinVar-like annotation source added to the automated and interactive ACMG scoring process
See how previous interpretations are integrated into your VSClinical analysis, whether they are for the current variant or are just in the genomic neighborhood
Cover the additional “Lookup in PubMed” variant search feature for finding supporting studies that may provide functional or clinical evidence for a variant
See in action the new ACMG Auto Scoring based templates for trio analysis and gene panel tests
Review somatic variant filtering and prioritizing in VarSeq and the updates to relevant public annotation sources including CiVIC, ICGC and a new and available to license COSMIC v86!
Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation Sources
Earlier this year we launched our latest product VSClinical featuring workflow support for the ACMG guidelines with advanced automation capabilities and per-criteria recommendations. It has been amazing to watch the adoption of this product in labs doing both germline and in some cases cancer variant interpretation. Our latest VarSeq 2.1 release demonstrates our approach to iterative product improvements based on our committed relationship with our customers and includes numerous enhancements to VSClinical.
In this webcast, we cover the new and updated capabilities that can add value to your genetic testing workflows as well as review the VarSeq workflow support somatic variant interpretation in tumors by leveraging our cancer-specific annotations sources. In this webcast, we:
-Demonstrate the new “Consortium Classification” support in VSClinical to have an additional ClinVar-like annotation source added to the automated and interactive ACMG scoring process.
-See how previous interpretations are integrated into your VSClinical analysis, whether they are for the current variant or are just in the genomic neighborhood.
-Cover the additional “Lookup in PubMed” variant search feature for finding supporting studies that may provide functional or clinical evidence for a variant.
-See in action the new ACMG Auto Scoring based templates for trio analysis and gene panel tests.
-Review somatic variant filtering and prioritizing in VarSeq and the updates to relevant public annotation sources including CiVIC, ICGC and a new and available to license COSMIC v86!
GIAB for AMP GeT-RM Forum
This document summarizes benchmarking of germline small variant calling using Genome in a Bottle (GIAB) reference materials. It highlights best practices for benchmarking, including using benchmarking tools like hap.py and stratified performance metrics. It demonstrates benchmarking an Illumina HiSeq dataset aligned and called against GRCh37 using hap.py and stratifications from the GA4GH benchmarking tool. The results show precision and recall metrics with confidence intervals to evaluate performance across variant classes and difficulty levels. Ongoing work includes developing GIAB resources for GRCh38 and structural variants.
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.
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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.
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.
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
From gene panels to whole genome, from short to long-read sequencing, the VarSeq suite is the solution for NGS analysis and reporting in a modern clinical lab. VarSeq handles the spectrum of variant types (SNV, Indel, CNV, Fusions) and provides automated classification and reporting capabilities following the ACMG and AMP guidelines. With our new PacBio partnership, we are more adaptable than ever with creating a spectrum of custom workflows to suit our unique user needs.
This webcast will review:
-Data analysis scaling from Gene Panel to Genome analysis with VarSeq and VSWarehouse.
-Analysis and annotation of SNVs, Indels, CNVs, and fusions.
-A close look at a PacBio long-read trio analysis.
Come join us for this showcase in modern VarSeq analysis capabilities.
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. The latest SVS release introduces a significant leap in capabilities, with a focus on advanced Polygenic Risk Score (PRS) calculations. PRS has become a fundamental tool in genomic research, enabling the identification of correlations between genotypic variants and phenotypes across large populations.
This enhancement is particularly relevant for researchers working on large cohorts and meta-analysis. Please join us as we explore:
-SVS Workflow Review: A review of the extensive capabilities of SVS to meaningful insights from large cohorts and association test result datasets
-Computing Polygenic Risk Scores: An overview of the PRS capabilities in SVS, including Clumping and Thresholding and creation of multiple PRS models
-Evaluating and Applying PRS: Evaluating PRS models in-sample and out-of-sample and applying PRS models to perform trait prediction
-Future Implications: Brief exploration of how these advancements in SVS could influence future genomic research.
This webcast will explore how SVS facilitates the creation of multiple PRS models from large-scale genomic data, such as those obtained from extensive cohort studies or comprehensive meta-analyses. Join us to discover how these latest updates in SVS are supporting large-scale genomic research.
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
With our recent launch of VarSeq 2.5.0, our ability to expedite somatic analysis for NGS labs is more accessible than ever before. Our recent webcasts have shown our range of updates, including our new oncogenicity classifier and carrier status workflows:
Identifying Oncogenic Variants in VarSeq
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
In this user perspective webcast, we will highlight how the combination of our new oncogenicity classifier and the updates to our CancerKB database streamline the interpretation of oncogenic variants. In addition, as NGS labs progress from gene panels to WES analysis for ideal genomic signature generation, we will demonstrate how a VarSeq somatic workflow can scale with these increased scopes of data analysis with ease.
Our user perspective webcast will cover:
Application of virtual panels to WES tumor/normal workflows.
Use of the oncogenicity classifier to streamline filter chains.
Updates to our CancerKB database to include the CancerKB gene track.
Including parallel germline secondary findings for the whole NGS workflow.
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
Golden Helix introduced new capabilities in VarSeq 2.5.0 to support carrier screening analysis through NGS data. Key features include the ability to import partnered samples, detect shared carrier variants between samples at the gene level using a couples carrier screening workflow, and generate clinical reports that calculate reproductive risks and include variant interpretations. The software is designed to scale from gene panels to whole exomes/genomes. A demo showed how these new features streamline the carrier screening analysis process from data import and filtering to clinical reporting.
Identifying Oncogenic Variants in VarSeq
The interpretation of somatic variants can be a challenging process. While AMP Guidelines provide detailed rules for accessing the clinical evidence associated with a specific variation, they do not specify criteria for determining if a variant is likely to be a driver mutation, which generates functional changes that enhance tumor cell proliferation. In this webcast, we will discuss a new VarSeq algorithm for estimating the oncogenicity of a variant. This will include a deep dive into our oncogenicity scoring system and a discussion of the various criteria used to distinguish driver mutations from benign variations and variants of uncertain significance.
What you will learn in this webcast:
-How to use the scoring algorithm to identify variants with evidence of oncogenicity
-Which criteria are used to assess a variant's oncogenicity
-How to evaluate the oncogenicity of a variant in VSClinical
Best Practices for Validating a Next-Gen Sequencing Workflow
Validating an NGS workflow is an iterative process that begins with collaboration with personnel and planning protocols for the entire workflow from sample preparation, sequencing and variant calling, all the way to data analysis and reporting. At Golden Helix, while we do not provide pre-validated black-box workflows, we provide our customers with support to validate workflows in a transparent manner, and assist them in reaching production deadlines. This webcast will be led by members of our Field Application Scientist team, and we will explore some of the best practices for NGS workflow validation that we have observed and helped to implement based on real-world examples from our customer base. Key topics for discussion will include:
Sample preparation and collection of adequate case/control data
Designing a robust workflow with special considerations for single versus family analyses and phenotypic considerations
Generating the desired output for clinical or other reports
Real world NGS workflow validation strategies
Tune in for tips and strategies that you can deploy when designing and validating your NGS workflow.
2023 Innovation Awards Winner, Dr. Muthukumaran
Expanded carrier screening in an infertile/affected Couple for determining carrier status for genetic mutations - VarSeq Couple Carrier Workflow
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
Mendelian disorders can be caused by various classes of genetic mutations, from small variants to CNVs and even Structural Variants. With the introduction of VarSeq 2.4.0, we are excited to unveil the latest advancements in VSClinical ACMG, focusing on the integration of Structural Variants and the enhanced automation capabilities that streamline your analysis process.
Join us in this webcast as we dive into the following topics:
Integration of Structural Variants: Learn how VarSeq 2.4.0 enables you to import and incorporate Structural Variants into your VSClinical ACMG evaluations and reports, providing a comprehensive understanding of the genetic landscape.
Advanced Automation in the ACMG Interface: Discover how evaluation scripts can be employed to automate the VSClinical ACMG interface, allowing you to perform custom actions or eliminate manual steps, thus increasing efficiency and reducing the risk of errors.
End-to-End Automation: Explore how VSPipeline can fully automate your analysis process, from raw VCF to report, ensuring a streamlined and consistent workflow that saves time and resources.
Harnessing the Power of VSClinical: Gain insights into how VarSeq 2.4.0 empowers you to tackle complex genomic data, enabling faster and more accurate identification of Mendelian disorders and facilitating personalized patient care.
With the advanced capabilities of VarSeq 2.4.0 and VSClinical, you can now unlock a new level of precision and efficiency in diagnosing Mendelian disorders. This webcast will showcase the latest innovations in variant interpretation and automation, exemplifying why the VarSeq Clinical Suite is the premier NGS analysis platform for germline and cancer testing.
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
There is a strong motivation for labs to bring most, if not all, of their next-gen sequencing pipeline in-house. This is especially relevant for clinical applications where there is a need to validate any routine diagnostics when seeking to provide genetic results to patients. The entirety of the NGS pipeline is highly automatable and comprised of multiple stages but from the geneticist's point of view, the tertiary stage requires the lengthiest review. This stage is where the geneticist sifts through the massive collection of genetic variants to find and report on those most relevant to the patient or population. Unfortunately, the tertiary stage can be a fairly sophisticated process and there aren’t many tools on the market that handle it comprehensively and simply. Many of the tools that are available may have severe limitations on the scale of genomic data they can process or limitations on the types of NGS assays that can be designed. Moreover, their license model may be on an individual sample basis and present cost-benefit hurdles for the user, especially when sample load will inevitably increase. Fortunately, none of these assay or cost-based issues are relevant with Golden Helix products.
The goal of this webcast is to expose our viewers to the versatility that GHI VarSeq provides when constructing your dream NGS assay. This demonstration will provide examples of germline and somatic workflows for both single and multi-sample analysis for a variety of different disorders. Please join us and learn more about the analytical possibilities you can achieve when using the VarSeq software.
Prenatal Genetic Screening with VarSeq
Our past webcast explored the current approaches for screening and diagnosis of genetic disorders in prenatal testing. While the methods available at the time were robust, they were severely limited, creating a need for a higher diagnostic yield and more efficient analysis for a wider range of genetic tests. The solution proposed was to improve and simplify prenatal screening and diagnosis with whole exome sequencing (WES).
During that webcast, we highlighted the advantages of WES over traditional methods such as karyotyping and chromosomal microarray, including improved accuracy, granularity, and cost-effectiveness. We also emphasized the potential of WES to expand diagnosis for many other adverse maternal-fetal complications beyond the large aneuploidy events previously covered. However, there was still an intimidation factor when it came to the massive data output from the exome. Fortunately, Golden Helix provided the necessary tools to build and standardize these genetic assays, simplifying the analytical process while leveraging increased diagnostic output. We explored our VarSeq software to demonstrate some example workflows of cases positive for Trisomy 21, an exon loss in DMD related to Duchenne Muscular Dystrophy, and detection of a single base change resulting in a LOF variant in RUNX1 relevant to hereditary leukemia.
Our goal was to expose our viewers to the methods of conquering this vast NGS-based data and play a role in dissolving any feeling of intimidation. Overall, exome sequencing has the potential to vastly improve diagnostic outcomes and widen discoveries in the research related to prenatal testing, and Golden Helix products are designed to facilitate this process.
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
NGS tests in the clinic cover more use cases than ever and are increasingly complex to implement. This leads to an increase in time to validate and bring tests to production, impacting a lab’s ability to be economically viable and serve the needs of patients. Core to the complexity is the expansion of tests to include multiple types of biomarkers and variants, including CNVs, gene fusions, and genomic signatures. The bioinformatics demands of these pipelines require powerful tools with built-in capabilities to handle the diverse needs of modern NGS tests and to integrate and automate the disparate steps leading to clinical insight.
Join us in this webinar as we explore the VarSeq suites’ capabilities as a fast, modular, and highly configurable solution for variant analysis and interpretation. We will cover:
The bioinformatic diversity of comprehensive genetic tests with NGS
Automation of FASTQ to clinical reports without losing control over the results of a test
Leverage built-in and custom automation capabilities in the VSClinical cancer guideline workflow to reduce work and improve accuracy
Reporting the relevant diagnostic and therapeutic findings for a patient based on the raw genomic data of modern NGS tests requires both human experience and advanced analysis software. We hope you can join us as we unpack how automation is a critical part of implementing NGS tests and furthering the application of precision medicine.
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
Comprehensive genomic testing via next generation sequencing (NGS) is being increasingly adapted as part of cancer care in conjunction with molecular and immunohistochemical tests. Comprehensive genomic profiling potentially expands the number of targeted therapies that are available to patients, improves patient diagnosis and prognosis, and increases the number of clinical trials that are relevant to patients. However, with these advancements come challenges such as gaps in expertise resulting in inadequate efforts to interpret genomic data accurately and efficiently, poorly coordinated efforts to implement precision care, patients being diagnosed and treated despite inadequate access to relevant information and subsequent lack of patient exposure to all available treatment options.
Golden Helix CancerKB v2.0 provides a means of closing the gap, whether you're a beginner who is trying to capture the vast amount of knowledge in the cancer field or an expert who has high sample volume AND needs to keep up with the ever-evolving knowledge of Tier II and III variants. In this webcast, we will discuss and apply Golden Helix CancerKB in the context of cancer precision medicine. Golden Helix CancerKB is systematically curated and reviewed by experts in the field and contains information about cancer genes, biomarkers, and treatments generated from several trusted cancer resources. With VarSeq 2.3.0’s added support for comprehensive cancer genomic profiling tests, Golden Helix CancerKB has expanded to include interpretations for genomic signatures, combination biomarkers, and more investigational (tier II) biomarkers, among several other additions that will be discussed. With the Golden Helix CancerKB database, users will experience a streamlined automatic matching of biomarkers to available drugs and trials which ultimately saves users massive amounts of time and effort while reducing the possibility for errors.
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
VarSeq 2.3.0 facilitates the evaluation of a multitude of somatic genomic variations with a more refined user interface to streamline variant evaluation. Our recent webcasts have shown the full range of these newly developed upgrades:
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Now, we are showing it all in action from the user’s perspective. This webcast will provide a comprehensive demonstration of performing somatic variation analysis and reporting. We will review how to use workflow automation to expedite the NGS project creation process and report rendering. We will also demonstrate the streamlined capture of knowledge during variant evaluation by leveraging our clinical expert-curated interpretations with the Golden Helix Cancer Knowledge Base (CancerKB).
We hope you will join us to see VarSeq 2.3.0 from a user’s perspective, covering:
-Somatic variant workflows: necessary algorithms and filtering strategies
-Import of all relevant biomarker and genomic signatures data from TSO-500
-Review content and value of clinically curated interpretations and treatments with CancerKB
-Interpretation of structural variants in the VSClinical AMP Guidelines workflow
-Workflow automation with VSPipeline
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
Next Generation Sequencing allows for the detection of a wide variety of genomic alterations. This includes small mutations, copy number variants and complex rearrangements. However, it can be difficult to annotate, filter, and interpret these alterations.
As part of our VarSeq 2.3.0 release, we have greatly simplified this process by allowing you to import, annotate, and filter mutations across all spectrums of genomic variation. This supports concurrent importation of small variants and CNVs as well as complex rearrangements. This release also includes strong support for structural variant annotation, filtering, and interpretation, including structural variant effect prediction. After filtering is complete, any clinically relevant structural variants can be interpreted with the VSClinical AMP Guidelines workflow and included in the final clinical report.
Come join us for this webcast to discuss VarSeq’s enhanced import and annotation capabilities, including:
Concurrent importation of variants CNVs and complex rearrangements
Improved multi-threaded import which dramatically speeds up the importation of large VCFs
Annotation of structural variants and prediction of effect
Interpretation of structural variants in the VSClinical AMP Guidelines workflow
Support for visualization and use of CRAM files as input for computing coverage statistics
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Precision medicine for cancer is rapidly accelerating because of the development and approval of targeted molecular therapies. These therapies require new genomic biomarkers as an indication for use, and require evaluating additional mutation types that are available in comprehensive genomic profiling assays as well as the small variants detected by Next-Generation Sequencing gene panels.
We are excited to announce VarSeq 2.3.0 which will update the VSClinical AMP workflow to meet the growing needs of labs conducting comprehensive genomic profiling (CGP) of tumors. This includes built-in support for the Illumina TruSight Oncology 500 (TSO-500) kit as well as similar kits from other vendors. The VSClinical AMP workflow has also gained native support for the bioinformatic outputs of CGP kits. Join us to learn about comprehensive genomic profiling in cancer, specifically:
Evaluation and clinical reporting of genomic signatures such as Microsatellite (MSI), Tumor mutation burden (TMB), PD-L1, Homologous recombination deficiency (HRD) statuses, and more.
Built-in TSO-500 import and expandable import capabilities for new genomic data types through the new advanced workflow scripting system.
Golden Helix CancerKB updates with report-ready genomic-signature interpretations written for approved therapies as well as gene interpretations for all 500 genes of the TSO-500 panel. In addition, CancerKB scopes have been extended to reference multiple relevant biomarkers in a single interpretation, capture approved therapies at the tumor type level, and include interpretations for clinically relevant negative findings.
Expanded clinical trial support to include international trials and the ability to search within proximity of European postal codes. VSClinical is accessing all active studies in AACT/ClinicalTrials.gov wherein users can search and select trials based on relevant drugs, biomarkers, and the geographic distance to the patient or testing site.
VarSeq 2.3.0 will deliver powerful capabilities for genomic profiling in cancer, enabling a new level of personalized and effective care for your patients. We look forward to demonstrating these updates and Golden Helix’s continued innovation making the VarSeq Clinical Suite the NGS analysis platform of choice for germline and cancer testing.
Single Sample and Family Based Genome Analysis With VarSeq
One major hurdle facing medicine is the need to quickly identify and assess the genetic components contributing to rare diseases. It has been estimated that nearly 350 million people suffer from rare diseases, 140 million of which are children, of whom ~30% do not live past their fifth birthday1,2. The specific issue to overcome is reducing morbidity by facilitating rapid diagnosis and treatment. Fortunately, the cost of whole genome sequencing has dropped below the $1000 mark, which not only makes the NGS approach more affordable but has become the status quo method of comprehensive diagnosis for these rare disorders. Currently, there are limited options in the market when it comes to quality software that can scale to this size of data and handle variant processing and evaluation in a timely fashion. Fortunately, Golden Helix has sought to set the market standard for top-quality NGS analysis with our bioinformatic software VarSeq. The focus of this webcast will be to explore example workflows tailored for rare disorders and elaborate on how best to expedite the NGS pipeline process with our command-line tool VSPipeline.
During the webcast, we will address the following:
Customizing clinically validated NGS workflows with VarSeq for both single sample and trios
Demonstrating the automation of ACMG-based guideline review in the VSClinical variant interpretation hub and rendering of customized clinical reports
Expediting the NGS workflow via Golden Helix command-line tool VSPipeline
We look forward to you joining us for our presentation, where we can demonstrate the value of our products when building your next-gen workflows. Ultimately, we wish to diminish the intimidation of genome workflow design and leave our future customers feeling confident that there is capable software to suit their needs.
Bick D, Jones M, Taylor SL, et al. Case for genome sequencing in infants and children with rare, undiagnosed or genetic disease. J Med Genet 2019; 56:783-791.
Owen M, Lefebvre S, Hansen C, et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13: 4057. https://doi.org/10.1038/s41467-022-31446-6
User perspective for somatic variant analysis in VSClinical AMP
Somatic analysis is a complex and precise process that is constantly evolving. As the volume of available data and the accessibility of sequencing technology increase, so too does the value of a versatile, well-vetted, and efficient workflow solution. In this webcast, we will take a deep dive into the current state of our AMP interpretation software and explore various ways to optimize workflows. For anyone from grizzled VarSeq veterans to those seeing our software for the first time and labs of any size, we will provide a practical overview of our somatic analysis capabilities and how those capabilities scale with improving technology.
Throughout this webcast we will be discussing the following:
- Universal principles of somatic workflows, providing baseline recommendations
- Specific tumor-normal and somatic-only use cases
- VSClinical AMP interpretation hub and some variants of interest
- Opportunities for automation and how to decrease time to report for increased throughput
Join us as we show off the versatility and scalability of our AMP interpretation capabilities!
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VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
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The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
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VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
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VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
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Alcohol Use: Immediate and long-term risks include impaired judgment, health issues, and social consequences.
Tobacco Use: Immediate effects include increased heart rate, while long-term risks encompass cancer and heart disease.
Drug Use: Risks vary depending on the drug type, including health and psychological implications.
Prevention Strategies: Education, healthy coping mechanisms, community support, and policies are vital in preventing substance use.
Harm Reduction Strategies: Safe use practices, medication-assisted treatment, and naloxone availability aim to reduce harm.
Seeking Help for Addiction: Recognizing signs, available treatments, support systems, and resources are essential for recovery.
Personal Stories: Real stories of recovery emphasize hope and resilience.
Interactive Q&A: Engage the audience and encourage discussion.
Conclusion: Recap key points and emphasize the importance of awareness, prevention, and seeking help.
Resources: Provide contact information and links for further support.
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Annotation capabilities
- 1. Advantages of VarSeq’s Annotation Capabilities Darby Kammeraad - Field Application Scientist 20 most promising Biotech Technology Providers Top 10 Analytics Solution Providers Hype Cycle for Life sciences
- 2. Golden Helix – Who We Are Golden Helix is a global bioinformatics company founded in 1998. GWAS Genomic Prediction Large-N-Population Studies RNA-Seq Large-N CNV-Analysis Variant Warehouse Centralized Annotations Hosted Reports Sharing and Integration Variant Calling Filtering and Annotation Clinical Reports CNV Analysis Pipeline: Run Workflows
- 3. Cited in over 1100 peer-reviewed publications
- 4. Over 350 customers globally
- 5. Golden Helix – Who We Are When you choose a Golden Helix solution, you get more than just software ▪ REPUTATION ▪ TRUST ▪ EXPERIENCE ▪ INDUSTRY FOCUS ▪ THOUGHT LEADERSHIP ▪ COMMUNITY ▪ TRAINING ▪ SUPPORT ▪ RESPONSIVENESS ▪ INNOVATION and SPEED ▪ CUSTOMIZATIONS
- 7. Annotation Options in VarSeq Types Description Popular Examples in VarSeq Gene Tracks Gene and effect on transcript(s) RefSeq, Ensemble, dbNSFP Assemblies Refence sequence and alignment review GRCh 37 hg19, GRCh 38/37 g1k Low complexity regions Microarray Probe Maps Matching variant with microarray probe location Affymetrix Cytogenetic/500K/SNP Variant/Function Allele frequencies and functional predictions gnomAD, ExAC, ICGC, CADD, OMIM, dbSNP, dbNSFP, OncoMD, ClinVar, COSMIC (cancer) Targeted Panels Disease specific regions TruSight (Cancer/Cardio/Autism), Ion AmpliSeq Disease Panel
- 8. Data Curation – A Peek Under The Hood ▪ Frequently update annotations – monthly for most (ClinVar, OncoMD, & others) ▪ From many disparate sources, researching the best representation of the raw data sources ▪ Variant normalization and transformation ensures the precision and sensitivity in matching genomic data source ▪ We work with creators of annotation sources providing feedback ▪ Substantial savings for clients – multiple Full Time Equivalents
- 9. Clinical assessment - ClinVar ▪ ClinVar – features 414,708 variants - This public archive from NCBI - Collaboration of many clinical labs (both commercial and academic) - Reports the relationship among human variations and phenotypes (supporting evidence from dbSNP) - Variants found in patient samples, their clinical significance, submitter information, and other supporting data - Alleles mapped to reference sequences and use HGVS standards - Submissions can be review by an expert panel.
- 10. Clinical assessment - OMIM ▪ OMIM (updated Monthly) - Contains information from all known Mendelian disorders - Variants (features 20,527 variants) These are specific variant assertions with clinical annotations and references - Genes (features 14,825 variants) Includes linked phenotypes and their inheritance pattern, with full HTML descriptions - Phenotypes (features 4,370 variants) Linked genes, alternative phenotype names, descriptions, and references
- 11. Annotations for Cancer ▪ CIViC (updated monthly) – features 634 variants - Variant Clinical Evidence Summaries & Region Clinical Evidence Summaries (exon and gene deletions/gains). - CIViC accepts public knowledge contributions but requires that experts review these submissions. - Evidence statements & records (response to therapy, prognostic, diagnostic, or predisposing for cancer. ▪ COSMIC Mutations Left Aligned 71 – features 2,151,007 variants - Catalogs somatic variants discovered in cancer samples. - Provides details about the frequency, tumor types and histology - Provides gene level annotations with relevant summary and curated oncology details - COSMIC breaks out each sample-variant pair into a record - VarSeq provides the fields in COSMIC with relevant hyperlinks.
- 12. Annotations for Cancer ▪ ICGC Simple Somatic Mutations 22 – features 47,879,813 variants - Collection of data from across 89 committed projects currently - Goals related to quality - Ensure that most cancer genes with frequency of >3% are discovered - High sequence level resolution - High quality standards - Control based data (tumor/normal pairs) - Somatic mutations in 21 primary cancer sites in 21k donors - Primary Site and affected donor frequency.
- 13. Annotations for Cancer ▪ OncoMD (updated Monthly) - Variant and Gene Summaries - Cancer related genes (onco and tumor suppressor genes) - Effect on protein - Publications/studies associated with the variant - Drug Targeting Mutations - List of open clinical trials
- 14. Frequency Tracks – From ExAC to gnomAD ▪ ExAC – features 10,324,246 variants ▪ gnomAD – features 17,439,605 variants - Major changes from ExAC – - Genome (15,496) and exome (123,136) - Gnomad is a new product (data processing perspective) - Cohort wider selection of ethnicities (Ashkenazi Jewish) - New/novel ways of flagging low quality variants
- 15. Frequency Tracks cont… – NHLBI and 1kgenome ▪ NHLBI - Features 2,029,948 variants - Current release is taken from 6503 samples - Focus on heart, lung, and blood disorders ▪ 1kGenome - Features 85,823,495 variants - Project ran from 2008 to 2015. One of the largest catalogs - Goal: ID variants with at least 1% frequencies
- 16. Functional Prediction Annotations ▪ dbNSFP Functional Predictions and Scores 3.0 – features 82,832,027 variants - 14 classifier/prediction algorithms: SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor, FATHMM, MetaSVM, MetaLR, VEST, PROVEAN, FATHMM-MKL coding and fitCons - 8 conservation scores (phyloP46way_primate, phyloP46way_placental, phyloP100way_vertebrate, phastCons46way_primate, phastCons46way_placental, phastCons100way_veterbrate, GERP++ and SiPhy) ▪ dbscSNV Splice Altering Predictions 1.1 – features 15,030,435 variants - Predicts all snps −3 to +8 at the 5’ splice site and −12 to +2 at the 3’ splice site - Two ensemble predictions scores, I can provide cut-offs for 95% specificity in calling splice altering mutations
- 17. Functional Prediction Annotations cont… ▪ GWAS Catalog 2015-12-29 – features 22,373 variants - Identifies location of SNPs - Lists associated publication where the SNP (assay <100,000 SNPS) ▪ CADD – Interpreting Variants of Clinical Significance - Provides C-scores of “deleteriousness” for SNVs and indels in the human genome. - Also scores coding/non-coding regions - Score based on multiple annotation types: - Conservation, population frequency, regulatory, functional/structural
- 18. Transcript Annotations ▪ RefSeq – features 84,950 variants - Includes genomic DNA, transcripts, and proteins - Effect of transcripts - HGVS notation - Sequence ontology of variant in all transcripts in database ▪ Ensembl – features 215,170 variants - Joint effort from EBI and WTSI - Annotate, analyze, and display