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.
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic VariationGolden Helix
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 2.4.0: VSClinical ACMG Workflow from the User PerspectiveGolden Helix
Earlier this year, we released VarSeq 2.3.0 which brought massive updates to our VSClinical AMP interface, such as enhanced capabilities for automation and analysis of structural variants in the cancer context. Naturally, we wanted to follow that up shortly with similar advancements to our VSClinical ACMG interface, and also make our customers doing germline variant analysis happy.
Our latest software release, VarSeq 2.4.0, was therefore focused on the advancements in VSClinical ACMG, namely support for importing and clinically evaluating structural variants, long read sequencing, advanced automation with evaluation scripts in VSClinical ACMG and end-to-end automation of ACMG workflows with VSPipeline. These new and improved features were discussed in a great webcast by our VP of Product and Engineering, Gabe Rudy, last month.
This upcoming webcast by our FAS team will be a user’s perspective on the new features in VarSeq 2.4.0 and VSClinical ACMG and how our tools can precisely and efficiently enable the full spectrum NGS analysis for Mendelian disorders.
Handling a Variety of CNV Caller Inputs with VarSeqGolden Helix
VarSeq has become renowned for the accuracy of its CNV Caller, and the ease with which VSClinical takes the user through CNV evaluation. Cited in many publications, this well-validated tool brings our customers the ability to run both variant and CNV interpretations in one program, on data ranging from Gene Panels to whole genomes. What is less well known about CNV analysis through VarSeq, is that our users are not only limited to CNVs called through our software. VarSeq CNV is able to import CNVs in several file formats (VCFs, text, or tsv) generated by a wide variety of secondary callers, allowing the user to analyze their externally derived data. In this webcast, we will take you through the basics of CNV analysis with both the VarSeq CNV caller and from several common external CNV callers.
Join us in this webinar as we cover:
Leveraging the Copy Number Probability and Segregation Algorithm to add power to a CNV Trio workflow.
Importing externally called CNVs.
Expediting the path to analysis with CNV specific templates.
Utilizing the auto-recommendations to efficiently analyze the pathogenicity of several CNV calls and generate clinical reports.
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic VariationGolden Helix
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 2.4.0: VSClinical ACMG Workflow from the User PerspectiveGolden Helix
Earlier this year, we released VarSeq 2.3.0 which brought massive updates to our VSClinical AMP interface, such as enhanced capabilities for automation and analysis of structural variants in the cancer context. Naturally, we wanted to follow that up shortly with similar advancements to our VSClinical ACMG interface, and also make our customers doing germline variant analysis happy.
Our latest software release, VarSeq 2.4.0, was therefore focused on the advancements in VSClinical ACMG, namely support for importing and clinically evaluating structural variants, long read sequencing, advanced automation with evaluation scripts in VSClinical ACMG and end-to-end automation of ACMG workflows with VSPipeline. These new and improved features were discussed in a great webcast by our VP of Product and Engineering, Gabe Rudy, last month.
This upcoming webcast by our FAS team will be a user’s perspective on the new features in VarSeq 2.4.0 and VSClinical ACMG and how our tools can precisely and efficiently enable the full spectrum NGS analysis for Mendelian disorders.
Handling a Variety of CNV Caller Inputs with VarSeqGolden Helix
VarSeq has become renowned for the accuracy of its CNV Caller, and the ease with which VSClinical takes the user through CNV evaluation. Cited in many publications, this well-validated tool brings our customers the ability to run both variant and CNV interpretations in one program, on data ranging from Gene Panels to whole genomes. What is less well known about CNV analysis through VarSeq, is that our users are not only limited to CNVs called through our software. VarSeq CNV is able to import CNVs in several file formats (VCFs, text, or tsv) generated by a wide variety of secondary callers, allowing the user to analyze their externally derived data. In this webcast, we will take you through the basics of CNV analysis with both the VarSeq CNV caller and from several common external CNV callers.
Join us in this webinar as we cover:
Leveraging the Copy Number Probability and Segregation Algorithm to add power to a CNV Trio workflow.
Importing externally called CNVs.
Expediting the path to analysis with CNV specific templates.
Utilizing the auto-recommendations to efficiently analyze the pathogenicity of several CNV calls and generate clinical reports.
This presentation gives an easy introduction to ChIP-seq analyses and is part of a bioinformatics workshop. The accompanying websites are available at http://sschmeier.github.io/bioinf-workshop/#!galaxy-chipseq/
Original Next Gen Seq Methods set of slides prepared for Technorazz Vibes 2016. There is also a shorter version.
This starts with an introduction to qPCR followed by an introduction to Library Complexity. Microarrays are discussed as well along with a very short introduction to FISH. Finally discussion of Next gen seq methods is done where generation of sequencers are discussed and a short discussion of the ILLUMINA protocol. Finally comparison of ILLUMINA amongst other 3rd gen sequencer, description of the standard pipeline and the omics technologies that have risen from this seq data.
Introduction to second generation sequencingDenis C. Bauer
An introduction to second generation sequencing will be given with focus on the basic production informatics: The approach of raw data conversion and quality control will be discussed.
Microsatellite are powerful DNA markers for quantifying genetic variations within & between populations of a species, also called as STR, SSR, VNTR. Tandemly repeated DNA sequences with the repeat/size of 1 – 6 bases repeated several times
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solutionGolden Helix
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.
VarSeq 2.5.0: VSClinical AMP Workflow from the User PerspectiveGolden Helix
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.
This presentation gives an easy introduction to ChIP-seq analyses and is part of a bioinformatics workshop. The accompanying websites are available at http://sschmeier.github.io/bioinf-workshop/#!galaxy-chipseq/
Original Next Gen Seq Methods set of slides prepared for Technorazz Vibes 2016. There is also a shorter version.
This starts with an introduction to qPCR followed by an introduction to Library Complexity. Microarrays are discussed as well along with a very short introduction to FISH. Finally discussion of Next gen seq methods is done where generation of sequencers are discussed and a short discussion of the ILLUMINA protocol. Finally comparison of ILLUMINA amongst other 3rd gen sequencer, description of the standard pipeline and the omics technologies that have risen from this seq data.
Introduction to second generation sequencingDenis C. Bauer
An introduction to second generation sequencing will be given with focus on the basic production informatics: The approach of raw data conversion and quality control will be discussed.
Microsatellite are powerful DNA markers for quantifying genetic variations within & between populations of a species, also called as STR, SSR, VNTR. Tandemly repeated DNA sequences with the repeat/size of 1 – 6 bases repeated several times
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solutionGolden Helix
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.
VarSeq 2.5.0: VSClinical AMP Workflow from the User PerspectiveGolden Helix
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.
Building Secure Analysis and Storage Systems with Golden HelixGolden 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.
Evaluating Cloud vs On-Premises for NGS Clinical WorkflowsGolden Helix
In the era where cloud-based solutions are the default for the modern office, it may not be obvious why many laboratories and testing centers choose to host their data and analysis pipelines on-premises or on self-managed cloud services. Next-generation sequencing enables a precision medicine approach to rare disease diagnostic and cancer therapeutics through its power to detect unique variants in individuals. This data is generated quickly and cheaply but requires a lot of disk space and processing power to arrive at clinically useful insights.
When providing a clinical lab service under a regulated environment: data security, long-term affordable storage, and versioning through locked-down pipelines are all factors that must go into the choice of whether to choose a hosted analytics platform versus on-premises solutions or self-managed cloud infrastructure.
Join us in this webinar as we cover:
The validation and regulatory requirements that inform infrastructure and hosting decisions for NGS labs
The cost structure of scaling NGS labs to exomes and genomes
Deployment and security architecture for on-premises and self-managed cloud infrastructure
Validating and versioning analysis pipelines with clinical tests through self-managed software lifecycles and versioned annotation sources
Cybersecurity, patient data privacy, and scalable unit economics play a bigger role than ever before in the planning of NGS lab’s infrastructure choices. We look forward to you joining us as we tackle the trade-offs and choices around these topics and how deployment flexibility is a core feature of the Golden Helix VarSeq Suite.
ACMG-Based Variant Classification with VSClinicalGolden Helix
Evaluating variants according to the ACMG guidelines can be an extensive process as it requires an in-depth understanding of all available criteria for any variant. Even the most adept clinicians familiar to the guidelines suffer from this tedious manual process and from the challenge of teaching these fundamentals to new technicians. VSClinical is an automated solution to the complex ACMG guidelines process. In this webcast, we will present how VSClinical follows the true-to-form ACMG classification rules. Additionally, users will discover the value of automating the ACMG guidelines to make variant classification consistent and simplify the interpretation process for those less familiar with ACMG criteria.
Integrating Custom Gene Panels for Variant InnovationsGolden Helix
The ability to use predefined sets of genes to isolate clinically relevant variants is an important aspect of clinical variant analysis. Golden Helix’s VarSeq product houses the tools, namely our Gene Panel Manager and Match Genes set of algorithms, that enable users to create and manage reusable gene lists within projects, incorporate the ACMG Secondary Findings v3.0 gene list for the reporting of incidental findings, make use of well validated publicly available gene panels with published evidence of disease associations and create gene panels based on specific disorders or phenotypes of interest. These capabilities were covered in a webcast “Creating and Managing Reusable Gene Lists with VSClinical” by Dr. Nathan Fortier our Director of Research. In the upcoming webcast, we will dive deeper into these capabilities, implementing our gene panel tools from the user’s perspective by focusing on two clinical use cases where custom virtual gene panels are particularly useful.
For the standard use case, users typically incorporate targeted gene panel-based data to hone in on any number of variants that fall within the scope of their targeted genes list. More recently, we have observed from the field application perspective, a trend among Golden Helix customers towards importing WES and WGS data followed by creating unique per sample gene panels. Therefore, the purpose of this webcast will be to showcase how simple it can be to construct and manage both styles of virtual gene panels within VarSeq in ways that will best suit the specific needs of your lab. We will share with you several clever shortcuts for users to implement filters on gene panels, to design and manage gene panels and calculate the coverage over these regions. We will also delve into the details of incorporating gene panel data into variant evaluation in VSClinical and bringing the relevant information into a final clinical report. Viewers tuning in to this webcast will be exposed to all the tools available in VarSeq for creating and managing their potential gene panel workflows.
Best Practices for Validating a Next-Gen Sequencing WorkflowGolden Helix
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.
Family-Based Workflows in VarSeq and VSClinicalGolden Helix
Golden Helix is a single testing paradigm that allows users to start with next-generation sequencing data and finish with a clinical report. Our solutions are comprehensive as they are all performed in one software suite, which can save time and money as they prevent the need to outsource to different companies. Furthermore, our software is fully transparent in that you have full control over the steps performed in your analysis. Golden Helix is also on the forefront in the clinical workspace as we have implemented the ACMG and AMP guidelines to evaluate single nucleotide variants, insertions and deletions, as well as structural variants.
Beyond these functionalities, Golden Helix provides the ability to perform family-based analysis. Our ACMG and Exome trio templates give users a starting point to understand the different inheritance models ranging from transmitted to de novo variants, but we also have features that can provide additional evidence for both traditional and nontraditional family-based workflows. Specifically, we have algorithms that can be implemented to look at extended pedigree information and sample relatedness as well as options for examining whether a given variant such as a CNV segregates among similarly affected family members. In this webcast, we would like to demonstrate these features and show some solutions for the analysis of different family structures.
As an overview, this webcast will cover:
- Implementing filter logics for different family structures
- Algorithms that can be used for establishing clinical significance in family-based workflows
- Visualization capabilities for further understanding of inheritance models
- Confirming and evaluating transmitted CNVs
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0Golden Helix
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
AMP-Based Variant Classification with VSClinicalGolden Helix
Evaluating somatic variants according to the cancer AMP guidelines can be an extensive process. In addition to the standard collection of all available, clinical evidence for any biomarkers, there is a need to define treatment options following final classification. Even the most adept clinicians familiar to the guidelines suffer from this arduous process and thus need a standardized approach for classifying, interpreting and reporting variants according to the AMP guidelines. VSClinical’s new AMP workflow alleviates these complexities by providing an automated workflow that captures and reports on all critical data present. With the VSClinical AMP workflow, users can also customize clinical reports to reflect your lab’s preferences and branding. This webcast will provide a simple AMP guideline-based demonstration from a user perspective with multiple examples of simple report customizations from the VSClinical interpretation hub.
What you will learn in this webcast:
How VSClinical integrates the tier system to evaluate somatic mutations according to the AMP guidelines, with a focus on SNPs, InDels, CNVs and fusions
Automating the AMP guidelines using Golden Helix CancerKB and lab-specific knowledge databases to streamline variant classifications
Multiple report examples to demonstrate simple Word-based report customization capability
Overall, VSClinical enables labs to test for both germline and somatic variants according to the ACMG and AMP guidelines in an automated fashion and allows users to obtain consistent and accurate results.
VSClinical: a complete clinical workflow solutionGolden Helix
Clinical variant analysis involves many steps and potentially requires the expertise and input from multiple individuals. For many, this process can be rather complex as it entails moving the data from user to user and possibly multiple platforms or internal bioinformatic pipelines. In general, this workflow can be broken down into three stages:
- Quality control (QC) and processing of the data. This step involves importing the data into a tertiary analysis platform and validating that the variants and samples are high quality.
- Variant evaluation using different genomic databases and annotation sources, which is then incorporated into a draft report.
- Assessment and assurance that the previous steps were performed correctly and a sign-off on the report.
Golden Helix offers VSClinical, a complete clinical workflow solution that simplifies and streamlines the clinical analysis process outlined above. VSClinical is a single testing paradigm that consolidates and automates the tertiary analysis workflow. With this software, users can perform variant and sample QC, create a variant evaluation using a plethora of public and licensed annotation sources and evaluate variants with the automated ACMG and AMP guidelines for SNVs, Indels, and CNVs. All this information can then be used to create a clinical report with our new word-based report templates.
In this webcast, we plan to demonstrate the full clinical analysis workflow within VSClinical, focusing on the topics below:
- How easy it is to perform the different stages of a tertiary analysis in VarSeq and VSClinical
- The fluidity in transferring data between different users
- Evaluating germline and somatic variants according to the ACMG and AMP guidelines
- Creating and signing off on a clinical report with the new word-based templates
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic AnalysisGolden Helix
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.
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...Golden Helix
As exome sequencing continues to gain momentum as a comprehensive and affordable genetic test, many labs are considering the transition from their various targeted gene panels to a single comprehensive exome test. Along with the various challenges in small-variant analysis and interpretation of exomes, CNVs also require exome-specific considerations and strategies. In this webcast, we will review new capabilities and updated algorithms in the latest VarSeq release that will assist in any clinical exome sequencing workflow. Please join us in this webcast, as we review:
A new VS-CNV best-practice workflow with specialized features for calling CNVs on exomes and large panels with more precision, enhanced quality flags and additional outputs.
Enhanced analysis of variants found in exome sequencing, including non-coding clinically relevant RNA variants and mitochondrial variants
Additional CNV analysis capabilities such as CNV export and import as VCFs
The identification and interpretation of easily missed variants, such as those introducing novel splice-sites using the ACMG auto-classification and interpretation workflow
Strategies for incorporating disease-specific virtual gene panel lists into the filtering, quality and reporting capabilities of VSClinical
Exome sequence analysis is complex, and the process to define and validate a clinical exome test can be daunting. The VarSeq clinical suite has the flexibility and best practice workflows built-in to define and implement a repeatable and comprehensive workflow for CNVs detection and analysis by exome sequencing. We hope you can join this webinar to learn how to go from FASTQ to clinical reports for exome-based clinical tests.
VSWarehouse; a scalable, rapid genomic repository solutionGolden Helix
Anyone handling NGS data understands the constant issue of not only storing all the variant data but also the difficulties in querying through a massive dataset. VarSeq has grown an excellent reputation for being a powerful filtration and annotation engine for NGS data. Tightly coupled with VarSeq is our genomic repository solution, VSWarehouse. VSWarehouse provides a means of storing all variant cohort data as well as rapid querying capabilities to quickly navigate through the, potentially, millions of variants you may amass over time. Just as important is the ability to store this data; users can find relief that VSWarehouse is designed to be installed behind a private network to ensure the protection of all genomic data. Join us in this webcast as we explore the key value points, usability, and direct scalability of VSWarehouse.
What will you learn in this webcast?
From VSWarehouse, how to access the browser to investigate:
-Querying updated clinical evidence against an existing variant cohort
-Filtering through stored projects for all relevant variant data
-Accessing the administrator-level permissions management site
From VarSeq, how to leverage variant data in VSWarehouse to:
-Filter out common variants in the store cohort
-Annotate and plot VSWarehouse content in the VarSeq project
-Utilize congruent assessment catalogs for storing variant classifications uniformly for all users
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP GuidelinesGolden Helix
Join us as we delve into VSWarehouse with a focus on our new capability of storing somatic variant projects and catalogs built for the AMP Guidelines within VSClinical.
We will also be demonstrating how VSWarehouse efficiently navigates through stored variants via the VSWarehouse Browser.
We hope you enjoy as we explore and leverage a comprehensive set of genomic data stored within VSWarehouse to ensure rapid workflow efficiency.
In this webcast, you will learn:
How to access the VSWarehouse terminal within VarSeq
Leverage the VSWarehouse genomic database in a VarSeq workflow
Explore the stored genomic data via the VSWarehouse Browser
You can read more about what this webcast covers over on our blog: https://blog.goldenhelix.com/vswarehouse-upgrade-somatic-variant-analysis-via-vsclinical-amp-guidelines/
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeqGolden Helix
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.
Exploring New Features and Clinical Reports in the ACMG Guideline WorkflowGolden Helix
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
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...Golden Helix
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.
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMPGolden Helix
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.
Updates to VSWarehouse: Storing your CNV & ACMG ResultsGolden Helix
Golden Helix has created VSWarehouse as a solution to store the massive collection of sample and variant data output from your tertiary analysis. The classic VSWarehouse application provides a means of storing and querying on all your variant data from VarSeq projects. On top of storing your variants, VSWarehouse also stores your assessment catalogs and clinical reports. Regarding VarSeq, we’ve made some massive workflow upgrades with CNV detection and ACMG guidelines in VSClinical. Recently, we’ve given plenty of attention to these analysis upgrades from the VarSeq perspective, but now we have upgraded VSWarehouse to store your CNV and VSClinical results. In this webcast we are not only going to explore the new Warehouse capabilities; demonstrating how a user can leverage recorded CNV and ACMG data, but also describe more fundamental values VSWarehouse delivers.
Similar to VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG (20)
Introducing VarSeq Dx as a Medical Device in the European UnionGolden Helix
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 VarSeqGolden Helix
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...Golden Helix
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.
Enhance Genomic Research with Polygenic Risk Score Calculations in SVSGolden Helix
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: Empowering Family Planning through Carrier Screening AnalysisGolden Helix
Over the past 50 years, partners with potential genetic risks have sought advanced genetic testing to guide family planning decisions. Carrier screening is a valuable tool in genetics and reproductive medicine that helps individuals and families make informed choices about family planning and reduce the risk of passing autosomal recessive or X-linked genetic disorders to their children. Several carrier screening panels are available for Next-Generation Sequencing platforms, ranging from those targeting prevalent disorders to expanded ones covering various inherited conditions. Since NGS offers an affordable, high-throughput solution, carrier screening has become a common practice in healthcare systems.
We are excited to announce that VarSeq and VSClinical now support a multi-sample carrier screening workflow. VarSeq 2.5.0 unlocks the ability to:
-Filter variants between samples and identify genes in which a variant from each partner sample is present.
-Apply the ACMG Carrier Screening gene panel or generate customized carrier screening panels to include in your analysis.
-Evaluate partnered samples side-by-side in a single VSClinical evaluation.
-Generate a combined sample clinical report that includes reproductive risk calculations for the most prevalent autosomal recessive and X-linked diseases.
Identifying Oncogenic Variants in VarSeqGolden Helix
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
Prenatal Genetic Screening with VarSeqGolden Helix
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.
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...Golden Helix
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.
Single Sample and Family Based Genome Analysis With VarSeqGolden Helix
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 AMPGolden Helix
Somatic analysis is a complex and precise process that is constantly evolving. As the volume of available data and the accessibility of sequencing technology increase, so too does the value of a versatile, well-vetted, and efficient workflow solution. In this webcast, we will take a deep dive into the current state of our AMP interpretation software and explore various ways to optimize workflows. For anyone from grizzled VarSeq veterans to those seeing our software for the first time and labs of any size, we will provide a practical overview of our somatic analysis capabilities and how those capabilities scale with improving technology.
Throughout this webcast we will be discussing the following:
- Universal principles of somatic workflows, providing baseline recommendations
- Specific tumor-normal and somatic-only use cases
- VSClinical AMP interpretation hub and some variants of interest
- Opportunities for automation and how to decrease time to report for increased throughput
Join us as we show off the versatility and scalability of our AMP interpretation capabilities!
Maximizing Profitability in your NGS Testing LabGolden Helix
The automation of clinical NGS workflows provides a number of important benefits for labs. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In turn, these benefits create higher profitability from a P&L perspective.
Golden Helix software is designed to meet these needs by automating the full analysis workflow from sequencer to clinical report on a fixed annual subscription model. We are looking forward to discussing the best practices of maximizing profitability in your NGS testing lab and how Golden Helix supports these efforts.
Join us in this webinar as we cover how to develop repeatable cancer and germline interpretation workflows that scale from panels to whole exomes and genomes.
As our users have come to know, VarSeq serves as a hub for variant annotation and the full interpretation/classification of germline (ACMG) and somatic (AMP) variants. Whether direct annotation or backend variant evidence is being presented to the user via VSClinical for the interpretation process, users greatly benefit from the hosted variant databases being available directly from VarSeq. Our team has automated much of the curation process and hosts the ongoing updates to these tracks so that users no longer suffer manual review of each database via the web or manual curation efforts. Useful databases include ClinVar and ClinGen for classification submissions, gnomAD exomes/genomes for filtering out common variants in the population, RefSeq for gene impact and sequence ontology assessment, and OMIM for phenotypic information. Obviously, there is a large collection of databases out there, and not all of them make it into our automated queue. However, GHI supports the utilization of custom databases in our software. This webcast will expose features of custom database curation/utilization in VarSeq to optimize your NGS workflows even further.
During the presentation, we will discuss many different approaches with custom annotations, including:
Interval Tracks: Bed files defining target regions for coverage calculations and CNV detection.
Assessment catalogs: record keeping of variant classification/interpretations in VSClinical.
Frequency catalogs: approaches to capture all variant allele frequencies at a project level and cohort level with VSWarehouse.
Automating Clinical Workflows with the VarSeq SuiteGolden Helix
The automation of clinical NGS workflows provides a number of important benefits. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In this webcast, we will discuss how the VarSeq Suite can be leveraged to automate the full analysis workflow from sequencer to clinical report. Join us as we demonstrate how VarSeq’s automation capabilities can enable your laboratory to:
Automatically perform secondary analysis when a new sequence run is complete
Go from FASTQ to BAM and high-quality variants in VCFs using Sentieon
Automatically start VSPipeline to go from raw VCFs to candidate variants
Compute coverage and call CNVs alongside small variants with VS-CNV
Efficiently interpret a small set of annotated candidate variants and CNVs
Draft reports with VarSeq and VSClinical
Join us as we discuss the automation of the clinical analysis process for NGS genetic tests from FASTQ to Clinical Reports using the VarSeq Suite and discover how your laboratory’s NGS workflows may benefit from these automation capabilities.
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do association testing and trait analysis on large cohorts of samples in both humans and other species. As samples size increase to do population-scale genomics, the analysis methods need to adapt to remain computable on your analysis workstation.
One of the most popular methods for determining population structure in SVS is Principal Component Analysis. In this webcast, we review the fundamentals of this methodology, as well as how we have advanced the state of the art by implementing a new “Large Data PCA” capability in SVS, handling over 10 times as many samples as previously possible at a fraction of the time. Join us as we cover:
A review of SVS association testing and trait analysis capabilities
Usage of Principle Component Analysis to discern population structure
Scaling PCA beyond the limitations of computer hardware Other SVS improvements based on ongoing feedback from the user community
SVS continues to move forward as a flexible and powerful tool to perform genotype and Large-N variant analysis. We hope you enjoy this webcast highlighting the exciting new features and select enhancements we have made.
Using Golden Helix CancerKB to Accelerate NGS Cancer TestingGolden Helix
Next Generation Sequencing is being rapidly integrated into the oncology field. From the clinical perspective, both somatic and germline NGS results are informative for hereditary cancer risk and treatment strategies. There are numerous scattered resources that inform the clinical significance of a somatic mutation for a patient’s tumor type. Similarly, there are many FDA-approved anti-cancer agents and drugs with changing indications, and opportunities for off-label use. Even more, there are clinical trials all over the world that though they require specific genetic alterations for enrollment eligibility, they could provide more treatment options for cancer patients.
What’s the bottom line? It is certainly a huge undertaking to evaluate a gene or biomarker’s role in cancer or clinical significance. It requires sifting through trials that are relevant for the patient from the abundance of literature available, not to mention staying well-informed on new research as it is published.
Golden Helix CancerKB offers a solution. We demonstrate the application of CancerKB and how easy somatic variant analysis can be in VSClinical. Namely, I will deep dive into the following topics:
The process our expert curators use to produce high-quality cancer interpretations
Examples of complex biomarker interpretations simplified using CancerKB
Report content filled in by CancerKB, even for rare genes
Integrating customer feedback and the future of CancerKB
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
Dr. Vidisha Kumari, a leading epidemiologist in Bangalore, emphasizes the importance of getting vaccinated. "The flu vaccine is our best defense against the influenza virus. It not only protects individuals but also helps prevent the spread of the virus in our communities," he says.
This year, the flu season is expected to coincide with a potential increase in other respiratory illnesses. The Karnataka Health Department has launched an awareness campaign highlighting the significance of flu vaccinations. They have set up multiple vaccination centers across Bangalore, making it convenient for residents to receive their shots.
To encourage widespread vaccination, the government is also collaborating with local schools, workplaces, and community centers to facilitate vaccination drives. Special attention is being given to ensuring that the vaccine is accessible to all, including marginalized communities who may have limited access to healthcare.
Residents are reminded that the flu vaccine is safe and effective. Common side effects are mild and may include soreness at the injection site, mild fever, or muscle aches. These side effects are generally short-lived and far less severe than the flu itself.
Healthcare providers are also stressing the importance of continuing COVID-19 precautions. Wearing masks, practicing good hand hygiene, and maintaining social distancing are still crucial, especially in crowded places.
Protect yourself and your loved ones by getting vaccinated. Together, we can help keep Bangalore healthy and safe this flu season. For more information on vaccination centers and schedules, residents can visit the Karnataka Health Department’s official website or follow their social media pages.
Stay informed, stay safe, and get your flu shot today!
NVBDCP.pptx Nation vector borne disease control programSapna Thakur
NVBDCP was launched in 2003-2004 . Vector-Borne Disease: Disease that results from an infection transmitted to humans and other animals by blood-feeding arthropods, such as mosquitoes, ticks, and fleas. Examples of vector-borne diseases include Dengue fever, West Nile Virus, Lyme disease, and malaria.
These lecture slides, by Dr Sidra Arshad, offer a quick overview of physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar leads (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
Pulmonary Thromboembolism - etilogy, types, medical- Surgical and nursing man...VarunMahajani
Disruption of blood supply to lung alveoli due to blockage of one or more pulmonary blood vessels is called as Pulmonary thromboembolism. In this presentation we will discuss its causes, types and its management in depth.
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Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
Report Back from SGO 2024: What’s the Latest in Cervical Cancer?bkling
Are you curious about what’s new in cervical cancer research or unsure what the findings mean? Join Dr. Emily Ko, a gynecologic oncologist at Penn Medicine, to learn about the latest updates from the Society of Gynecologic Oncology (SGO) 2024 Annual Meeting on Women’s Cancer. Dr. Ko will discuss what the research presented at the conference means for you and answer your questions about the new developments.
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
Preoperative Management of Patients on GLP-1 Receptor Agonists like Ozempic and Semiglutide
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Explore natural remedies for syphilis treatment in Singapore. Discover alternative therapies, herbal remedies, and lifestyle changes that may complement conventional treatments. Learn about holistic approaches to managing syphilis symptoms and supporting overall health.
ARTIFICIAL INTELLIGENCE IN HEALTHCARE.pdfAnujkumaranit
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3. VarSeq 2.4.0: Structural Variants and
Advanced Automation in VSClinical ACMG
May 17, 2023
Presented by Gabe Rudy, VP of Product & Engineering
4. NIH Grant Funding Acknowledgments
4
• Research reported in this publication was supported by the National Institute Of General Medical Sciences of
the National Institutes of Health under:
o Award Number R43GM128485-01
o Award Number R43GM128485-02
o Award Number 2R44 GM125432-01
o Award Number 2R44 GM125432-02
o Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005
• PI is Dr. Andreas Scherer, CEO of Golden Helix.
• The content is solely the responsibility of the authors and does not necessarily represent the official views of the
National Institutes of Health.
5. Who Are We?
5
Golden Helix is a global bioinformatics company founded in 1998
Filtering and Annotation
ACMG & AMP Guidelines
Clinical Reports
CNV Analysis
CNV Analysis
GWAS | Genomic Prediction
Large-N Population Studies
RNA-Seq
Large-N CNV-Analysis
Variant Warehouse
Centralized Annotations
Hosted Reports
Sharing and Integration
Pipeline: Run Workflows
8. The Golden Helix Difference
8
FLEXIBLE DEPLOYMENT
On premise or in a private
cloud
BUSINESS MODEL
Annual fee for software,
training and support
CLIENT CENTRIC
Unlimited support from the
very beginning
SINGLE SOLUTION
Comprehensive cancer and
germline diagnostics
SCALABILITY
Gene panels to whole
exomes or genomes
THROUGHPUT
Automated pipeline
capabilities
QUALITY
Clinical reports correct the
first time
9. Today’s Agenda
9
Gabe Rudy
VP of Product & Engineering
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
10. Content Overview
10
Demonstration
1) Review cancer fusions with TSO-500
2) Example structural variants in WGS
VSClinical Interpretation Support
AMP and ACMG support all these variant types in
annotation, interpretation and reporting
NGS Mutation Types
Overview of types of mutations that impact
diagnosis and prognosis that can be detected
with NGS tests
11. Keys to Profitability: Capability, flexibility, automation
11
The core tenets of long-term success
Ability to create new tests
quickly according to
market demand
Bottom line-oriented
business partners enabling
your lab
Scalable solutions and a
high degree of automation
12. 12
• Local-first algorithm and data strategy
• Building from-scratch algorithms and
integrated data storage strategies
• FASTQ to clinical reporting in one solution,
with training and support
• Industry standard guidelines:
o ACMG: Germline interpretation for
diagnosis and hereditary disease risk
o AMP: Somatic interpretation for targeted
molecular therapy and cancer prognostics
• Automation and customization of lab-
specific needs
• Long term data storage and knowledgebase
management with VSWarehouse
Bottom Line-Oriented Partners Enabling your Lab
Golden Helix Clinical Suite
14. Evolving use of Structural Variants in NGS tests
14
Use in both Oncology and Germline testing
• CNVs and SVs are involved in genetic disorders
• Clear use case in cancer, and extended to ACMG germline scoring
• Driving forces to adoption in NGS tests
• Affordability and accuracy of long-read technology (PacBio, Nanopore)
• Kits that simplify and integrate RNA detection with DNA
• Adoption of whole genome sequencing with callable structural variants
• Comprehensive tests can increase diagnosis yield, fewer tests
PacBio read length histogram
https://www.pacb.com/technology/hifi-sequencing/how-it-works/
15. More than one type of genetic mutation can drive disorders
• Mutations that activate genes:
o Missense
o In-frame insertions/deletions
o Fusions
o Copy number amplifications
• Functions that inhibit or disable genes:
o Gene deletions
o Loss of function nonsense, frameshift indels
o Disabling fusions, structural variants
o Genomic Signatures that describe overall state of
the mutated genome
Comprehensive Genomic Profiling Tests
15
Copy Number
Rearrangements
Base Substitutions
Deletions
Insertions
Genomic Signatures
16. TruSight Oncology 500
16
Illumina TSO500 Comprehensive Cancer Panel Kit
• 523 genes
• DNA + RNA
• DNA: small variants, CNVs, TMB, MSI (HRD)
• RNA: fusions, exon skipping
• Solid tumor vs liquid biopsy (does not require biospy of tumor)
• Bioinformatic pipeline that computes calls, produces files
17. Multi-Variant Type Analysis Workflow
18
1. Import Wizard
• “Records” are split based on their type
• Variants, CNVs, Break-end Pairs
2. Variant Type Specific Tables
• Annotate and filter variant types individually
• Gene impact analysis
• Type-specific annotations
• Auto-classifiers (ACMG, CNV, AMP)
3. VSClinical Analysis
• Brings in variants from VarSeq tables
• Only analyze filtered or “marked” variants, CNVs, fusions
• Import sample QC details, phenotype, clinical features
4. Integrated Reporting
• Report sections: Primary, Secondary, VUS
• All variant types can be reported in any section
18. Interpreting Break-end Events in VarSeq
19
Break-end Location
• Rearrangements within and in between
chromosomes
• Coding genes, non-coding genes,
introns
Orientation and SV Type
• Translocations
• Deletions
• Duplications
• Inversions
Effect on Gene
• In-frame Fusion
• Frameshift fusion
• Transcript ablation,
frameshift, start
loss
• Transcript fusion
• Non-functional
rearrangement
• Intronic, intergenic,
upstream,
downstream, start
gain
Gene 2
Gene 1
Exon 3
Exon 34
Gene 1 e3 :: Gene 2 e34
19. VSClinical Interpretation of Structural Variants
20
• Adding SVs to an Evaluation
o Filtered result of break-end table
o Selected SVs for analysis based on Record Sets
o Automation with Evaluation Scripts
• Add all variants, CNVs, SVs
• Sync with Report Status using Record Sets
o Manually
• Structural Variant Analysis
o Interpretation and classification
o SV Catalog to save assessments
• Reporting
o Report SNVs, CNVs and SVs together in one report
o Report as primary and secondary findings or uncertain significance
o Customized report templates
20. VarSeq Suite: Automate Inputs and Outputs
21
• VarSeq built for flexibility and automation
• A modular set of capabilities at the disposal
• Support all records in VCF 4.3
• Custom pipelines support built-in:
• VCFs with all types of variants
• Custom callers output such as ArcherDx
• Sample or patient info
• Automation of VSClinical input and outputs
• Reduction or elimination of custom work
21. 22
Automation in Review
Powerful, modular NGS testing
Secondary Analysis Tertiary Analysis Interpretation
• Strong Starting points with Sentieon
• Ability to import results of any secondary
pipeline
• Reliance on validated, reproducible
VarSeq templates
• Thorough automation options with
VSPipeline
• Automatically pull from vast, expert-
review repositories like CancerKB
• Interface with VSWarehouse to track
assessments across your institution
23. Wrapping up
24
A snapshot of the vast capabilities of automation
• Structural variants support allows for
comprehensive NGS tests for both cancer and
germline use cases
• VarSeq Suite can accommodate automation from
the straightforward to the complex
• Overall reduction in work and human error, while
retaining expert input
• We invite you to give our software a try!
24. NIH Grant Funding Acknowledgments
25
• Research reported in this publication was supported by the National Institute Of General Medical Sciences of
the National Institutes of Health under:
o Award Number R43GM128485-01
o Award Number R43GM128485-02
o Award Number 2R44 GM125432-01
o Award Number 2R44 GM125432-02
o Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005
• PI is Dr. Andreas Scherer, CEO of Golden Helix.
• The content is solely the responsibility of the authors and does not necessarily represent the official views of the
National Institutes of Health.
26. 25 Licenses for 25 Months
27
Celebrating 25 Years in Business
• Limited quantity
• Licenses are 25-month license periods
• Available to new customers only
• Orders must be received by June 15, 2023
• Visit goldenhelix.com/forms/25-for-25 or
scan the QR code below
27. Conferences
28
European Human Genetics Conference, Booth #566
• June 10 – 13, 2023
• Glasgow, UK
• Monday, June 12, 12:00 - Corporate Satellite Talk (ALSH 1,
Level 0) Achieving Economic Success as an NGS Lab:
Strategy and Implementation
AMP Europe, Milan, Italy, Booth #14
• June 18 – 20, 2023
• Milan, Italy
• Monday, June 19, 1:00 – Industry Symposium Achieving
Economic Success as an NGS Lab: Strategy and
Implementation
Before we start diving into the subject, I wanted mention our appreciation for our grant funding from NIH.
The research reported in this publication was supported by the National institute of general medical sciences of the national institutes of health under the listed awards.
We are also grateful to have received local grant funding from the state of Montana. Our PI is Dr. Andreas Scherer who is also the CEO at Golden Helix and the content described today is the responsibility of the authors and does not officially represent the views of the NIH.
So with that covered, lets take just a few minutes to talk a little bit about our company Golden Helix.
Golden Helix is a global bioinformatics software and analytics company that enables research and clinical practices to analyze large genomic datasets. We were originally founded in 1998 based off pharmacogenomics work performed at GlaxoSmithKline, who is still a primary investor in our company.
VarSeq, our flagship product, serves as a clinical tertiary analysis tool. At its core, it serves as a variant annotation and filtration engine. Additionally, however, users have access to automated AMP or ACMG variant guidelines. VarSeq also have the capability to detect copy number variations scaling from single exome to large aneuploidy events. Lastly, the finalization of variant interpretation and classification is further optimized with the VarSeq clinical reporting capability. Users can integrate all of these features into a standardized workflow.
Paired with VarSeq are VSWarehouse and VSPipeline. VSWarehouse serves as a repository for the large amount of useful genomic data wrangled by our customers. Warehouse not only solves the issue of data storage for ever-increasing genomic content, but also is fully queryable and auditable and allows for the definability of user access for project managers or collaborators. In tandem with this, VSPipeline, which will be a large part of today's discussion, allows for the automated execution of routine workflows, further optimizing users' abilities to handle large amounts of data and throughput.
Lastly, our research platform, SVS, enables researchers to perform complex analysis and visualizations on genomic and phenotypic data. SVS has a range of tools to perform GWAW, genomic prediction, and RNA-Seq analysis, among other common research applications.
Our software has been very well received by the industry. We have been cited in thousands of peer-reviewed publications, and that’s a testament to our customer base.
We work with over 400 organizations all over the globe. This includes top-tier institutions, like Stanford and yale, government organizations like the NCI and NIH, clinics such as Sick Kids, and many other genetic testing labs. We now have well over 20,000 installs of our products and with 1,000’s of unique users.
So how is this relevant to you?
At Golden Helix, we focus on the seven pillars of customer success. Golden Helix offers a single software solution that encompasses germline, somatic, and CNV analysis. Our software is also highly scalable, supporting gene panel to whole genome sequencing workflows. With our complete automation capabilities, we now offer a FASTQ or VCF to report pipeline. Our software can be locally deployed, or installed in cloud, and our business model of annual subscription per user means you are able to increase your workload without increasing analysis fees. And it goes without saying, that our FAS team is here to support you on your analysis journey.
Today, you'll be hearing from myself, Solomon Reinman, a Technical Field Application Scientist, and Gabe Rudy, our VP of Product & Engineering. We've both put a lot of blood, sweat, and tears into the realm of automation, and dare I say we even enjoy most of it.
I'm now going to hand things over to Gabe to talk a little bit about VarSeq before we dissect the complexity of the automation problem and the full scale of improvement organizations can see with effective automation. Gabe, take it away.
Casey: Intro
Solomon: 1-9
Gabe: 10-13
Solomon 14/15
Gabe: 16-19
Solomon: Demo part 1
Gabe: Demo part2
Solomon Wrap-up, hand to Casey for Marketing & QA
Review the steps and various technology components of an NGS test
This will make it clear that there is a need to integrate quite a few pieces of technology
Review how automation can tackle this problem, both the complexity of the integration but also improving quality of your test output
Demonstrations in two parts: How far automation can take you: fastq to report, and how human interpretation and review is still incorporated into the process with the rich VSClinical interface
ESHG talk pitch
Labs are successful when then have a test in production that is economical to run.
But this is a changing landscpape
Need to respond to the marketplace, improving tests and adding new tests
So for both new labs and existing labs, the time it takes to take a test through the design and validation process and move to production can be the key to profitability
Choosing your vendors wisely can make all the difference. Do they have the capability, flexibility and ability to automate these process.
Once in production, do they scale with you. Both performance and per-unit costs.
The Golden Helix stack provides the capability to start with an initial FASTQ file all the way down to a clinical report. This is achievable through our partnership with Sentieon providing the alignment and variant calling steps to produce the VCF and BAM files. This output serves as the basis for CNV detection and import data for your tertiary analysis in VarSeq. If you are performing NGS based CNV analysis, Golden Helix is the market leader; supported by studies like Robarts Research Institute showing 100% concordance with MLPA. Additionally, the imported variants in your VarSeq project can be run through VSClinical’s automated ACMG and AMP guidelines. After completing secondary and tertiary processing, all analysis can be rendered into a clinical report which can be stored in VSWarehouse providing researchers and clinicians with access to this information and to view previous findings.
Overview of somatic workflow in VarSeq/VSClinical
Previously used CMA, fusion detection PCR kits
FoundationOne CDx broke ground as the first FDA-approved CGP for all solid tumors.
MSK-IMPACT was FDA approved for their large panel test that included MSI
Wea added support for this in VarSeq 2.3.0, we can no bring in all these mutation types into the cancer interpretation workflow for AMP
Diagram of going from vcf => three table => one evaluation (fan out and fan in)
Variants (SNVs, InDels 100bp
CNVs (Deletion, Duplications, LOH)
Break-end Pairs (resulting in fusions, inversions etc)
Can result in both CNV and break-end
We do a lot of work on import and with our gene annotation algorithm
Additional inserted sequences can be called insertion inversions
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.
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.
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.
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.
Thanks for the great demo Gabe, and thanks to all of our viewers for being here today. We hope you've been impressed with the breadth of complexity that is handled by the VarSeq suite and our demonstration of how far we can take automation. We'd love to work with you to explore how you can reduce the overall amount of work, mitigate human error, and maintain control through automation of your NGS testing capabilities. We invite you to demo and evaluate our software if you are interested. The evaluation process with Golden Helix is a comprehensive look at both our software and the support we provide our users in getting started and keeping at it. If you'd like to see how your workflow can be integrated and automated with VarSeq, please reach out to us so we can get you to your production goals.
Before wrapping up, we'd like to again state our appreciation for the grants included here. And with that, I'll hand things back to Casey to talk about some exciting marketing updates and take us through a Q&A session.
Again, I want to mention how grateful we are we are thankful of grants such as this which support the advancement and development of our software to create the high quality software you'll see today.
So with that covered, lets take a few minutes to talk a little bit about our company Golden Helix.