A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
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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
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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:
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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.
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Use of the oncogenicity classifier to streamline filter chains.
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Including parallel germline secondary findings for the whole NGS workflow.
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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.
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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
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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
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Leverage built-in and custom automation capabilities in the VSClinical cancer guideline workflow to reduce work and improve accuracy
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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
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The individualized nature of tumors requires genomic testing for providing the best outcomes for patients. Next-Generation Sequencing enables the detection of small mutations, copy number changes, and common fusions affordably and with high precision. However, the interpretation of these detected variants is arduous without a comprehensive analytical workflow that can incorporate all the bioinformatics and clinical evidence involved in following the AMP guidelines for the scoring and reporting of somatic mutations.
Please join us as we reveal the AMP guidelines workflow support in VSClinical. We will cover the entire post-sequencing analytical workflow from FASTQ to clinical report, including:
- Apply the AMP Tiers to the available clinical evidence for Drug Sensitivity, Drug Response, Prognostics and Diagnostics
Support small mutations (SNPs, InDels) along with CNVs, fusions and wild-types as relevant biomarkers for the reporting of clinical evidence
- Develop a lab-specific knowledgebase of interpretations that allow maximum re-use of interpretations and descriptions from one patient to the next
- Leverage the built-in Golden Helix CancerKB interpretation knowledgebase that covers many common genes and biomarkers
- When detecting inherited and not somatic variants in a patient, score and classify them using the ACMG guidelines and report as secondary germline findings
- Use the Oncogenicity scoring system for evaluating the impact of variants in cancer
- Customize your clinical report using Word to reflect your lab's preferences and branding
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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.
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!
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!
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
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
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Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Interpreting somatic variants for the clinical genetic testing of tumors requires hands-on time of the most skilled clinical lab personnel. Various clinical and genomic sources must be queried, papers and guidelines referenced, and an evaluation of the clinical actionability of the mutation determined by the following the AMP guidelines. Yet, there is tremendous potential for reuse of this time consuming and valuable work!
Earlier this summer we launched our VSClinical AMP Guidelines workflow which integrates a lab-specific knowledgebase that saves every biomarkers interpretation in up to seven different snippets that ar reusable across various genomic and clinical contexts. Furthermore, our cancer workflow is bundled with the Golden Helix CancerKB, our expert-curated interpretations of the most common biomarkers for the most common cancer types, reducing the time to your first precision medicine report.
Follow along as we cover:
The interpretation of clinically actionable biomarkers for targeted molecular therapy and diagnostic/prognostic clinical reports for cancer
The different levels and scopes of re-use of the interpretation for each biomarker
Saving, re-using and updating these interpretations over time by multiple users within a clinical lab with an integrated lab-specific knowledgebase
The built in Golden Helix CancerKB that provides default interpretations for most cancer genes, biomarkers and many clinically actionable Tier I/II drug sensitivity and resistance interpretations.
In the world of genomics shaping precision medicine in oncology, the limiting factor is the time-to-sign-off on fully interpreted molecular profile reports.
Integrating Custom Gene Panels for Variant Innovations
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.
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
ACMG-Based Variant Classification with VSClinical
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.
VSClinical: a complete clinical workflow solution
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
Family-Based Workflows in VarSeq and VSClinical
Golden Helix is a single testing paradigm that allows users to start with next-generation sequencing data and finish with a clinical report. Our solutions are comprehensive as they are all performed in one software suite, which can save time and money as they prevent the need to outsource to different companies. Furthermore, our software is fully transparent in that you have full control over the steps performed in your analysis. Golden Helix is also on the forefront in the clinical workspace as we have implemented the ACMG and AMP guidelines to evaluate single nucleotide variants, insertions and deletions, as well as structural variants.
Beyond these functionalities, Golden Helix provides the ability to perform family-based analysis. Our ACMG and Exome trio templates give users a starting point to understand the different inheritance models ranging from transmitted to de novo variants, but we also have features that can provide additional evidence for both traditional and nontraditional family-based workflows. Specifically, we have algorithms that can be implemented to look at extended pedigree information and sample relatedness as well as options for examining whether a given variant such as a CNV segregates among similarly affected family members. In this webcast, we would like to demonstrate these features and show some solutions for the analysis of different family structures.
As an overview, this webcast will cover:
- Implementing filter logics for different family structures
- Algorithms that can be used for establishing clinical significance in family-based workflows
- Visualization capabilities for further understanding of inheritance models
- Confirming and evaluating transmitted CNVs
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.
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
Clinical Validation of Copy Number Variants Using the AMP Guidelines
The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you to utilize your existing NGS data and perform the analysis all in one suite. Coupled with this innovative feature is the ability to annotate CNV events against a variety of databases, and by incorporating our VSClinical AMP workflow, we can now assess CNVs as potential biomarkers. Most importantly, Golden Helix CancerKB is an AMP workflow feature that provides expert-curated biomarker interpretations, including those for common somatic CNVs, that will streamline the analysis time and report generation.
In this demonstration we will cover:
Setting up the VS-CNV caller using BAM files from whole exome data
Filtering down to high quality, high confidence CNV events
Annotating CNVs using publicly curated catalogs and databases
Adding clinically relevant CNVs to the VSClinical AMP workflow
Utilizing Golden Helix CancerKB to obtain expert-curated interpretations
Showing updated features and polishes to the software
Together, VarSeq incorporates the ability to accurately call and annotate CNVs and evaluate germline and somatic mutations according to the ACMG and AMP guidelines, respectively. This webcast demonstration will provide insight into these best practice workflows and will hopefully show you how you can implement this top-quality software into your pipeline solution.
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.
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
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.
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
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.
Introducing Drugs & Trials for Cancer Diagnostics
When interpreting a variant using the AMP/ASCO guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials, FDA approved therapies and peer-reviewed studies. Unfortunately, strong evidence linking specific genetic biomarkers to FDA-approved therapies only exists for a small number of cancers. Thus, most variants require an exploration of clinical practice guidelines, peer-reviewed literature, and large-scale cancer mutation databases to effectively assess the clinical significance of a given mutation.
This webcast explores this new incorporation of Drugs & Trials Annotations in VSClinical's AMP Workflow covering:
Identification of relevant clinical evidence for drug sensitivity and resistance based on patient biomarkers and tumor type
Review of clinical trial information including inclusion criteria, trial status, and contact information
Management of citations associated with relevant, targeted therapies
Evaluation of a biomarkers clinical evidence tier based on available evidence for drug sensitivity and resistance
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
New & Improved COSMIC Database for NGS Cancer Analyses
With Next-Gen Sequencing becoming a routine method of rapidly investigating cancer mutations, having access to accurate and large somatic variant catalogs is paramount. We at Golden Helix are excited to announce our newly released COSMIC 87 track. This updated version of the world's largest and most comprehensive somatic track provides a number of significant improvements. This includes not only an increase of ~1.1 million variants but also improvements on evidence accessibility and as always maintaining data quality. As a result of our 20+ years of bioinformatics experience, users have come to trust and rely on our data curation since our goal is to ensure highly efficient and accurate variant analysis. With this webcast, we are going to focus on the new capabilities users have when integrating COSMIC into their cancer workflow. We will also discuss the implications and value of relying on top data quality data curation maintained here at Golden Helix. Please join us as we seek to inform you on methods to optimize your cancer variant analysis!
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
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.
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.
More Related Content
Similar to A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
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.
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!
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!
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
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
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Interpreting somatic variants for the clinical genetic testing of tumors requires hands-on time of the most skilled clinical lab personnel. Various clinical and genomic sources must be queried, papers and guidelines referenced, and an evaluation of the clinical actionability of the mutation determined by the following the AMP guidelines. Yet, there is tremendous potential for reuse of this time consuming and valuable work!
Earlier this summer we launched our VSClinical AMP Guidelines workflow which integrates a lab-specific knowledgebase that saves every biomarkers interpretation in up to seven different snippets that ar reusable across various genomic and clinical contexts. Furthermore, our cancer workflow is bundled with the Golden Helix CancerKB, our expert-curated interpretations of the most common biomarkers for the most common cancer types, reducing the time to your first precision medicine report.
Follow along as we cover:
The interpretation of clinically actionable biomarkers for targeted molecular therapy and diagnostic/prognostic clinical reports for cancer
The different levels and scopes of re-use of the interpretation for each biomarker
Saving, re-using and updating these interpretations over time by multiple users within a clinical lab with an integrated lab-specific knowledgebase
The built in Golden Helix CancerKB that provides default interpretations for most cancer genes, biomarkers and many clinically actionable Tier I/II drug sensitivity and resistance interpretations.
In the world of genomics shaping precision medicine in oncology, the limiting factor is the time-to-sign-off on fully interpreted molecular profile reports.
Integrating Custom Gene Panels for Variant Innovations
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.
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
ACMG-Based Variant Classification with VSClinical
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.
VSClinical: a complete clinical workflow solution
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
Family-Based Workflows in VarSeq and VSClinical
Golden Helix is a single testing paradigm that allows users to start with next-generation sequencing data and finish with a clinical report. Our solutions are comprehensive as they are all performed in one software suite, which can save time and money as they prevent the need to outsource to different companies. Furthermore, our software is fully transparent in that you have full control over the steps performed in your analysis. Golden Helix is also on the forefront in the clinical workspace as we have implemented the ACMG and AMP guidelines to evaluate single nucleotide variants, insertions and deletions, as well as structural variants.
Beyond these functionalities, Golden Helix provides the ability to perform family-based analysis. Our ACMG and Exome trio templates give users a starting point to understand the different inheritance models ranging from transmitted to de novo variants, but we also have features that can provide additional evidence for both traditional and nontraditional family-based workflows. Specifically, we have algorithms that can be implemented to look at extended pedigree information and sample relatedness as well as options for examining whether a given variant such as a CNV segregates among similarly affected family members. In this webcast, we would like to demonstrate these features and show some solutions for the analysis of different family structures.
As an overview, this webcast will cover:
- Implementing filter logics for different family structures
- Algorithms that can be used for establishing clinical significance in family-based workflows
- Visualization capabilities for further understanding of inheritance models
- Confirming and evaluating transmitted CNVs
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.
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
Clinical Validation of Copy Number Variants Using the AMP Guidelines
The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you to utilize your existing NGS data and perform the analysis all in one suite. Coupled with this innovative feature is the ability to annotate CNV events against a variety of databases, and by incorporating our VSClinical AMP workflow, we can now assess CNVs as potential biomarkers. Most importantly, Golden Helix CancerKB is an AMP workflow feature that provides expert-curated biomarker interpretations, including those for common somatic CNVs, that will streamline the analysis time and report generation.
In this demonstration we will cover:
Setting up the VS-CNV caller using BAM files from whole exome data
Filtering down to high quality, high confidence CNV events
Annotating CNVs using publicly curated catalogs and databases
Adding clinically relevant CNVs to the VSClinical AMP workflow
Utilizing Golden Helix CancerKB to obtain expert-curated interpretations
Showing updated features and polishes to the software
Together, VarSeq incorporates the ability to accurately call and annotate CNVs and evaluate germline and somatic mutations according to the ACMG and AMP guidelines, respectively. This webcast demonstration will provide insight into these best practice workflows and will hopefully show you how you can implement this top-quality software into your pipeline solution.
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.
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
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.
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
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.
Introducing Drugs & Trials for Cancer Diagnostics
When interpreting a variant using the AMP/ASCO guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials, FDA approved therapies and peer-reviewed studies. Unfortunately, strong evidence linking specific genetic biomarkers to FDA-approved therapies only exists for a small number of cancers. Thus, most variants require an exploration of clinical practice guidelines, peer-reviewed literature, and large-scale cancer mutation databases to effectively assess the clinical significance of a given mutation.
This webcast explores this new incorporation of Drugs & Trials Annotations in VSClinical's AMP Workflow covering:
Identification of relevant clinical evidence for drug sensitivity and resistance based on patient biomarkers and tumor type
Review of clinical trial information including inclusion criteria, trial status, and contact information
Management of citations associated with relevant, targeted therapies
Evaluation of a biomarkers clinical evidence tier based on available evidence for drug sensitivity and resistance
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
New & Improved COSMIC Database for NGS Cancer Analyses
With Next-Gen Sequencing becoming a routine method of rapidly investigating cancer mutations, having access to accurate and large somatic variant catalogs is paramount. We at Golden Helix are excited to announce our newly released COSMIC 87 track. This updated version of the world's largest and most comprehensive somatic track provides a number of significant improvements. This includes not only an increase of ~1.1 million variants but also improvements on evidence accessibility and as always maintaining data quality. As a result of our 20+ years of bioinformatics experience, users have come to trust and rely on our data curation since our goal is to ensure highly efficient and accurate variant analysis. With this webcast, we are going to focus on the new capabilities users have when integrating COSMIC into their cancer workflow. We will also discuss the implications and value of relying on top data quality data curation maintained here at Golden Helix. Please join us as we seek to inform you on methods to optimize your cancer variant analysis!
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
Similar to A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0 (20)
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates
User perspective for somatic variant analysis in VSClinical AMP
User perspective for somatic variant analysis in VSClinical AMP
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...
Integrating Custom Gene Panels for Variant Innovations
Integrating Custom Gene Panels for Variant Innovations
VSWarehouse: Tracking Changing Variant Evidence and Classifications
VSWarehouse: Tracking Changing Variant Evidence and Classifications
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
Creating & Managing Reusable Gene Lists with VSClinical
Creating & Managing Reusable Gene Lists with VSClinical
Clinical Validation of Copy Number Variants Using the AMP Guidelines
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Introducing VSPGx: Pharmacogenomics Testing in VarSeq
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VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
Single Sample and Family Based Genome Analysis With VarSeq
Single Sample and Family Based Genome Analysis With VarSeq
New & Improved COSMIC Database for NGS Cancer Analyses
New & Improved COSMIC Database for NGS Cancer Analyses
Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
More from Golden Helix
Introducing VarSeq Dx as a Medical Device in the European Union
A transition period regarding in vitro medical device (IVD) regulation in the European Union (EU) is upon us. The former IVDD regulations are phasing out and IVDR 2017/746 has already taken its place as the acting regulation for IVD manufacturers but also lab developed tests (LDTs) and health institutions. In our upcoming webcast we will talk about the roles and significance of IVDR and ISO 13485 certification for clinical labs and for Golden Helix as a medical device manufacturer.
Join us as we will introduce VarSeq 2.6.1 complete with Dx Mode, which offers the use of VarSeq as CE marked medical device. Even more we will also present strategies to facilitate the transition of Golden Helix customers to operate in accordance with IVDR.
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.
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: Empowering Family Planning through Carrier Screening Analysis
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 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
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.
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
Maximizing Profitability in your NGS Testing Lab
The automation of clinical NGS workflows provides a number of important benefits for labs. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In turn, these benefits create higher profitability from a P&L perspective.
Golden Helix software is designed to meet these needs by automating the full analysis workflow from sequencer to clinical report on a fixed annual subscription model. We are looking forward to discussing the best practices of maximizing profitability in your NGS testing lab and how Golden Helix supports these efforts.
Join us in this webinar as we cover how to develop repeatable cancer and germline interpretation workflows that scale from panels to whole exomes and genomes.
Handling a Variety of CNV Caller Inputs with VarSeq
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.
Evaluating Cloud vs On-Premises for NGS Clinical Workflows
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.
VarSeq Custom Database Curation Capabilities.pdf
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 Suite
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.
Large Scale PCA Analysis in SVS
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.
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Introducing VarSeq Dx as a Medical Device in the European Union
Introducing VarSeq Dx as a Medical Device in the European Union
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
Best Practices for Validating a Next-Gen Sequencing Workflow
Best Practices for Validating a Next-Gen Sequencing Workflow
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
Handling a Variety of CNV Caller Inputs with VarSeq
Handling a Variety of CNV Caller Inputs with VarSeq
Evaluating Cloud vs On-Premises for NGS Clinical Workflows
Evaluating Cloud vs On-Premises for NGS Clinical Workflows
Automating Clinical Workflows with the VarSeq Suite
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Physiology of Chemical Sensation of smell.pdf
Title: Sense of Smell
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 primary categories of smells and the concept of odor blindness.
Explain the structure and location of the olfactory membrane and mucosa, including the types and roles of cells involved in olfaction.
Describe the pathway and mechanisms of olfactory signal transmission from the olfactory receptors to the brain.
Illustrate the biochemical cascade triggered by odorant binding to olfactory receptors, including the role of G-proteins and second messengers in generating an action potential.
Identify different types of olfactory disorders such as anosmia, hyposmia, hyperosmia, and dysosmia, including their potential causes.
Key Topics:
Olfactory Genes:
3% of the human genome accounts for olfactory genes.
400 genes for odorant receptors.
Olfactory Membrane:
Located in the superior part of the nasal cavity.
Medially: Folds downward along the superior septum.
Laterally: Folds over the superior turbinate and upper surface of the middle turbinate.
Total surface area: 5-10 square centimeters.
Olfactory Mucosa:
Olfactory Cells: Bipolar nerve cells derived from the CNS (100 million), with 4-25 olfactory cilia per cell.
Sustentacular Cells: Produce mucus and maintain ionic and molecular environment.
Basal Cells: Replace worn-out olfactory cells with an average lifespan of 1-2 months.
Bowman’s Gland: Secretes mucus.
Stimulation of Olfactory Cells:
Odorant dissolves in mucus and attaches to receptors on olfactory cilia.
Involves a cascade effect through G-proteins and second messengers, leading to depolarization and action potential generation in the olfactory nerve.
Quality of a Good Odorant:
Small (3-20 Carbon atoms), volatile, water-soluble, and lipid-soluble.
Facilitated by odorant-binding proteins in mucus.
Membrane Potential and Action Potential:
Resting membrane potential: -55mV.
Action potential frequency in the olfactory nerve increases with odorant strength.
Adaptation Towards the Sense of Smell:
Rapid adaptation within the first second, with further slow adaptation.
Psychological adaptation greater than receptor adaptation, involving feedback inhibition from the central nervous system.
Primary Sensations of Smell:
Camphoraceous, Musky, Floral, Pepperminty, Ethereal, Pungent, Putrid.
Odor Detection Threshold:
Examples: Hydrogen sulfide (0.0005 ppm), Methyl-mercaptan (0.002 ppm).
Some toxic substances are odorless at lethal concentrations.
Characteristics of Smell:
Odor blindness for single substances due to lack of appropriate receptor protein.
Behavioral and emotional influences of smell.
Transmission of Olfactory Signals:
From olfactory cells to glomeruli in the olfactory bulb, involving lateral inhibition.
Primitive, less old, and new olfactory systems with different path
Report Back from SGO 2024: What’s the Latest in Cervical Cancer?
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.
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Acute scrotum is a general term referring to an emergency condition affecting the contents or the wall of the scrotum.
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Tom Selleck Health: A Comprehensive Look at the Iconic Actor’s Wellness Journey
Tom Selleck, an enduring figure in Hollywood. has captivated audiences for decades with his rugged charm, iconic moustache. and memorable roles in television and film. From his breakout role as Thomas Magnum in Magnum P.I. to his current portrayal of Frank Reagan in Blue Bloods. Selleck's career has spanned over 50 years. But beyond his professional achievements. fans have often been curious about Tom Selleck Health. especially as he has aged in the public eye.
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Introduction
Many have been interested in Tom Selleck health. not only because of his enduring presence on screen but also because of the challenges. and lifestyle choices he has faced and made over the years. This article delves into the various aspects of Tom Selleck health. exploring his fitness regimen, diet, mental health. and the challenges he has encountered as he ages. We'll look at how he maintains his well-being. the health issues he has faced, and his approach to ageing .
Early Life and Career
Childhood and Athletic Beginnings
Tom Selleck was born on January 29, 1945, in Detroit, Michigan, and grew up in Sherman Oaks, California. From an early age, he was involved in sports, particularly basketball. which played a significant role in his physical development. His athletic pursuits continued into college. where he attended the University of Southern California (USC) on a basketball scholarship. This early involvement in sports laid a strong foundation for his physical health and disciplined lifestyle.
Transition to Acting
Selleck's transition from an athlete to an actor came with its physical demands. His first significant role in "Magnum P.I." required him to perform various stunts and maintain a fit appearance. This role, which he played from 1980 to 1988. necessitated a rigorous fitness routine to meet the show's demands. setting the stage for his long-term commitment to health and wellness.
Fitness Regimen
Workout Routine
Tom Selleck health and fitness regimen has evolved. adapting to his changing roles and age. During his "Magnum, P.I." days. Selleck's workouts were intense and focused on building and maintaining muscle mass. His routine included weightlifting, cardiovascular exercises. and specific training for the stunts he performed on the show.
Selleck adjusted his fitness routine as he aged to suit his body's needs. Today, his workouts focus on maintaining flexibility, strength, and cardiovascular health. He incorporates low-impact exercises such as swimming, walking, and light weightlifting. This balanced approach helps him stay fit without putting undue strain on his joints and muscles.
Importance of Flexibility and Mobility
In recent years, Selleck has emphasized the importance of flexibility and mobility in his fitness regimen. Understanding the natural decline in muscle mass and joint flexibility with age. he includes stretching and yoga in his routine. These practices help prevent injuries, improve posture, and maintain mobilit
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A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
- 1. A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0 December 7, 2022 Presented by the Golden Helix Field Application Scientist Team Jennifer Dankoff, PhD, Rana Smalling, PhD, and Solomon Reinman,TechnicalFAS
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- 3. A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0 December 7, 2022 Presented by the Golden Helix Field Application Scientist Team Jennifer Dankoff, PhD, Rana Smalling, PhD, and Solomon Reinman,TechnicalFAS
- 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/STTRMatching Funds ProgramGrant 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
- 6. Cited in 1,000s of Peer-Reviewed Publications 6
- 7. Over 400 Customers Globally 7
- 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. 9
- 10. Today’s Agenda A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0 10 Solomon Reinman Technical Field Application Scientist • Somatic workflow design • The joys of automation Rana Smalling, PhD Field Application Scientist • Optimizing somatic variant evaluation • Updates to CancerKB Jennifer Dankoff, PhD Field Application Scientist • Completing an evaluation • New report templates
- 11. 11
- 12. Basic considerations for somatic workflows 12 August 2022 Webcast by Solomon Reinman - User perspective for somatic analysis in VSClinical AMP • Common Filtering Strategies: o Variant Quality o Remove Common o Gene Impact o ACMG Classifier to remove benign variants o Somatic/tumor panels/phenotypes • Project versus template • Built into template o NGS coverage reporting o CNV calling and analysis o Sample demographics
- 13. 13 VCF & BAM/ CRAM Import Annotation & Filtering Evaluation & Report • Import all major genomic variant classes, i.e. comprehensive genomic profiling (CGP): o SNVs/Indels o Copy number variations o Breakends/Fusions o Splice variants • Genomic signatures that describe overall state of somatic genome • Improved automation in VarSeq 2.3.0’s VSPipeline o Value: Increasing automation capability to 100% VSPipeline: automating import to clinical report
- 14. The Value of NGS Automation 14 Test Size and Volume • Increased number of NGS samples • Scale increasing from panels to WES and WGS • Comprehensive NGS workflows • Fixed cost licensing Automation • VSPipeline automates NGS analysis • CancerKB auto-applies to evaluation biomarkers • Scriptable AMP evaluation • Auto-generate Clinical Reports Warehouse • Cohort variant frequencies • Host Interpretation Knowledgebase • Integration with external systems
- 15. Golden Helix CancerKB V2.0 15 • High-quality expert-curated biomarker and drug interpretations • Accurate information, up-to-date with what is available in the cancer field • Each interpretation reviewed by expert curator • Knowledge base updated monthly • Key to VSPipeline -> VSClinical automation • New and exciting features!
- 16. TSO-500 genes Interpretation for all 523 genes included in TSO-500 kit Updates to CancerKB 16 Copy Number Base Substitutions Expanded Interpretations Increased Tier 1 and 2 interpretations Genomic Signatures 17 new Genomic Signatures Drug descriptions 147 new drug descriptions with indications Combination biomarkers Report on combinations of biomarkers including negative findingsand biomarker impacts Tumor Specific FDA therapies 82 new interpretations for FDA approved therapies at tumor type level
- 17. New biomarker typesand genomic signatures 17 • TSO-500 genes, fusions and more • Genomic signatures including but not limited to: o TMB o MSI o PD-L1 o PMSA • Combination biomarkers o BRAF negative findings • Gene impact o BRAF Activating o Loss/Gain of Function
- 18. New drug interpretations 18 • Detailed drug descriptions o Commercial label- “Keytruda" o Mechanism of action- “Anti PD-1" o Status- "Approved" vs "Investigational" o Indications for use- "Solid Tumors with MSI-high" o Drug Class- "Immune Checkpoint inhibitor" • Lists available clinical trials
- 19. New Report Templates 19 • New somatic report templates include: o Report MSI, TMB o Other Genomic Signatures o Structural variants o Negative findings Put template screenshot here
- 20. Example Biomarkers 20 • Colorectal cancer sample: o MSH6 LOF o Gene Signature: TMB High o Gene signature: MSI High o BRAF/KRAS negative finding – colorectal Put variants to evaluate screenshot here?
- 21. 21 Product Demo
- 22. NIH Grant Funding Acknowledgments 22 • 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/STTRMatching Funds ProgramGrant 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.
- 23. 23
- 24. eBook Update: Clinical Variant Analysis for Cancer 24 Want a free copy? Request one in the questions or chat panel and our team will follow up with you!
- 25. Innovation Awards 25 The 2023 Golden Helix Innovation Awards will run from Dec. 1st, 2022 - Feb. 28th, 2023 • We want to see how YOU are using our tools to the best of their ability. • Anyone using Golden Helix Software tools is eligible to submit for entry, and no prior publication of research is required. • Submissions can be for clinical or hospital laboratory work, academic research, government, or commercial, we just want to see great examples of your workflows. • 3 winners, each receiving 1 user license for either SVS or VarSeq, and first place receiving in addition a Dell Latitude 5000 series laptop. • All winners will receive the opportunity to present their research via webcast. Goldenhelix.com/events/Innovation_Awards
- 26. Awards 26
- 27. 27