Bioanalytical Capabilities -- Thought-Leading Science Armed with the Latest Technology
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Helping your drug development program succeed is what we do. Keeping your timeline on track requires scientific expertise, operational experience and up-to-date knowledge of the regulatory environment. Whether you need preclinical or clinical bioanalysis, local support or global capabilities, Covance is the partner that you can trust to help deliver on your bioanalytical timelines every day, every time.
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Bioanalytical Capabilities - Thought-Leading Science Armed with the Latest Te...
Covance offers comprehensive bioanalytical capabilities to support drug development from preclinical through clinical trials. They have scientific and regulatory expertise across multiple species and sample types. Their services include method development, validation, sample analysis, biomarker services, and specialized mass spectrometry solutions. Covance has laboratories around the world and experience supporting over 1,000 projects annually to help clients succeed in developing new drugs.
North America Toxicology Laboratories Market Analysis | Coherent Market Insights
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The document summarizes a market analysis report on the North America toxicology laboratories market from 2019 to 2027. It finds that the market is estimated to reach $317.1 million by 2027, driven by increasing awareness of conventional toxicology testing and cost-effective methods. However, point-of-care toxicology devices and limited efficacy of conventional techniques may hamper growth. Opportunities exist in increased government testing spending and integrating toxicology results with cloud computing. Major players are focused on expanding services, product launches, and partnerships.Performing a Trio Analysis in VSClinical
We recently have exposed the powerful application of our newly released product, VSClinical and the included ACMG Guidelines. Our previous webcasts covered some basics on new algorithms and annotations behind the variant scoring and classification. Taking a step back for a moment, there are many long-time VarSeq users are familiar with our Trio template that comes packaged with the software. But, how does the Trio analysis fit into VSClinical?
In this webcast, we are going to explore some modifications to our baseline trio template showing how to incorporate the ACMG classification results into the various workflows. This will include capturing de novo, compound heterozygous, and dominant heterozygous variants. We will score criteria related to variant frequency, gene impact, and available study information. Additionally, we will also investigate the clinical section of the ACMG guideline tool to see how to leverage the inheritance and allelic state of each variant. After this webcast, the user will discover new avenues of examining trio data by utilizing the ACMG classifier to improve upon one of our classic templates.
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
QPS Bioanalysis
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Annotation capabilities
VarSeq provides powerful annotation capabilities for variant analysis including gene tracks, assemblies, variant functions, frequency tracks, functional predictions, and transcript annotations. It integrates information from over 20 public databases and sources and updates annotations monthly to provide the most current clinically relevant information for researchers. By centralizing variant annotations from disparate sources, VarSeq saves customers significant time and resources compared to manual curation of this data.
Automating the ACMG Guidelines with VSClinical
Clinical Genetic testing requires a complex analysis using the totality of our knowledge about the clinical relevance of a variant and a gene. This includes bioinformatic evidence as well as clinical evidence. The ACMG Guidelines provided a framework in which to score variants based on this evidence, and while some of those scoring criteria require close consultation of the clinical context for a given patient, much of it can be automated.
In this webcast, we review how VSClinical automates the ACMG scoring guidelines while integrating the collective lab expertise from previously classified variants and preferences about genes. We will cover:
Using the ACMG Auto Classifier as part the filtering strategy for gene panels and trio workflows
How gene preferences such as the default transcript, inheritance model, and disorder are updated and saved from VSClinical and used in all future analysis
How the per-variant recommendation engine builds on the auto-classification with descriptive reasons for answering each criterion yes or no
Using the auto-interpretation to present the evidence for all scored criteria in a human-readable paragraph
Working with VSClinical’s self-learning knowledgebase that incorporates previously classified variants and genes inform the interpretation of new variants!
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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Bioanalytical Capabilities - Thought-Leading Science Armed with the Latest Te...
Covance offers comprehensive bioanalytical capabilities to support drug development from preclinical through clinical trials. They have scientific and regulatory expertise across multiple species and sample types. Their services include method development, validation, sample analysis, biomarker services, and specialized mass spectrometry solutions. Covance has laboratories around the world and experience supporting over 1,000 projects annually to help clients succeed in developing new drugs.
North America Toxicology Laboratories Market Analysis | Coherent Market Insights
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The document summarizes a market analysis report on the North America toxicology laboratories market from 2019 to 2027. It finds that the market is estimated to reach $317.1 million by 2027, driven by increasing awareness of conventional toxicology testing and cost-effective methods. However, point-of-care toxicology devices and limited efficacy of conventional techniques may hamper growth. Opportunities exist in increased government testing spending and integrating toxicology results with cloud computing. Major players are focused on expanding services, product launches, and partnerships.Performing a Trio Analysis in VSClinical
We recently have exposed the powerful application of our newly released product, VSClinical and the included ACMG Guidelines. Our previous webcasts covered some basics on new algorithms and annotations behind the variant scoring and classification. Taking a step back for a moment, there are many long-time VarSeq users are familiar with our Trio template that comes packaged with the software. But, how does the Trio analysis fit into VSClinical?
In this webcast, we are going to explore some modifications to our baseline trio template showing how to incorporate the ACMG classification results into the various workflows. This will include capturing de novo, compound heterozygous, and dominant heterozygous variants. We will score criteria related to variant frequency, gene impact, and available study information. Additionally, we will also investigate the clinical section of the ACMG guideline tool to see how to leverage the inheritance and allelic state of each variant. After this webcast, the user will discover new avenues of examining trio data by utilizing the ACMG classifier to improve upon one of our classic templates.
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
QPS Bioanalysis
Whether your focus is on small molecules, proteins, bio-therapeutics, vaccines, or gene therapy, QPS provides a full range of bioanalytical solutions to support drug development from discovery through clinical development and filing.
Annotation capabilities
VarSeq provides powerful annotation capabilities for variant analysis including gene tracks, assemblies, variant functions, frequency tracks, functional predictions, and transcript annotations. It integrates information from over 20 public databases and sources and updates annotations monthly to provide the most current clinically relevant information for researchers. By centralizing variant annotations from disparate sources, VarSeq saves customers significant time and resources compared to manual curation of this data.
Automating the ACMG Guidelines with VSClinical
Clinical Genetic testing requires a complex analysis using the totality of our knowledge about the clinical relevance of a variant and a gene. This includes bioinformatic evidence as well as clinical evidence. The ACMG Guidelines provided a framework in which to score variants based on this evidence, and while some of those scoring criteria require close consultation of the clinical context for a given patient, much of it can be automated.
In this webcast, we review how VSClinical automates the ACMG scoring guidelines while integrating the collective lab expertise from previously classified variants and preferences about genes. We will cover:
Using the ACMG Auto Classifier as part the filtering strategy for gene panels and trio workflows
How gene preferences such as the default transcript, inheritance model, and disorder are updated and saved from VSClinical and used in all future analysis
How the per-variant recommendation engine builds on the auto-classification with descriptive reasons for answering each criterion yes or no
Using the auto-interpretation to present the evidence for all scored criteria in a human-readable paragraph
Working with VSClinical’s self-learning knowledgebase that incorporates previously classified variants and genes inform the interpretation of new variants!
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.
Advanced VSClinical Reports with Scripting and Custom Integrations
Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines for the evaluation of variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since VSClinical was introduced, we have provided a powerful Word-based templating system that allows labs to customize reports to include their specific content and branding.
Although powerful, this capability has been limited to customizing the contents of a Word file. Sometimes, the next logical step for the VSClinical analysis result is not a Word file, but some other file or target system: A database, LIMS, EMR, or even just a custom structured text file.
Join us in this webinar, as we discuss the next version of VarSeq, which will introduce a powerful scripting and custom integration engine built into VSClinical Reports. We will cover:
Capabilities and outputs of the workflows of VSClinical ACMG and Cancer
Content of VSClinical reports, including sample-QC, coverage statistics, custom gene panels, and data providence
The shipped report templates that range from gene panels to exome trios and comprehensive cancer testing
The new custom script-based reports and example workflows it enables
The tools enabling a powerful developer experience when building custom outputs and integrations
The VarSeq Suite holds customization and extendibility as core values, allowing the powerful capabilities of variant analysis to be truly customized to the needs of a specific laboratory and NGS test. The new scripting and integration capabilities build on this tradition for the VSClinical workflows. We hope you can join us as we explore this topic in-depth in this webinar.
Automating NGS Gene Panel Analysis Workflows with Golden Helix
In a clinical setting, investing in automatable workflows provides two pay-backs: First, less time is spent by the constraint resource of laboratory staff and medical professionals. Second, and more importantly, the possibilities for errors is reduced. In this webcast, we will cover the full analysis workflow from sequencer to clinical report and how each component can be automated with the Golden Helix clinical stack. Producing high-quality genetic test reports requires the experience of an entire lab and a robust and repeatable process. Join us to see how automation can enable your laboratory to:
Automatically start secondary analysis pipelines when new sequence runs are complete
Go from FASTQ to BAM and high-quality variants in VCFs hands-off with Sentieon
Automatically start VSPipeline to go from raw VCFs to candidate variants
Compute coverage and call CNVs alongside small variants with VS-CNV
Generate short-list previously scored variants, annotated full candidate variant lists and draft reports with VarSeq and VSClinical
Join us for a tour de force of NGS analytics powered by the Golden Helix VarSeq clinical stack and learn about how each component of your laboratory NGS analysis process may benefit from automation capabilities.
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.
AMP-Based Variant Classification with VSClinical
The document discusses Golden Helix's VSClinical software and its capabilities for analyzing biomarkers and variants according to AMP and ACMG guidelines. VSClinical provides a four-phased workflow to 1) filter variants, 2) assess evidence, 3) develop classifications, and 4) include interpretations in clinical reports. It leverages Golden Helix's CancerKB knowledgebase to accelerate variant interpretation and standardized reporting. The document demonstrates VSClinical's analysis and reporting of variants from a myeloid gene panel according to AMP guidelines.
Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation Sources
Earlier this year we launched our latest product VSClinical featuring workflow support for the ACMG guidelines with advanced automation capabilities and per-criteria recommendations. It has been amazing to watch the adoption of this product in labs doing both germline and in some cases cancer variant interpretation. Our latest VarSeq 2.1 release demonstrates our approach to iterative product improvements based on our committed relationship with our customers and includes numerous enhancements to VSClinical.
In this webcast, we cover the new and updated capabilities that can add value to your genetic testing workflows as well as review the VarSeq workflow support somatic variant interpretation in tumors by leveraging our cancer-specific annotations sources. In this webcast, we:
-Demonstrate the new “Consortium Classification” support in VSClinical to have an additional ClinVar-like annotation source added to the automated and interactive ACMG scoring process.
-See how previous interpretations are integrated into your VSClinical analysis, whether they are for the current variant or are just in the genomic neighborhood.
-Cover the additional “Lookup in PubMed” variant search feature for finding supporting studies that may provide functional or clinical evidence for a variant.
-See in action the new ACMG Auto Scoring based templates for trio analysis and gene panel tests.
-Review somatic variant filtering and prioritizing in VarSeq and the updates to relevant public annotation sources including CiVIC, ICGC and a new and available to license COSMIC v86!
Splice Site Algorithms for Clinical Genomics
To fully interpret variants in the context of clinical genomics, as outlined by the ACMG interpretation guidelines, variants near canonical splice boundaries must be evaluated for their potential to disrupt gene splicing and thus be classified as a gene-damaging mutation. Five splicing methods have been canonized for this purpose in the clinical testing market: GeneSplicer, MaxEntScan, NNSplice, and Position Weight Matrix (PWM). Although these algorithms vary wildly in their performance characteristics, such as sensitivity and specificity, they are treated as black-box oracles on equal footing when being used by variant curators to classify variants.
In this presentation, we will review these algorithms and their technical strengths and weakness from the perspective of clinical variant interpretation. Additionally, we will present our approach to splice site prediction within VarSeq, demonstrating how we improve on the status quo by employing these algorithms both in the batch annotation and genomic visualization contexts. Finally, we will demonstrate how these methods can be leveraged during the interpretation of variants following the ACMG guidelines within our upcoming product, VSClinical.
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
We have seen the widespread adoption of VarSeq in the clinic. It is chosen for its versatility and flexibility as well as the extensive catalog of annotations provided by Golden Helix. In a genetic testing scenario, VarSeq provides the annotated and filtered list of high-quality variants to that are ready for the user to classify and interpret.
In this webcast, we introduce a new product VSClinical that enables the interpretation of variants following the ACMG Guidelines. By incorporating new algorithms and annotation sources, detailed variant scoring and classification can occur right within VarSeq and without the need for additional external tools or resources.
Join us to see these upcoming capabilities:
Streamline the ACMG scoring guidelines with supportive recommendation and incorporated historical precedence
See the new algorithms behind the automated recommendation algorithm, and how they provide various levels of evidence
Drill down to an unprecedented level of supporting evidence for mutation hot spots, splice site predictions, and related clinical assertions
Build your own lab practices around new capabilities of blinded interpretations, collaborative interpretation review and detailed audit logs for CLIA compliance
Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation
In combination, this can be a game-changer for any clinical lab looking to improve their efficiency and reproducibility of the most complex step in the genetic testing workflow.
Golden Helix's End-to-End Solution for Clinical Labs
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
Advanced Report Customization via VSClinical
This document provides a summary of a presentation about advanced customization capabilities for clinical reports using VSClinical software:
- VSClinical allows customization of clinical reports through custom HTML, XML, JSON templates and scripts to enhance Word reports and integrate with REST APIs.
- Templates are provided for germline and somatic variant analysis that include ACMG/AMP guidelines and can be further customized.
- Reports can include additional data such as gene impact analysis, drug/trial information, and machine-readable outputs like JSON can be generated.
- A product demo was given to showcase report customization features.
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Golden Helix is a bioinformatics company that has developed software tools like CancerKB to help accelerate next-generation sequencing (NGS) cancer testing. CancerKB is a curated knowledgebase that provides clinically relevant information and interpretations of cancer variants to help generate standardized clinical reports. It is updated based on current guidelines, literature, and customer feedback to integrate the most relevant cancer data and help clinicians evaluate NGS results more efficiently. Golden Helix also acknowledges funding support from the National Institutes of Health.
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Efficient Application of NGS Family-Based Analysis
Golden Helix is committed to providing next-gen sequencing solutions that are comprehensive and efficient. A significant portion of our user base processes pediatric cases or requires the ability to run family-based analyses that can be applied to all inheritance models in order to identify rare variants in Mendelian disorders and cancer. To increase diagnostic yield and reduce time to clinical results, these models and workflows must be easy to set up and used efficiently. Optimization can involve all the steps, including data import, workflow design (variant filtering), a detailed evaluation of variant impact and clinical relevance via ACMG guidelines and AMP guidelines, as well as providing a full clinical report.
VarSeq is the best tool to accomplish this task. VarSeq, our tertiary analytics platform, is designed to process all sizes of genomic data. It can filter through all variants in order to identify clinically relevant variants. The results are evaluated using automated and standardized guidelines. This webcast will demonstrate workflows tailored to different pedigree scenarios. It will also demonstrate VarSeq features designed to speed up analysis time while maintaining consistency with outcomes.
In this webcast, we will cover the following topics:
Explore various family-based project designs (includes trio and duo & extended families)
Discuss various inheritance models (compound het, de novo, dominant inherited, etc)
Briefly examine the ACMG guidelines relevant to inheritance and review an example trio clinical report
Demonstrate how VSPipeline can automate the creation of projects
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A Walk Through GWAS
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Exploring New Features and Clinical Reports in the ACMG Guideline Workflow
For the past year, Golden Helix has been preparing a VarSeq release that includes ACMG Guidelines scoring and classification for not only single nucleotide variants but also copy number variants. In the past few months, our webcasts have introduced these guidelines and explored example CNVs that demonstrated the automated scoring of CNVs according to the new ACMG CNV Guidelines. However, there are many other new features and upgrades that have been incorporated into this VarSeq release. These upgrades have largely been driven by input from VarSeq users! That’s why I am very excited to explore these features together in the upcoming webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”. In this webcast, we will walk through a workflow with SNVs and CNVs highlighting many of the new features and upgrades that will improve and streamline your ACMG workflow. Notably, we will see how these new features can also be incorporated into clinical reports.
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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
An Exploration of Clinical Workflows in VarSeq
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Cancer Workflows in VarSeq
Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go from an unfiltered variant file created by a secondary analysis pipeline to a report containing information about interesting variants.
This webcast will highlight VarSeq's support for Cancer Gene Panels and Tumor-Normal workflows by demonstrating:
• Variant, Region and Sample Quality Assurance
• Filtering to variants in targeted cancer genes relevant to the tumor type
• Summarizing variants in a clinical report
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Advanced VSClinical Reports with Scripting and Custom Integrations
Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines for the evaluation of variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since VSClinical was introduced, we have provided a powerful Word-based templating system that allows labs to customize reports to include their specific content and branding.
Although powerful, this capability has been limited to customizing the contents of a Word file. Sometimes, the next logical step for the VSClinical analysis result is not a Word file, but some other file or target system: A database, LIMS, EMR, or even just a custom structured text file.
Join us in this webinar, as we discuss the next version of VarSeq, which will introduce a powerful scripting and custom integration engine built into VSClinical Reports. We will cover:
Capabilities and outputs of the workflows of VSClinical ACMG and Cancer
Content of VSClinical reports, including sample-QC, coverage statistics, custom gene panels, and data providence
The shipped report templates that range from gene panels to exome trios and comprehensive cancer testing
The new custom script-based reports and example workflows it enables
The tools enabling a powerful developer experience when building custom outputs and integrations
The VarSeq Suite holds customization and extendibility as core values, allowing the powerful capabilities of variant analysis to be truly customized to the needs of a specific laboratory and NGS test. The new scripting and integration capabilities build on this tradition for the VSClinical workflows. We hope you can join us as we explore this topic in-depth in this webinar.
Automating NGS Gene Panel Analysis Workflows with Golden Helix
In a clinical setting, investing in automatable workflows provides two pay-backs: First, less time is spent by the constraint resource of laboratory staff and medical professionals. Second, and more importantly, the possibilities for errors is reduced. In this webcast, we will cover the full analysis workflow from sequencer to clinical report and how each component can be automated with the Golden Helix clinical stack. Producing high-quality genetic test reports requires the experience of an entire lab and a robust and repeatable process. Join us to see how automation can enable your laboratory to:
Automatically start secondary analysis pipelines when new sequence runs are complete
Go from FASTQ to BAM and high-quality variants in VCFs hands-off with Sentieon
Automatically start VSPipeline to go from raw VCFs to candidate variants
Compute coverage and call CNVs alongside small variants with VS-CNV
Generate short-list previously scored variants, annotated full candidate variant lists and draft reports with VarSeq and VSClinical
Join us for a tour de force of NGS analytics powered by the Golden Helix VarSeq clinical stack and learn about how each component of your laboratory NGS analysis process may benefit from automation capabilities.
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.
AMP-Based Variant Classification with VSClinical
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Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation Sources
Earlier this year we launched our latest product VSClinical featuring workflow support for the ACMG guidelines with advanced automation capabilities and per-criteria recommendations. It has been amazing to watch the adoption of this product in labs doing both germline and in some cases cancer variant interpretation. Our latest VarSeq 2.1 release demonstrates our approach to iterative product improvements based on our committed relationship with our customers and includes numerous enhancements to VSClinical.
In this webcast, we cover the new and updated capabilities that can add value to your genetic testing workflows as well as review the VarSeq workflow support somatic variant interpretation in tumors by leveraging our cancer-specific annotations sources. In this webcast, we:
-Demonstrate the new “Consortium Classification” support in VSClinical to have an additional ClinVar-like annotation source added to the automated and interactive ACMG scoring process.
-See how previous interpretations are integrated into your VSClinical analysis, whether they are for the current variant or are just in the genomic neighborhood.
-Cover the additional “Lookup in PubMed” variant search feature for finding supporting studies that may provide functional or clinical evidence for a variant.
-See in action the new ACMG Auto Scoring based templates for trio analysis and gene panel tests.
-Review somatic variant filtering and prioritizing in VarSeq and the updates to relevant public annotation sources including CiVIC, ICGC and a new and available to license COSMIC v86!
Splice Site Algorithms for Clinical Genomics
To fully interpret variants in the context of clinical genomics, as outlined by the ACMG interpretation guidelines, variants near canonical splice boundaries must be evaluated for their potential to disrupt gene splicing and thus be classified as a gene-damaging mutation. Five splicing methods have been canonized for this purpose in the clinical testing market: GeneSplicer, MaxEntScan, NNSplice, and Position Weight Matrix (PWM). Although these algorithms vary wildly in their performance characteristics, such as sensitivity and specificity, they are treated as black-box oracles on equal footing when being used by variant curators to classify variants.
In this presentation, we will review these algorithms and their technical strengths and weakness from the perspective of clinical variant interpretation. Additionally, we will present our approach to splice site prediction within VarSeq, demonstrating how we improve on the status quo by employing these algorithms both in the batch annotation and genomic visualization contexts. Finally, we will demonstrate how these methods can be leveraged during the interpretation of variants following the ACMG guidelines within our upcoming product, VSClinical.
Introducing VSClinical: Streamlining ACMG Variant Interpretation Guidelines
We have seen the widespread adoption of VarSeq in the clinic. It is chosen for its versatility and flexibility as well as the extensive catalog of annotations provided by Golden Helix. In a genetic testing scenario, VarSeq provides the annotated and filtered list of high-quality variants to that are ready for the user to classify and interpret.
In this webcast, we introduce a new product VSClinical that enables the interpretation of variants following the ACMG Guidelines. By incorporating new algorithms and annotation sources, detailed variant scoring and classification can occur right within VarSeq and without the need for additional external tools or resources.
Join us to see these upcoming capabilities:
Streamline the ACMG scoring guidelines with supportive recommendation and incorporated historical precedence
See the new algorithms behind the automated recommendation algorithm, and how they provide various levels of evidence
Drill down to an unprecedented level of supporting evidence for mutation hot spots, splice site predictions, and related clinical assertions
Build your own lab practices around new capabilities of blinded interpretations, collaborative interpretation review and detailed audit logs for CLIA compliance
Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation
In combination, this can be a game-changer for any clinical lab looking to improve their efficiency and reproducibility of the most complex step in the genetic testing workflow.
Golden Helix's End-to-End Solution for Clinical Labs
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
Advanced Report Customization via VSClinical
This document provides a summary of a presentation about advanced customization capabilities for clinical reports using VSClinical software:
- VSClinical allows customization of clinical reports through custom HTML, XML, JSON templates and scripts to enhance Word reports and integrate with REST APIs.
- Templates are provided for germline and somatic variant analysis that include ACMG/AMP guidelines and can be further customized.
- Reports can include additional data such as gene impact analysis, drug/trial information, and machine-readable outputs like JSON can be generated.
- A product demo was given to showcase report customization features.
Using Golden Helix CancerKB to Accelerate NGS Cancer Testing
Golden Helix is a bioinformatics company that has developed software tools like CancerKB to help accelerate next-generation sequencing (NGS) cancer testing. CancerKB is a curated knowledgebase that provides clinically relevant information and interpretations of cancer variants to help generate standardized clinical reports. It is updated based on current guidelines, literature, and customer feedback to integrate the most relevant cancer data and help clinicians evaluate NGS results more efficiently. Golden Helix also acknowledges funding support from the National Institutes of Health.
NeoGenomics Company Overview for June 2015
This presentation provides an overview of the company, which provides cancer genetic testing services. It highlights the company's fast growth, experienced management team, expanding product and service offerings including next generation sequencing and liquid biopsy tests. The company has achieved significant reductions in costs per test through economies of scale and innovation. Financial metrics show accelerating revenue, earnings, and cash flow in recent years through both organic growth and acquisition.
Efficient Application of NGS Family-Based Analysis
Golden Helix is committed to providing next-gen sequencing solutions that are comprehensive and efficient. A significant portion of our user base processes pediatric cases or requires the ability to run family-based analyses that can be applied to all inheritance models in order to identify rare variants in Mendelian disorders and cancer. To increase diagnostic yield and reduce time to clinical results, these models and workflows must be easy to set up and used efficiently. Optimization can involve all the steps, including data import, workflow design (variant filtering), a detailed evaluation of variant impact and clinical relevance via ACMG guidelines and AMP guidelines, as well as providing a full clinical report.
VarSeq is the best tool to accomplish this task. VarSeq, our tertiary analytics platform, is designed to process all sizes of genomic data. It can filter through all variants in order to identify clinically relevant variants. The results are evaluated using automated and standardized guidelines. This webcast will demonstrate workflows tailored to different pedigree scenarios. It will also demonstrate VarSeq features designed to speed up analysis time while maintaining consistency with outcomes.
In this webcast, we will cover the following topics:
Explore various family-based project designs (includes trio and duo & extended families)
Discuss various inheritance models (compound het, de novo, dominant inherited, etc)
Briefly examine the ACMG guidelines relevant to inheritance and review an example trio clinical report
Demonstrate how VSPipeline can automate the creation of projects
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This document summarizes a presentation given by Gabe Rudy, VP of Product & Engineering at Golden Helix, on updated strategies and expanded capabilities for exome analysis with VS-CNV and VSClinical. The presentation demonstrates new features for enhanced variant analysis, including analyzing splice site, non-coding RNA, and mitochondrial variants. It also reviews improvements to Golden Helix's exome CNV calling in VarSeq, including a new low-quality target filter strategy that reduces the number of CNVs called while maintaining sensitivity and precision. Additional capabilities discussed include generating synchronized clinical reports and incorporating virtual gene panels.
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This document provides a report card format for assessing the status and commercialization progress of organ-on-chip technologies. It introduces challenges facing new technologies, the market need for organ-on-chip, and technical and commercial factors for evaluation. Example scores are given to different players for technical and commercial criteria. The report recommends refining the scoring system and revisiting it each year to track the field's progress towards successfully commercializing organ-on-chip technologies.
A Walk Through GWAS
Genome-wide association studies (GWAS) have been providing valuable insight to the genetics of common and complex diseases for many years. In this webcast we will walk through one possible workflow for completing GWAS in Golden Helix SNP & Variation Suite (SVS) with special attention paid to adjusting analysis for population stratification.
Clinical Reporting Made Easy
This webcast will walk through preparing a template for report generation, reviewing the generated report and performing some report customizations.
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
An Exploration of Clinical Workflows in VarSeq
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
Cancer Workflows in VarSeq
Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go from an unfiltered variant file created by a secondary analysis pipeline to a report containing information about interesting variants.
This webcast will highlight VarSeq's support for Cancer Gene Panels and Tumor-Normal workflows by demonstrating:
• Variant, Region and Sample Quality Assurance
• Filtering to variants in targeted cancer genes relevant to the tumor type
• Summarizing variants in a clinical report
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The document discusses the development of the PanDx integrated diagnostic platform by UC Berkeley. It provides an overview of the project, which aims to create a portable diagnostic device that can quickly diagnose diseases like HIV, TB, and malaria using different sample types in resource-limited settings. The device is being designed to be affordable, reliable, and able to function in areas with limited electricity. Updates are provided on the development progress, including demonstration cartridges being tested for tuberculosis, HIV p24 antigen, and ALT clinical chemistry assays. The goal is to have fully functional breadboard prototypes and performance data from hundreds of demonstration cartridge tests in multiple assays by the end of the current development phase in September 2015.
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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.
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Discovering New Innovations in Oncology
To learn more visit:
https://insidescientific.com/webinar/cutting-edge-conversations-discovering-new-innovations-in-oncology/
Starting off the conversation, Dr. David Bunka will present specific case studies for prostate cancer, multiple myeloma and chronic myelomonocytic leukaemia, highlighting the ability of Optimer technology to deliver novel targeted therapeutics for cancer treatment. Optimer binders are small, highly target specific oligonucleotide-based affinity binders. The Optimer platform offers the ability to develop specific binders targeted to a specific biomarker or to an oncological cell phenotype without the need for known biomarkers. Optimer therapeutics are enabling new strategies in cancer treatment, including the targeted delivery of diverse payloads to cancer cells for precision chemotherapy, or gene therapy approaches.
Dr. Cathie Miller will discuss how archived tissues contain valuable information for clinical research. For over thirty years, BioIVT has worked to expand the characterization of their archived tissues. BioIVT offers complete NGS project management that ensures success. In this presentation, Dr. Miller will review BioIVT’s comprehensive process, their strengths in sample collection through library prep, their in-house and validated partnership capabilities and how BioIVT elevates science.
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Plant Metabolism Studies: Options for Plant Cultivation
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Biocide Authorization Timeline
This document outlines the timeline and key steps involved in obtaining biocide authorization, which can take up to 30 months to complete:
1) An initial data gap analysis is conducted to structure the product family, identify existing data, and determine what additional testing may be required.
2) Dossier preparation involves completing Iuclid datasets for the active substance and products, drafting supporting documents like exposure scenarios, and finalizing the dossier for submission via R4BP.
3) Translation of dossier documents may be required for mutual recognition applications in other countries in parallel to the primary authorization process.
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Bioanalytical Capabilities -- Thought-Leading Science Armed with the Latest Technology
- 1. BIOANALYTICAL CAPABILITIES Expert Navigation & Delivery to Help You Reach Your Preclinical & Clinical Objectives Helping your drug development program succeed is what we do. Keeping your timeline on track requires scientific expertise, operational experience and up-to-date knowledge of the regulatory environment. Whether you need preclinical or clinical bioanalysis, local support or global capabilities, Covance is the partner that you can trust to help deliver on your bioanalytical timelines every day, every time. Covance offers unique perspectives that have helped to develop more than 80 percent of all 2016 FDA approved new drugs. We partner to help you determine the best strategy for your drug candidate and to implement a solution that delivers the most value from your program. We will work collaboratively with you to meet your needs, leveraging experience gained from developing more than 1,000 methods annually and supporting more than 260 unique compounds annually. Small Molecule & Biologics Bioanalytical Solutions Translational Biomarker Solutions Specialized LC-MS Solutions 188,500 feet2 (17,512 meters2 ) of Operational Space (as of June 2019) ▶ Feasibility, method development, transfer, validation and sample analysis ▶Scientific and regulatory expertise across multiple species and sample matrices ▶ High-throughput discovery, nonclinical (GLP) and clinical studies ▶ Fit-for-purpose validation ▶ CLIA-certified laboratories ▶ GLP/GCP-compliant services ▶ Discovery and clinical biomarker services ▶ Multiplexing capabilities ▶ Multiple platforms including MSD and Luminex ▶ Immunogenicity studies using a tiered approach • Screening • Confirmatory (immunodepletion) • Titer assessment (quantification, semi-quantification) • Cell-based neutralizing antibody detection ▶ Cell-based bioassay development, validation and sample analysis ELISA-Based ▶ Ligand-binding assays ▶ Targeted biomarker assay development and validation ▶ Biomarker discovery Mass Spectrometry-Based ▶ Targeted biomarker assay development and validation ▶ Biomarker discovery (proteomics and metabonomics) ▶ Oligonucleotides (siRNA, DNA) ▶ Peptides and proteins (mAbs) ▶ Targeted proteomics ▶ Antibody-drug conjugates ▶ Tissues ▶ Indianapolis, IN: 51,000 ft2 ▶ Salt Lake City, UT: 29,000 ft2 ▶ Chantilly, VA: 42,500 ft2 ▶ Dried Matrix Spot analysis ▶ Microfluidics and microsampling analysis ▶ High-resolution accurate mass (HRAM)-MS ▶ Madison, WI: 25,000 ft2 ▶ Harrogate, UK: 22,000 ft2 ▶ Shanghai, CN: 19,000 ft2
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