Using VarSeq to Improve Variant Analysis Research WorkflowsGolden Helix Inc
In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.
Comprehensive Clinical Workflows for Copy Number Variants in VarSeqGolden Helix
While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
Golden Helix has developed and validated with our clinical partners a specialized NGS-based CNV caller capable of detecting deletion and duplication events as small as single-exons and as large as whole chromosome aneuploidy events.
As this capability is applied to large panels and exomes with many putative CNVs per sample, it is important to distinguish between rare and common CNV regions as well as pull in clinical assessments done on similar CNVs that match the clinical phenotype under test.
Enjoy this webcast recording where we review the expanded capabilities of CNV analysis in VarSeq including how to:
Annotate CNV against genes, population catalogs, and clinical sources
Automate the prioritizing of CNVs in your test-specific workflows with customized annotation and filtering steps
Interpret CNVs in your samples in conjunction with NGS variants with both visual and algorithm support
Capture the expert curation of variants in your labs in a CNV based Assessment Catalog
Expand your clinical reports with annotated and interpreted CNVs alongside your existing NGS variants
Centralize your knowledge-base in VSWarehouse for both variants and CNVs
We hope you enjoy this as we review and demonstrate the comprehensive support for CNVs in VarSeq and how these concepts apply to your clinical genetic tests.
Getting Started with VSWarehouse - The User ExperienceGolden Helix Inc
Built on the algorithms and high-performance storage technology that powers the VarSeq software, VSWarehouse offers a scalable, multi-project warehouse for NGS variant call sets, clinical reports, and a knowledge base of variant classifications.
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.
VSWarehouse; a scalable, rapid genomic repository solutionGolden Helix
Anyone handling NGS data understands the constant issue of not only storing all the variant data but also the difficulties in querying through a massive dataset. VarSeq has grown an excellent reputation for being a powerful filtration and annotation engine for NGS data. Tightly coupled with VarSeq is our genomic repository solution, VSWarehouse. VSWarehouse provides a means of storing all variant cohort data as well as rapid querying capabilities to quickly navigate through the, potentially, millions of variants you may amass over time. Just as important is the ability to store this data; users can find relief that VSWarehouse is designed to be installed behind a private network to ensure the protection of all genomic data. Join us in this webcast as we explore the key value points, usability, and direct scalability of VSWarehouse.
What will you learn in this webcast?
From VSWarehouse, how to access the browser to investigate:
-Querying updated clinical evidence against an existing variant cohort
-Filtering through stored projects for all relevant variant data
-Accessing the administrator-level permissions management site
From VarSeq, how to leverage variant data in VSWarehouse to:
-Filter out common variants in the store cohort
-Annotate and plot VSWarehouse content in the VarSeq project
-Utilize congruent assessment catalogs for storing variant classifications uniformly for all users
Performing a Trio Analysis in VSClinicalGolden Helix
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.
Automating NGS Gene Panel Analysis Workflows with Golden HelixGolden 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.
Using VarSeq to Improve Variant Analysis Research WorkflowsGolden Helix Inc
In this webinar presentation, we will review workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.
Comprehensive Clinical Workflows for Copy Number Variants in VarSeqGolden Helix
While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
Golden Helix has developed and validated with our clinical partners a specialized NGS-based CNV caller capable of detecting deletion and duplication events as small as single-exons and as large as whole chromosome aneuploidy events.
As this capability is applied to large panels and exomes with many putative CNVs per sample, it is important to distinguish between rare and common CNV regions as well as pull in clinical assessments done on similar CNVs that match the clinical phenotype under test.
Enjoy this webcast recording where we review the expanded capabilities of CNV analysis in VarSeq including how to:
Annotate CNV against genes, population catalogs, and clinical sources
Automate the prioritizing of CNVs in your test-specific workflows with customized annotation and filtering steps
Interpret CNVs in your samples in conjunction with NGS variants with both visual and algorithm support
Capture the expert curation of variants in your labs in a CNV based Assessment Catalog
Expand your clinical reports with annotated and interpreted CNVs alongside your existing NGS variants
Centralize your knowledge-base in VSWarehouse for both variants and CNVs
We hope you enjoy this as we review and demonstrate the comprehensive support for CNVs in VarSeq and how these concepts apply to your clinical genetic tests.
Getting Started with VSWarehouse - The User ExperienceGolden Helix Inc
Built on the algorithms and high-performance storage technology that powers the VarSeq software, VSWarehouse offers a scalable, multi-project warehouse for NGS variant call sets, clinical reports, and a knowledge base of variant classifications.
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.
VSWarehouse; a scalable, rapid genomic repository solutionGolden Helix
Anyone handling NGS data understands the constant issue of not only storing all the variant data but also the difficulties in querying through a massive dataset. VarSeq has grown an excellent reputation for being a powerful filtration and annotation engine for NGS data. Tightly coupled with VarSeq is our genomic repository solution, VSWarehouse. VSWarehouse provides a means of storing all variant cohort data as well as rapid querying capabilities to quickly navigate through the, potentially, millions of variants you may amass over time. Just as important is the ability to store this data; users can find relief that VSWarehouse is designed to be installed behind a private network to ensure the protection of all genomic data. Join us in this webcast as we explore the key value points, usability, and direct scalability of VSWarehouse.
What will you learn in this webcast?
From VSWarehouse, how to access the browser to investigate:
-Querying updated clinical evidence against an existing variant cohort
-Filtering through stored projects for all relevant variant data
-Accessing the administrator-level permissions management site
From VarSeq, how to leverage variant data in VSWarehouse to:
-Filter out common variants in the store cohort
-Annotate and plot VSWarehouse content in the VarSeq project
-Utilize congruent assessment catalogs for storing variant classifications uniformly for all users
Performing a Trio Analysis in VSClinicalGolden Helix
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.
Automating NGS Gene Panel Analysis Workflows with Golden HelixGolden 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.
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.
Automating Clinical Workflows with the VarSeq SuiteGolden Helix
The automation of clinical NGS workflows provides a number of important benefits. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In this webcast, we will discuss how the VarSeq Suite can be leveraged to automate the full analysis workflow from sequencer to clinical report. Join us as we demonstrate how VarSeq’s automation capabilities can enable your laboratory to:
Automatically perform secondary analysis when a new sequence run is complete
Go from FASTQ to BAM and high-quality variants in VCFs using Sentieon
Automatically start VSPipeline to go from raw VCFs to candidate variants
Compute coverage and call CNVs alongside small variants with VS-CNV
Efficiently interpret a small set of annotated candidate variants and CNVs
Draft reports with VarSeq and VSClinical
Join us as we discuss the automation of the clinical analysis process for NGS genetic tests from FASTQ to Clinical Reports using the VarSeq Suite and discover how your laboratory’s NGS workflows may benefit from these automation capabilities.
Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeqGolden Helix Inc
As Precision Medicine is taking off, the number of samples in a testing lab and the associated data volume is increasing exponentially. In order to organize the data and build a knowledge base of cases that can be used for future analysis as well as ongoing research, labs need to leverage state of the art warehousing technology.
Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation SourcesDelaina Hawkins
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!
Updates to VSWarehouse: Storing your CNV & ACMG ResultsGolden Helix
Golden Helix has created VSWarehouse as a solution to store the massive collection of sample and variant data output from your tertiary analysis. The classic VSWarehouse application provides a means of storing and querying on all your variant data from VarSeq projects. On top of storing your variants, VSWarehouse also stores your assessment catalogs and clinical reports. Regarding VarSeq, we’ve made some massive workflow upgrades with CNV detection and ACMG guidelines in VSClinical. Recently, we’ve given plenty of attention to these analysis upgrades from the VarSeq perspective, but now we have upgraded VSWarehouse to store your CNV and VSClinical results. In this webcast we are not only going to explore the new Warehouse capabilities; demonstrating how a user can leverage recorded CNV and ACMG data, but also describe more fundamental values VSWarehouse delivers.
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP GuidelinesGolden Helix
Join us as we delve into VSWarehouse with a focus on our new capability of storing somatic variant projects and catalogs built for the AMP Guidelines within VSClinical.
We will also be demonstrating how VSWarehouse efficiently navigates through stored variants via the VSWarehouse Browser.
We hope you enjoy as we explore and leverage a comprehensive set of genomic data stored within VSWarehouse to ensure rapid workflow efficiency.
In this webcast, you will learn:
How to access the VSWarehouse terminal within VarSeq
Leverage the VSWarehouse genomic database in a VarSeq workflow
Explore the stored genomic data via the VSWarehouse Browser
You can read more about what this webcast covers over on our blog: https://blog.goldenhelix.com/vswarehouse-upgrade-somatic-variant-analysis-via-vsclinical-amp-guidelines/
Golden Helix's End-to-End Solution for Clinical LabsGolden Helix
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!
New & Improved COSMIC Database for NGS Cancer AnalysesGolden Helix
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!
Using Golden Helix CancerKB to Accelerate NGS Cancer TestingGolden Helix
Next Generation Sequencing is being rapidly integrated into the oncology field. From the clinical perspective, both somatic and germline NGS results are informative for hereditary cancer risk and treatment strategies. There are numerous scattered resources that inform the clinical significance of a somatic mutation for a patient’s tumor type. Similarly, there are many FDA-approved anti-cancer agents and drugs with changing indications, and opportunities for off-label use. Even more, there are clinical trials all over the world that though they require specific genetic alterations for enrollment eligibility, they could provide more treatment options for cancer patients.
What’s the bottom line? It is certainly a huge undertaking to evaluate a gene or biomarker’s role in cancer or clinical significance. It requires sifting through trials that are relevant for the patient from the abundance of literature available, not to mention staying well-informed on new research as it is published.
Golden Helix CancerKB offers a solution. We demonstrate the application of CancerKB and how easy somatic variant analysis can be in VSClinical. Namely, I will deep dive into the following topics:
The process our expert curators use to produce high-quality cancer interpretations
Examples of complex biomarker interpretations simplified using CancerKB
Report content filled in by CancerKB, even for rare genes
Integrating customer feedback and the future of CancerKB
Processing Hereditary Cancer Panels in VarSeqGolden Helix
Processing variants related to cancer is an incredibly critical process and a primary goal is to not only assess the variants rapidly but also accurately. A major improvement to cancer panel workflow efficiency is to utilize VarSeq for variant filtering, annotating, and interpretation. In this webcast we’ll cover some important quality assurance capabilities VarSeq provides, multiple approaches to build targeted panels, how to access/utilize numerous cancer annotations, and finally work through the ACMG guideline process on the selected germline cancer variants. The overall goal is to cover the basics of building the cancer gene panel project template so that it can be used routinely in high throughput environments.
In this presentation we will demonstrate how to customize your VarSeq workflow to handle the following family scenarios:
*Full Quad (mother, father and 2 affected children)
*Siblings with different affection status (mother, father, 1 affected and 1 unaffected child)
*No parents (2 affected siblings)
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...Golden Helix
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.
Building Secure Analysis and Storage Systems with Golden HelixGolden Helix
Genetic testing labs deal with personal data in categories with the highest level of security requirements: personal identity and medical records. Given the liability and risk associated with a breach of this secure information, it is not surprising that many labs and institutes that aggregate genomic data prefer if not require on-premise analysis and storage solutions.
Golden Helix is in a unique position to provide completely on-premise analysis solutions with a history of building analysis software from the ground-up on first principles and a focus on providing integrated, turn-key solutions. This allows for a licensing model based on training and supporting users, not tracking per-sample usage of cloud resources. As the regulatory environment around the world strengthens the privacy rights of individuals and the outcry around data breaches raises the stakes for building a secure system, we have developed a number of best practices for building secure, offline genomic analysis pipelines. Watch as we cover:
- Building a FASTQ to clinical reports pipeline behind a firewall
- On-premise analysis, warehouse and data servers independent of the internet
- Single sign-on based on local credential systems and without internet access
- Storage and network considerations for the analysis of patient-linked data
- Choose when to update and validate new pipelines, data sources and software versions
We hope you enjoy as we review the capabilities and best practices in building the most secure environment for hosting the analytics behind your precision medicine tests.
Annotating and Cataloging CNVs in VarSeqGolden Helix
In this webcast recording, we will be showing users the process of annotating and filtering CNVs in VarSeq. This will include a discussion of available annotation sources and a demonstration of how these annotations may be utilized in VarSeq filter chains to identify clinically relevant CNVs. We will also discuss CNV assessment catalogs as a mechanism for tracking common CNVs and identifying relevant previously classified events.
Στα πλαίσια του προγράμματος Erasmus+, “ Help the Earth: Reduce, Reuse, Recycle.” και της Δράσης “Stop hurting the earth/change.org”, το κάθε τμήμα του σχολείου μας,του Γυμνασίου Νέου Σκοπού, προτείνει έναν εφικτό τρόπο προστασίας της γης μας.
MM-KBAC – Using Mixed Models to Adjust for Population Structure in a Rare-var...Golden Helix Inc
Confounding from population structure, extended families and inbreeding can be a significant issue for burden and kernel association tests on rare variants from next generation DNA sequencing. An obvious solution is to combine the power of a mixed model regression analysis with the ability to assess the rare variant burden using methods such as KBAC or CMC. Recent approaches have adjusted burden and kernel tests using linear regression models; this method adjusts for the relatedness of samples and includes that directly into a logistic regression model.
Pentyrch bowling club horse racing nightkrakoweric
On Friday 11th July 2014 Pentyrch bowling Club held a fundraising evening at Pentyrch Rugby Club. A night at the horse races raised almost £1000. A great effort especially by Brian Ilbery who drove the project along with help from all the social committee and Andres and Ruth Davies who ran the races and the technology.
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.
Automating Clinical Workflows with the VarSeq SuiteGolden Helix
The automation of clinical NGS workflows provides a number of important benefits. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In this webcast, we will discuss how the VarSeq Suite can be leveraged to automate the full analysis workflow from sequencer to clinical report. Join us as we demonstrate how VarSeq’s automation capabilities can enable your laboratory to:
Automatically perform secondary analysis when a new sequence run is complete
Go from FASTQ to BAM and high-quality variants in VCFs using Sentieon
Automatically start VSPipeline to go from raw VCFs to candidate variants
Compute coverage and call CNVs alongside small variants with VS-CNV
Efficiently interpret a small set of annotated candidate variants and CNVs
Draft reports with VarSeq and VSClinical
Join us as we discuss the automation of the clinical analysis process for NGS genetic tests from FASTQ to Clinical Reports using the VarSeq Suite and discover how your laboratory’s NGS workflows may benefit from these automation capabilities.
Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeqGolden Helix Inc
As Precision Medicine is taking off, the number of samples in a testing lab and the associated data volume is increasing exponentially. In order to organize the data and build a knowledge base of cases that can be used for future analysis as well as ongoing research, labs need to leverage state of the art warehousing technology.
Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation SourcesDelaina Hawkins
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!
Updates to VSWarehouse: Storing your CNV & ACMG ResultsGolden Helix
Golden Helix has created VSWarehouse as a solution to store the massive collection of sample and variant data output from your tertiary analysis. The classic VSWarehouse application provides a means of storing and querying on all your variant data from VarSeq projects. On top of storing your variants, VSWarehouse also stores your assessment catalogs and clinical reports. Regarding VarSeq, we’ve made some massive workflow upgrades with CNV detection and ACMG guidelines in VSClinical. Recently, we’ve given plenty of attention to these analysis upgrades from the VarSeq perspective, but now we have upgraded VSWarehouse to store your CNV and VSClinical results. In this webcast we are not only going to explore the new Warehouse capabilities; demonstrating how a user can leverage recorded CNV and ACMG data, but also describe more fundamental values VSWarehouse delivers.
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP GuidelinesGolden Helix
Join us as we delve into VSWarehouse with a focus on our new capability of storing somatic variant projects and catalogs built for the AMP Guidelines within VSClinical.
We will also be demonstrating how VSWarehouse efficiently navigates through stored variants via the VSWarehouse Browser.
We hope you enjoy as we explore and leverage a comprehensive set of genomic data stored within VSWarehouse to ensure rapid workflow efficiency.
In this webcast, you will learn:
How to access the VSWarehouse terminal within VarSeq
Leverage the VSWarehouse genomic database in a VarSeq workflow
Explore the stored genomic data via the VSWarehouse Browser
You can read more about what this webcast covers over on our blog: https://blog.goldenhelix.com/vswarehouse-upgrade-somatic-variant-analysis-via-vsclinical-amp-guidelines/
Golden Helix's End-to-End Solution for Clinical LabsGolden Helix
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!
New & Improved COSMIC Database for NGS Cancer AnalysesGolden Helix
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!
Using Golden Helix CancerKB to Accelerate NGS Cancer TestingGolden Helix
Next Generation Sequencing is being rapidly integrated into the oncology field. From the clinical perspective, both somatic and germline NGS results are informative for hereditary cancer risk and treatment strategies. There are numerous scattered resources that inform the clinical significance of a somatic mutation for a patient’s tumor type. Similarly, there are many FDA-approved anti-cancer agents and drugs with changing indications, and opportunities for off-label use. Even more, there are clinical trials all over the world that though they require specific genetic alterations for enrollment eligibility, they could provide more treatment options for cancer patients.
What’s the bottom line? It is certainly a huge undertaking to evaluate a gene or biomarker’s role in cancer or clinical significance. It requires sifting through trials that are relevant for the patient from the abundance of literature available, not to mention staying well-informed on new research as it is published.
Golden Helix CancerKB offers a solution. We demonstrate the application of CancerKB and how easy somatic variant analysis can be in VSClinical. Namely, I will deep dive into the following topics:
The process our expert curators use to produce high-quality cancer interpretations
Examples of complex biomarker interpretations simplified using CancerKB
Report content filled in by CancerKB, even for rare genes
Integrating customer feedback and the future of CancerKB
Processing Hereditary Cancer Panels in VarSeqGolden Helix
Processing variants related to cancer is an incredibly critical process and a primary goal is to not only assess the variants rapidly but also accurately. A major improvement to cancer panel workflow efficiency is to utilize VarSeq for variant filtering, annotating, and interpretation. In this webcast we’ll cover some important quality assurance capabilities VarSeq provides, multiple approaches to build targeted panels, how to access/utilize numerous cancer annotations, and finally work through the ACMG guideline process on the selected germline cancer variants. The overall goal is to cover the basics of building the cancer gene panel project template so that it can be used routinely in high throughput environments.
In this presentation we will demonstrate how to customize your VarSeq workflow to handle the following family scenarios:
*Full Quad (mother, father and 2 affected children)
*Siblings with different affection status (mother, father, 1 affected and 1 unaffected child)
*No parents (2 affected siblings)
Efficiently Following the AMP Guidelines with VSClinical and Golden Helix Can...Golden Helix
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.
Building Secure Analysis and Storage Systems with Golden HelixGolden Helix
Genetic testing labs deal with personal data in categories with the highest level of security requirements: personal identity and medical records. Given the liability and risk associated with a breach of this secure information, it is not surprising that many labs and institutes that aggregate genomic data prefer if not require on-premise analysis and storage solutions.
Golden Helix is in a unique position to provide completely on-premise analysis solutions with a history of building analysis software from the ground-up on first principles and a focus on providing integrated, turn-key solutions. This allows for a licensing model based on training and supporting users, not tracking per-sample usage of cloud resources. As the regulatory environment around the world strengthens the privacy rights of individuals and the outcry around data breaches raises the stakes for building a secure system, we have developed a number of best practices for building secure, offline genomic analysis pipelines. Watch as we cover:
- Building a FASTQ to clinical reports pipeline behind a firewall
- On-premise analysis, warehouse and data servers independent of the internet
- Single sign-on based on local credential systems and without internet access
- Storage and network considerations for the analysis of patient-linked data
- Choose when to update and validate new pipelines, data sources and software versions
We hope you enjoy as we review the capabilities and best practices in building the most secure environment for hosting the analytics behind your precision medicine tests.
Annotating and Cataloging CNVs in VarSeqGolden Helix
In this webcast recording, we will be showing users the process of annotating and filtering CNVs in VarSeq. This will include a discussion of available annotation sources and a demonstration of how these annotations may be utilized in VarSeq filter chains to identify clinically relevant CNVs. We will also discuss CNV assessment catalogs as a mechanism for tracking common CNVs and identifying relevant previously classified events.
Στα πλαίσια του προγράμματος Erasmus+, “ Help the Earth: Reduce, Reuse, Recycle.” και της Δράσης “Stop hurting the earth/change.org”, το κάθε τμήμα του σχολείου μας,του Γυμνασίου Νέου Σκοπού, προτείνει έναν εφικτό τρόπο προστασίας της γης μας.
MM-KBAC – Using Mixed Models to Adjust for Population Structure in a Rare-var...Golden Helix Inc
Confounding from population structure, extended families and inbreeding can be a significant issue for burden and kernel association tests on rare variants from next generation DNA sequencing. An obvious solution is to combine the power of a mixed model regression analysis with the ability to assess the rare variant burden using methods such as KBAC or CMC. Recent approaches have adjusted burden and kernel tests using linear regression models; this method adjusts for the relatedness of samples and includes that directly into a logistic regression model.
Pentyrch bowling club horse racing nightkrakoweric
On Friday 11th July 2014 Pentyrch bowling Club held a fundraising evening at Pentyrch Rugby Club. A night at the horse races raised almost £1000. A great effort especially by Brian Ilbery who drove the project along with help from all the social committee and Andres and Ruth Davies who ran the races and the technology.
PnPAuthors Promotional Magazine is about authors, poets, and artist. Peter Cacciolfi, President, and Pattimari Sheets Cacciolfi is VP.
They interview authors and talk about their published books.
They display artists' work.
They publish poets' poems
Στα πλαίσια του μαθήματος της Αρχαίας Ελληνικής Ιστορίας,
οι μαθήτριες της Α΄1 τάξης του γυμνασίου Νέου Σκοπού, Καμακάμη Ευαγγελία και Κουζουτζίδου Παρασκευή,παρουσιάζουν τη Διατροφή στην Αρχαία Ελλάδα
Οι μαθήτριες της Α΄2 τάξης, Τσώνη Σταυρούλα, Ράντου Χρύσα και Σέκρα Σοφία, ζωγραφίζουν και δραματοποιούν τη συνομιλία του Τηλέμαχου με την Αθηνά- Μέντη
Οι μαθητές της Β΄1 τάξης του Γυμνασίου Νέου Σκοπού Σερρών με αφορμή το κείμενο της Νεοελληνικής Λογοτεχνίας,
"Ο μικρός πρίγκιπας και η αλεπού" του Αντουάν ντε-Σαιντ Εξυπερύ, μιλούν για την αληθινή φιλία.
As the number of samples and associated data volume in a testing lab increases, it becomes imperative for labs to leverage state of the art warehousing technology that not only organizes data, but also aides and enables researchers and clinicians to perform further analysis, and ongoing research.
Built on the algorithms and high-performance storage technology that powers the VarSeq software, VSWarehouse offers a scalable, multi-project warehouse for NGS variant call sets, clinical reports, and a knowledge base of variant classifications.
In this webinar, we will discuss 4 topics:
1. How to use VSWarehouse as an annotation source. We will explore questions like:
Have I ever seen this variant before?
At what frequency? (How many heterozygous and homozygous genotypes?)
Have I used this variant in a clinical report for any previous samples?
2. Using VSWarehouse to alert for changes in public annotations that warrant a review of previously reported decisions. We can use this to answer questions such as:
What has changed in public databases like ClinVar since I last accessed this variant?
3. How researchers with lots of data can use VSWarehouse to create a single repository of clinical samples that allows for retrospective cohort research studies.
4. Using the VSWarehouse API to query for information such as:
How many samples have been added to the warehouse in the past day/week/month/year?
How many tests did I conduct in the past day/week/month/year?
These questions and many more are answered by our integrated variant warehousing solution. VSWarehouse retains data from sample VCFs or their genomic annotations, even as new samples and updated annotations are added. VSWarehouse creates a single annotated matrix of all unique variants for all uploaded samples and can be accessed through multiple interfaces.
RIQAS is the largest international External Quality Assessment (EQA)/ Proficiency Testing (PT) scheme, there are currently more than 45,000 participants in 133 countries.
Using Clinical Reports as a part of a Gene Panel PipelineGolden Helix Inc
This webcast will walk through preparing a template for automatic report generation, running new data through the pipeline and reviewing the generated report.
Evaluating Cloud vs On-Premises for NGS Clinical WorkflowsGolden Helix
In the era where cloud-based solutions are the default for the modern office, it may not be obvious why many laboratories and testing centers choose to host their data and analysis pipelines on-premises or on self-managed cloud services. Next-generation sequencing enables a precision medicine approach to rare disease diagnostic and cancer therapeutics through its power to detect unique variants in individuals. This data is generated quickly and cheaply but requires a lot of disk space and processing power to arrive at clinically useful insights.
When providing a clinical lab service under a regulated environment: data security, long-term affordable storage, and versioning through locked-down pipelines are all factors that must go into the choice of whether to choose a hosted analytics platform versus on-premises solutions or self-managed cloud infrastructure.
Join us in this webinar as we cover:
The validation and regulatory requirements that inform infrastructure and hosting decisions for NGS labs
The cost structure of scaling NGS labs to exomes and genomes
Deployment and security architecture for on-premises and self-managed cloud infrastructure
Validating and versioning analysis pipelines with clinical tests through self-managed software lifecycles and versioned annotation sources
Cybersecurity, patient data privacy, and scalable unit economics play a bigger role than ever before in the planning of NGS lab’s infrastructure choices. We look forward to you joining us as we tackle the trade-offs and choices around these topics and how deployment flexibility is a core feature of the Golden Helix VarSeq Suite.
Clinical labs need to be able to process samples down to a shortlist of variants and publish a professional report. Two common clinical applications for genetic tests include Cancer Gene Panels and Whole Exome Trios. Using VarSeq and VSReports, we will demonstrate how easy it is to go from a variant file created by a secondary analysis pipeline containing unfiltered variants to a report containing information for variants of interest. Along the way, we will discuss tips and tricks and answer frequently asked questions to help you get the most out of your data!
This webcast will present a thorough overview of VarSeq's support for clinics:
Cancer Gene Panel:
- Variant, Region and Sample Quality Assurance
- Filtering to variants in targeted cancer genes relevant to the tumor type
- Summarizing variants in a clinical report
Whole Exome Trio:
- Variant Quality Assurance
- Filtering to variants matching several inheritance patterns
- Summarizing variants in a clinical report
Two Clinical Workflows - From Unfiltered Variants to a Clinical ReportGolden Helix Inc
Clinical labs need to be able to process samples down to a short list of variants and publish a professional report. Two common clinical applications for genetic tests include Cancer Gene Panels and Whole Exome Trios. Using VarSeq and VSReports, we will demonstrate how easy it is to go from a variant file created by a secondary analysis pipeline containing unfiltered variants to a report containing information for variants of interest. Along the way we will discuss tips and tricks and answer frequently asked questions to help you get the most out of your data!
Clinical labs need to be able to process samples down to a shortlist of variants and publish a professional report. VSReports helps scientists and clinicians alike create timely, actionable reports that can improve clinical decision making and streamline patient care by seamlessly incorporating the results of tertiary analysis into a customizable clinical report.
Reports are fully customizable, containing focused and actionable data. Additionally, reports can be branded and styled to match the documents that your lab typically produces. With tight integration to your analysis results, you can also pull in additional annotation sources relevant to the sample being tested.
This webcast will walk through preparing a template for report generation, reviewing the generated report and performing some report customizations.
Webinar: Is Phase-Appropriate Validation the Right Choice for your Cell or Ge...Merck Life Sciences
Participate in the interactive webinar now: http://bit.ly/CGTWebinar
This webinar will introduce phase-appropriate validation and why it may be advantageous for cell and gene therapy development. We will also describe how validated platform assays can help you meet your critical development timelines.
Explore our webinar library: www.merckmillipore.com/webinars
Webinar: Is Phase-Appropriate Validation the Right Choice for your Cell or Ge...MilliporeSigma
Participate in the interactive webinar now: http://bit.ly/CGTWebinar
This webinar will introduce phase-appropriate validation and why it may be advantageous for cell and gene therapy development. We will also describe how validated platform assays can help you meet your critical development timelines.
Explore our webinar library: www.emdmillipore.com/webinars
Best Practices for Validating a Next-Gen Sequencing WorkflowGolden Helix
Validating an NGS workflow is an iterative process that begins with collaboration with personnel and planning protocols for the entire workflow from sample preparation, sequencing and variant calling, all the way to data analysis and reporting. At Golden Helix, while we do not provide pre-validated black-box workflows, we provide our customers with support to validate workflows in a transparent manner, and assist them in reaching production deadlines. This webcast will be led by members of our Field Application Scientist team, and we will explore some of the best practices for NGS workflow validation that we have observed and helped to implement based on real-world examples from our customer base. Key topics for discussion will include:
Sample preparation and collection of adequate case/control data
Designing a robust workflow with special considerations for single versus family analyses and phenotypic considerations
Generating the desired output for clinical or other reports
Real world NGS workflow validation strategies
Tune in for tips and strategies that you can deploy when designing and validating your NGS workflow.
Consolidate all of your digital test results for mobile and web to gain end-to-end quality insights and drive improvements
• Quality dashboard: Gain up-to-date quality status and key insights for all of your applications
• Test coverage analysis: Use automated analysis to ensure your testing program covers all required scenarios and platforms
• Root cause analysis: Shorten investigation times with automated root-cause analysis
• Eliminate test fluctuations: Leverage a large results database to obtain a clear indication of end-to-end quality
• Collaboration: Streamline the fault investigation process for better decision making and faster resolution
• Customizable reports: Leverage your accumulated test data to drive business insights with tailored views and reports
• Support for all test platforms and types: Unit, Smoke, Sanity, Functional, non-functional, UI functional, Persistence, Accessibility
Lars Wolff - Performance Testing for DevOps in the Cloud - Codemotion Amsterd...Codemotion
Performance tests are not only an important instrument for understanding a system and its runtime environment. It is also essential in order to check stability and scalability – non-functional requirements that might be decisive for success. But won't my cloud hosting service scale for me as long as I can afford it? Yes, but… It only operates and scales resources. It won't automatically make your system fast, stable and scalable. This talk shows how such and comparable questions can be clarified with performance tests and how DevOps teams benefit from regular test practise.
Similar to Authoring Clinical Reports in VarSeq (20)
The premedical competencies as outlined in a recent American Association of Medical Colleges (AAMC)-HHMI report on Scientific Foundation for Future Physicians calls for stronger connections between course content and the underlying principles in health and medicine. To meet this need, I am developing chemistry courses at the University of Illinois for pre-health professionals that teach concepts and content in a personally meaningful way, thereby stimulating deep student interest and promoting curiosity-driven learning. Scientific evidence shows that people who feel curious devote more attention to an activity, process information more critically, remember information more effectively and persist on task until goals are met.
We are excited to announce and demonstrate some new and highly requested features in this webcast, including predicting phenotypes by applying existing GBLUP or Bayesian models and meta-analysis for GWAS studies.
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 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.
Big Data at Golden Helix: Scaling to Meet the Demand of Clinical and Research...Golden Helix Inc
With a focus on scalable architecture and optimized native code that fully utilizes the CPU and RAM available, we can scale genomic analysis into sizes conventionally considered Big Data on a single host. In this webcast, we demonstrate recent innovations and features in Golden Helix solutions that enable the analysis of big data on your own terms.
Join us in this webcast to see how we have written an open-source C++ port of Beagle v4.1 that is fully integrated into SVS and allows you to run your genotype phasing and imputation on human and animal data as part of your SVS analytics workflow.
Population Structure & Genetic Improvement in LivestockGolden Helix Inc
The genetic improvement of livestock has been a hot topic for almost a century, bringing together researchers, industry, and producers to work towards a common goal. Many countries currently employ extensive genetic selection programs in their cattle with pigs, sheep, and chicken close behind.
In this webcast, Heather J. Huson, Ph.D. from Cornell University will focus on population dynamics and trait association in cattle and goats using high density SNP datasets. Population structure plays a critical role in understanding the relatedness among livestock, ancestral origins of traits, and identification of unique sub-populations or breeds for production improvement and conservation. This also lays the foundation for understanding and improving species such as the goat which is a vital food source in developing countries but has little recorded production or health data.
Understanding population structure is essential for designing complex trait association studies such as those related to production and health characteristics. Here, Huson shows examples of her lab's investigation into population structure in both goats and cattle to identify distinct groups and study traits such as thermo-tolerance.
GWA studies are perhaps most often used for studying the genetic basis of human diseases, but this technology also has great utility for studying the natural variation of other organisms.
In this webcast, Ashley Hintz, Field Application Scientist, will discuss the utility of SVS for analyzing plant GWA data, using publicly available SNP data for Arabidopsis thaliana as a case study. Along the way, Ashley will demonstrate how SVS can be used to manage data, analyze population structure, perform genotype QA and ultimately replicate a published genetic association in A. thaliana using EMMAX regression. She will also address the flexibility of SVS for analyzing the genomes of other plant and animal species.
MM - KBAC: Using mixed models to adjust for population structure in a rare-va...Golden Helix Inc
Confounding from population structure, extended families and inbreeding can be a significant issue for burden and kernel association tests on rare variants from next generation DNA sequencing. An obvious solution is to combine the power of a mixed model regression analysis with the ability to assess the rare variant burden using methods such as KBAC or CMC. Recent approaches have adjusted burden and kernel tests using linear regression models; this method adjusts for the relatedness of samples and includes that directly into a logistic regression model.
This webcast will focus on the details of bringing Mixed Model Regression and KBAC together, including: deriving an optimal logistic mixed model algorithm for calculating the reduced model score, how the kinship or random effects matrix should be specified, and how it all comes together into one algorithm. Results from applying the method to variants from the 1000 Genomes project will also be presented and compared to famSKAT.
New Study Identifies High-Risk Variants Associated with Autism Spectrum Disor...Golden Helix Inc
A growing body of evidence suggests a genetic contribution in the development of autism spectrum disorders (ASD). Since 2002, Lineagen has been building the largest proprietary collection of ASD-related genetic variants and, in 2011, spearheaded a study to increase the clinical yield of the company's genetic diagnostic test, FirstStepDx. To find candidate variants, Linegean selected the Golden Helix services team as well as the Children's Hospital of Philadelphia Center for Applied Genomics to concurrently perform quality control, analyze the data, and interpret the results. The results of this study were recently published in PLoS ONE: "Identification of Rare Recurrent Copy Number Variants in High-Risk Autism Families and their Prevalence in a Large ASD Population."
In this 90-minute webcast, Dr. Hakonarson, Dr. Leppert, Dr. Paul, and Dr. Hensel will outline the study and methodology approach utilized by Lineagen to achieve a two-fold increase in detection rate of genetic variants in individuals with ASD, and Dr. Christensen will share the analytic processes Golden Helix used in this valuable research.
AGBT 2013: Home Brewed Personalized Genomics - The Quest for Meaningful Analy...Golden Helix Inc
Personalized genomics may be moving into a new era with whole-exome and whole-genome sequencing becoming affordable and available to consumers. 23andMe recently piloted a more affordable 80x exome to their existing customers. But it remains to be seen whether this wealth of raw genomic data can be analyzed to provide meaningful results for both healthy and symptomatic individuals.
By acquiring 23andMe exomes on his family, Gabe puts himself in the position of a bioinformatically inclined consumer, but non-clinician, to approach this question with his own analysis. His trio consists of a healthy father and son, and a mother with clinically-diagnosed idiopathic rheumatoid arthritis.
The following goals were set for the analysis: 1) How accurate are variant calls from direct-to-consumer NGS services? 2) How useful and durable is the list of risk variants provided by 23andMe? 3) Can a healthy individual's exome provide additional risk information over standard genotype-array-based risk prediction? and 4) Can the state of our current understanding of the complex genomic architecture of autoimmune diseases be enough to to find potential driver variants and genes to explain the diagnosis of a single case?
Here Gabe presents his findings of this analysis and discuss how individualized genomics might change in the world of affordable sequencing.
Insights: Identification of Candidate Variants using Exome Data in Ophthalmic...Golden Helix Inc
Technological advances in next generation sequencing provide clinicians and researchers with more effective methods to identify pathogenic gene mutations for heritable diseases. To date, the National Eye Institute Bank lists over 450 genes associated with eye-related disorders. Analytical processing of large datasets generated can be cumbersome for all parties involved and some issues that can cause inefficiencies include learning programming languages and reliance on inconsistent freeware. In this webcast, we demonstrate the ability to maximize Golden Helix tools to find potential pathogenic variants in rare ocular diseases.
Knowing Your NGS Upstream: Alignment and VariantsGolden Helix Inc
Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output.
This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
Knowing Your NGS Downstream: Functional PredictionsGolden Helix Inc
Next-Generation Sequencing analysis workflows typically lead to a list of candidate variants that may or may not be associated with the phenotype of interest. Any given analysis may result in tens, hundreds, or even thousands of genetic variants which must be screened and prioritized for experimental validation before a causal variant may be identified. To assist with this screening process, the field of bioinformatics has developed numerous algorithms to predict the functional consequences of genetic variants. Algorithms like SIFT and PolyPhen-2 are firmly established in the field and are cited frequently. Other tools, like MutationAssessor and FATHMM are newer and perhaps not known as well.
This presentation will review several of the functional prediction tools that are currently available to help researchers determine the functional consequences of genetic alterations. The biological principals underlying functional predictions will be discussed together with an overview of the methodology used by each of the predictive algorithms. Finally, we will discuss how these predictions can be accessed and used within the Golden Helix SNP & Variation Suite (SVS) software.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
3. Golden Helix – Who We Are
Golden Helix is a global bioinformatics
company founded in 1998.
We are cited in over 900 peer-reviewed publications
4. Our Customers
Over 200 organizations world wide, and thousands of users, trust our software.
5. Golden Helix – Who We Are
When you choose a Golden Helix solution, you get more than just software
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6. Use the Questions pane in
your GoToWebinar window
Questions during
the presentation
8. Clinical Gene Panel Tests
Sample Prep
• Extract DNA
• Ensure size and
quality
Library Prep
• Multiplex
• Bind adapters
• QC
NGS
Sequencing
• Load and monitor
flow cell, chips
Bioinformatics
• De-Multiplex
• Alignments
• Call Variants
• Annotate, Filter,
Interpret, Report
QC variants and target regions
Annotations current & accurate
Visualize NGS alignment, context
Capture variant assesements, results
Export captured and computed data
Annotate, Filter, Interpret, Report
Human hands-on-time most variable
Lab tech and MD time highly valued
Some analytics can be automated
Interpretation platform optimizes for:
Efficient interpretation
Integrated with lab workflow
Economics
9. What is VarSeq?
VarSeq
Simple
Flexible
Scalable
Variant annotation, filtering
and interpretation
Repeatable workflows
Rich visualizations with
GenomeBrowse built-in
Powerful GUI and
command-line interfaces
10. VarSeq Clinical Suite
Gene panel testing
Whole exome and whole
genome analysis
Cancer diagnostics
Repeatable workflows
Coverage statistics
Multiple sample support
Variant assesement
database
VarSeq
Tertiary analysis to report
in one click
Focused and actionable
data
Modeled on ACMG
guidelines
Hereditary and cancer
templates
OMIM included
VSReports
Command line runner
Integrate with your current
bioinformatics pipeline
Create repeatable clinical
workflows for CLIA and
CAP certified analysis
Supports high throughput
scenarios
VSPipeline
Gene panel testing
Whole exome and whole
genome analysis
Cancer diagnostics
Repeatable workflows
Coverage statistics
Multiple sample support
Variant assesement
database
VarSeq
Tertiary analysis to report
in one click
Focused and actionable
data
Modeled on ACMG
guidelines
Hereditary and cancer
templates
OMIM included
VSReports
Command line runner
Integrate with your current
bioinformatics pipeline
Create repeatable clinical
workflows for CLIA and
CAP certified analysis
Supports high throughput
scenarios
VSPipeline
14. Setting up a Clinical Test with VarSeq
New Workflow
• Project Templates
• Representable Sample
Tune QC to
Assay
• Use Provided VCF Fields
• Tune Threshold
Annotations &
Filters
• Add from Public Catalog
• Curate Internal/Licensed
• Add and Tune Filters
Save Project
Template
• Captures all Settings
• Document and Version
Run Workflow
& Interpret
• Variant Interpretation
• Export Tables
• Fill in Reports
15. Data Curation of Annotation Sources
- 1kG Phase3 Variant
Frequencies
- ClinVar, NCBI
- ClinVitae, Invitae
- COSMIC
- dbNSFP Functional
Predictions
- dbSNP
- ExAC
- RefSeq Genes,
NCBI
- Supercentenarian
17 Variant
Frequencies
Your workflows lock down specific
versions
VarSeq is backed by an extensive list of
curated data sources
OMIM – Variant, Gene and Phenotype
- Bundled with Clinical Reports
- Updated monthly
- Rich integration of hyperlinks, references
16. Workflows: What is it Capturing and How?
Save as Template
- Import Settings
- Annotations and Algorithms
- Filters (can be locked)
- View choices (Reports, Browser etc)
Create New Projects
- Shipped “starter” templates
- Your custom template
Automated and Logged
- Log contains what, when, whom
- Prompts to downloaded missing sources
17. VSReports
Customize a “Report Template”
- ACMG Standard Germline Report
- Configurable Global Settings
- Logo
- Lab Information
- Test Description / Disclaimers
Customizable Sample Inputs
- Patient Information
- Test Results
Select Variants to Include
- Per-variant classification
- Interpretation prefilled from project data
Customizable
20. Define a Workflow that is Repeated for “Batches” of Samples
• Steps in RED are done once
when designing a new
workflow to be tuned to the
upstream pipeline and test
thresholds
• Steps in BLUE are done for
each sample or set of
samples that should repeat
the workflow
• Steps in BLUE can be
automated with VSPIPELINE
START DESIGN
PROJECT
DEFINE
WORKFLOW
SAVE PROJECT
TEMPLATE
NEW PROJECT
W/ TEMPLATE
FINISH
INTERPRET
EACH SAMPLE
RUN EXPORTS
Batch Analysis Workflow
21. VSPipeline: High Throughput, Automated
Produce Automated “Deliverables”
- Filtered and annotated variant lists
- Exported to Excel, VCF, Text
- VarSeq Projects (openable by VarSEq,
VarSeq Viewer)
Deploy a Project Template
- Support validation (like CAP/CLIA)
- All steps logged
Integrated
- Run as part of pipeline that produces
BAM/VCF files.
Works with VSReports!
22. FREE Reader of VarSeq Projects
VarSeq projects are a perfect
preservation of an analysis,
and can be opened at any
time with the FREE VarSeq
Viewer.
VarSeq Viewer is VarSeq
without an active subscription
license. It can be downloaded
by anyone at anytime.
VIEW FILTERED
View tables
Investigate results
EXPORT
Excel Rich Reports
Text and VCF
SHARE
Relocatable Projects
Efficient Storage
Anybody can Open
VISUALIZE
GenomeBrowse
BAM and VCF
Save Screenshots
Available Now: VarSeq Viewer
23. Questions or
more info:
Email
info@goldenhelix.com
Request an evaluation of
the software at
www.goldenhelix.com