VSWarehouse; a scalable, rapid genomic repository solution

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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

Healthcare

VSWarehouse;
a scalable, rapid genomic repository solution
Darby Kammeraad
Field Application Scientist Manager
20 Most Promising Biotech
Technology Providers
Top 10 Analytics
Solution Providers
Hype Cycle for Life sciences

NIH Grant Funding Acknowledgments
• Research reported in this publication was supported by the National Institute Of General Medical
Sciences of the National Institutes of Health under:
• Award Number R43GM128485-01
• Award Number R43GM128485-02
• Award Number 2R44 GM125432-01
• Award Number 2R44 GM125432-02
• Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005
• PI is Dr. Andreas Scherer, CEO Golden Helix.
• The content is solely the responsibility of the authors and does not necessarily represent the official
views of the National Institutes of Health.

Who Are We?
Golden Helix is a global bioinformatics company founded in 1998
Filtering and Annotation
ACMG Guidelines
Clinical Reports
CNV Analysis
Pipeline: Run Workflows
Variant Warehouse
Centralized Annotations
Hosted Reports
Sharing and Integration
CNV Analysis
GWAS | Genomic Prediction
Large-N Population Studies
RNA-Seq
Large-N CNV-Analysis

Cited in 1,000s of Peer-Reviewed Publications

SIMPLE, SUBSCRIPTION-
BASED BUSINESS MODEL
o Yearly fee
o Unlimited training & support
SOFTWARE IS VETTED
o 20,000+ users at 400+ organizations
o Quality & feedback
DEEPLY ENGRAINED IN
SCIENTIFIC COMMUNITY
o Give back to the community
o Contribute content and support
INNOVATIVE SOFTWARE SOLUTIONS
o Cited in 1,000s of publications
When you choose Golden Helix,
you receive more than just the software

VarSeq Suite
Simple Flexible Scalable
Variant annotation
filtering, and interpretation
Powerful GUI with
rich visualizations
Repeatable
workflows

• Archive full VCFs for Sample Cohort
o Optimized repository infrastructure for rapid queried through millions of
variants
• Centralized Genomic Data Hosting
o Integrated with other systems
• Query Variant Warehouse
o Have I seen this variant in my cohort?
o Has the classification changed with new evidence in ClinVar?
o How do I ensure consistency of CNV/variant interpretations across all
users?
VSWarehouse - Variant Warehouse Server

• From VarSeq to VSWarehouse
 Upload full cohort data
 Upload variant classification/interpretations
 Upload clinical reports
• From VSWarehouse to VarSeq
 Annotate with cohort data
o Variant frequencies
 Annotate with classified variants
 Access congruent Assessment Catalogs & Reports
• VSWarehouse Browser
 Query all genomic data
o Reports, catalogs, projects
 Evidence updates with ClinVar
 Manage access permissions
Integration with VarSeq

VSWarehouse – Centralized Collaboration
Project A
Project B
VSWarehouse Server
Group A Group B Collaborators

• Part I – Exploring VSWarehouse Browser
o General variant search
o Filtering/query
o Classification changes in ClinVar
• Part II – VarSeq & VSWarehouse
o Filtering out common variants
Example Project

Scalable Variant Warehouse for VarSeq
Project Demonstration >

What's hot

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.

Automating NGS Gene Panel Analysis Workflows with Golden Helix

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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.

Building Secure Analysis and Storage Systems with Golden Helix

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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!

Golden Helix's End-to-End Solution for Clinical Labs

Golden Helix

Annotation sources are constantly evolving, sometimes quite literally overnight. This is especially true in the case of cancer databases. These ever-evolving annotation sources, coupled with increasing research publications, make it difficult to do variant analysis with up-to-date scientific knowledge. With the resources available to an individual clinician or single lab, this may even prove impossible. Fortunately, VSClinical provides access to the most current clinical annotation sources - automating scoring and interpreting variants according to the most recent ACMP and AMPO guidelines. This includes many fast-changing sources such as ClinVar and COSMIC, as well as expert-curated reviews of literature and the latest drug-labeling from regulatory bodies. In this webcast, we demonstrate the automation of a cancer workflow with enhanced cancer annotations for somatic and germline cancer variants: - Golden Helix’s own CancerKB database has been updated to include new interpretations for genes and biomarkers with AMP Tier Level I evidence for drug sensitivity, resistance, diagnostic, and prognostic information. - We feature a new Golden Helix curated annotation source that automates the scoring of TP53 variants with the special rule specifications by ClinGen’s TP53 Expert Panel. - The ClinGen Expert Curated Interpretation of Variants has always been available as an annotation source for VarSeq projects, but now the expert comments and interpretations can automatically be pulled into VSClinical and used for clinical reports. This webcast walks through a hematological-focused cancer workflow that shows off the enhanced cancer annotations and CancerKB updates!

Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB Updates

Golden 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

Using Golden Helix CancerKB to Accelerate NGS Cancer Testing

Golden Helix

When performing variant analysis on whole exome or large gene panels, clinicians must sort through thousands of variants to determine which variants are most likely to be associated with the patient’s phenotypes. To assist with this process, we have implemented the PhoRank algorithm, which incorporates phenotypic associations to highlight the most relevant genes with potentially damaging variants. PhoRank 1.0 supports researchers leveraging all possible gene-disease associations by traversing multiple gene and pathway ontologies. Recent papers have demonstrated new techniques that have improved ranking performance in a clinical context. We have incorporated these new strategies into PhoRank 2.0: providing better ranking and improved computational performance for most clinically diagnostic and testing scenarios. Join us in this webinar as we cover: Utility of gene ranking in genetic testing Scenarios that warrant the use of PhoRank 2.0 New ranking strategies provided by recent papers Benchmarks of PhoRank 2.0 on published datasets Golden Helix provides a comprehensive solution for NGS testing labs to perform best practice guidelines such as ACMG and AMP. Our gene ranking methods provide a vital role in scaling tests to large gene panels and exomes. Please join us as we review the testing workflow and how this significant update to our gene ranking algorithm fits into the testing workflow.

PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq

Golden Helix

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

Efficient Application of NGS Family-Based Analysis

Golden Helix

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.

Splice Site Algorithms for Clinical Genomics

Golden Helix

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.

Advanced VSClinical Reports with Scripting and Custom Integrations

Golden Helix

Evaluating somatic variants according to the cancer AMP guidelines can be an extensive process. In addition to the standard collection of all available, clinical evidence for any biomarkers, there is a need to define treatment options following final classification. Even the most adept clinicians familiar to the guidelines suffer from this arduous process and thus need a standardized approach for classifying, interpreting and reporting variants according to the AMP guidelines. VSClinical’s new AMP workflow alleviates these complexities by providing an automated workflow that captures and reports on all critical data present. With the VSClinical AMP workflow, users can also customize clinical reports to reflect your lab’s preferences and branding. This webcast will provide a simple AMP guideline-based demonstration from a user perspective with multiple examples of simple report customizations from the VSClinical interpretation hub. What you will learn in this webcast: How VSClinical integrates the tier system to evaluate somatic mutations according to the AMP guidelines, with a focus on SNPs, InDels, CNVs and fusions Automating the AMP guidelines using Golden Helix CancerKB and lab-specific knowledge databases to streamline variant classifications Multiple report examples to demonstrate simple Word-based report customization capability Overall, VSClinical enables labs to test for both germline and somatic variants according to the ACMG and AMP guidelines in an automated fashion and allows users to obtain consistent and accurate results.

AMP-Based Variant Classification with VSClinical

Golden Helix

When interpreting a variant using the AMP/ASCO guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials, FDA approved therapies and peer-reviewed studies. Unfortunately, strong evidence linking specific genetic biomarkers to FDA-approved therapies only exists for a small number of cancers. Thus, most variants require an exploration of clinical practice guidelines, peer-reviewed literature, and large-scale cancer mutation databases to effectively assess the clinical significance of a given mutation. This webcast explores this new incorporation of Drugs & Trials Annotations in VSClinical's AMP Workflow covering: Identification of relevant clinical evidence for drug sensitivity and resistance based on patient biomarkers and tumor type Review of clinical trial information including inclusion criteria, trial status, and contact information Management of citations associated with relevant, targeted therapies Evaluation of a biomarkers clinical evidence tier based on available evidence for drug sensitivity and resistance

Introducing Drugs & Trials for Cancer Diagnostics

Golden Helix

CNV Analysis in VarSeq

Golden Helix Inc

Advanced Report Customization via VSClinical

Golden Helix

Clinical Reporting Made Easy

Golden Helix Inc

As exome sequencing continues to gain momentum as a comprehensive and affordable genetic test, many labs are considering the transition from their various targeted gene panels to a single comprehensive exome test. Along with the various challenges in small-variant analysis and interpretation of exomes, CNVs also require exome-specific considerations and strategies. In this webcast, we will review new capabilities and updated algorithms in the latest VarSeq release that will assist in any clinical exome sequencing workflow. Please join us in this webcast, as we review: A new VS-CNV best-practice workflow with specialized features for calling CNVs on exomes and large panels with more precision, enhanced quality flags and additional outputs. Enhanced analysis of variants found in exome sequencing, including non-coding clinically relevant RNA variants and mitochondrial variants Additional CNV analysis capabilities such as CNV export and import as VCFs The identification and interpretation of easily missed variants, such as those introducing novel splice-sites using the ACMG auto-classification and interpretation workflow Strategies for incorporating disease-specific virtual gene panel lists into the filtering, quality and reporting capabilities of VSClinical Exome sequence analysis is complex, and the process to define and validate a clinical exome test can be daunting. The VarSeq clinical suite has the flexibility and best practice workflows built-in to define and implement a repeatable and comprehensive workflow for CNVs detection and analysis by exome sequencing. We hope you can join this webinar to learn how to go from FASTQ to clinical reports for exome-based clinical tests.

Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...

Golden 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.

Performing a Trio Analysis in VSClinical

Golden Helix

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 VSClinical ACMG Guidelines & a Tour of Cancer Annotation Sources

Delaina Hawkins

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.

Large Scale PCA Analysis in SVS

Golden Helix

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.

Using VarSeq to Improve Variant Analysis Research Workflows

Golden Helix Inc

What's hot (19)

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Using Golden Helix CancerKB to Accelerate NGS Cancer Testing

PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq

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AMP-Based Variant Classification with VSClinical

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CNV Analysis in VarSeq

Advanced Report Customization via VSClinical

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Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...

Performing a Trio Analysis in VSClinical

Updates to VSClinical ACMG Guidelines & a Tour of Cancer Annotation Sources

Large Scale PCA Analysis in SVS

Using VarSeq to Improve Variant Analysis Research Workflows

Similar to VSWarehouse; a scalable, rapid genomic repository solution

Over the years, VarSeq has evolved into a powerfully efficient next-gen sequencing variant analysis platform. Some of the recent advances Golden Helix has made to this software have been to implement the standard ACMG and AMP guidelines for variant classification and interpretation. The guidelines are composed of many criteria impacting any variant final classification. These criteria consider topics such as frequency of the variant among the population, functional predictions, hotspot pathogenic rich regions in the gene, as well as known clinical submissions from other labs. The reality with this guideline review is that variant evidence can changeover time. Among the long list of databases needed to automate this guideline process, many databases have massive updates or are frequently updated perhaps on a month-to-month basis. So, it follows that any classification can be altered once discoveries for these variants are made. A problem that arises is, how to manage changing classifications, retroactively review previous patient outcomes and updatevariant classifications accordingly. Fortunately, Golden Helix has solved this dilemma with the use of our VSWarehouse genomic repository. In this webcast, we are going to explore the value and application of VSWarehouse. Our example variants will showcase a situation where variants of uncertain significance ultimately reach a pathogenic classification based on updates to ClinVar. This change will be presented not only in VarSeq with listings of previous samples but also shown directly from the VSWarehouse browser in a ClinVar classification tracker. We will also look at an alternative situation where the classification may change to benign for some previously reported variants which would require follow-up with the patient. The importance of a tool like the ClinVar tracker in VSWarehouse cannot be understated as it is a simple way to comprehensively review the backlog of changing variant classifications when users must update their locked down validated NGS pipeline. Please join us in the upcoming webcast to explore how these features in VarSeq and VSWarehouse work to allow users thorough accountability in updating historical patient results with new variant evidence

VSWarehouse: Tracking Changing Variant Evidence and Classifications

Golden Helix

Evaluating variants according to the ACMG guidelines can be an extensive process as it requires an in-depth understanding of all available criteria for any variant. Even the most adept clinicians familiar to the guidelines suffer from this tedious manual process and from the challenge of teaching these fundamentals to new technicians. VSClinical is an automated solution to the complex ACMG guidelines process. In this webcast, we will present how VSClinical follows the true-to-form ACMG classification rules. Additionally, users will discover the value of automating the ACMG guidelines to make variant classification consistent and simplify the interpretation process for those less familiar with ACMG criteria.

ACMG-Based Variant Classification with VSClinical

Golden Helix

Golden Helix is a single testing paradigm that allows users to start with next-generation sequencing data and finish with a clinical report. Our solutions are comprehensive as they are all performed in one software suite, which can save time and money as they prevent the need to outsource to different companies. Furthermore, our software is fully transparent in that you have full control over the steps performed in your analysis. Golden Helix is also on the forefront in the clinical workspace as we have implemented the ACMG and AMP guidelines to evaluate single nucleotide variants, insertions and deletions, as well as structural variants. Beyond these functionalities, Golden Helix provides the ability to perform family-based analysis. Our ACMG and Exome trio templates give users a starting point to understand the different inheritance models ranging from transmitted to de novo variants, but we also have features that can provide additional evidence for both traditional and nontraditional family-based workflows. Specifically, we have algorithms that can be implemented to look at extended pedigree information and sample relatedness as well as options for examining whether a given variant such as a CNV segregates among similarly affected family members. In this webcast, we would like to demonstrate these features and show some solutions for the analysis of different family structures. As an overview, this webcast will cover: - Implementing filter logics for different family structures - Algorithms that can be used for establishing clinical significance in family-based workflows - Visualization capabilities for further understanding of inheritance models - Confirming and evaluating transmitted CNVs

Family-Based Workflows in VarSeq and VSClinical

Golden 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.

Evaluating Cloud vs On-Premises for NGS Clinical Workflows

Golden Helix

Mendelian disorders can be caused by various classes of genetic mutations, from small variants to CNVs and even Structural Variants. With the introduction of VarSeq 2.4.0, we are excited to unveil the latest advancements in VSClinical ACMG, focusing on the integration of Structural Variants and the enhanced automation capabilities that streamline your analysis process. Join us in this webcast as we dive into the following topics: Integration of Structural Variants: Learn how VarSeq 2.4.0 enables you to import and incorporate Structural Variants into your VSClinical ACMG evaluations and reports, providing a comprehensive understanding of the genetic landscape. Advanced Automation in the ACMG Interface: Discover how evaluation scripts can be employed to automate the VSClinical ACMG interface, allowing you to perform custom actions or eliminate manual steps, thus increasing efficiency and reducing the risk of errors. End-to-End Automation: Explore how VSPipeline can fully automate your analysis process, from raw VCF to report, ensuring a streamlined and consistent workflow that saves time and resources. Harnessing the Power of VSClinical: Gain insights into how VarSeq 2.4.0 empowers you to tackle complex genomic data, enabling faster and more accurate identification of Mendelian disorders and facilitating personalized patient care. With the advanced capabilities of VarSeq 2.4.0 and VSClinical, you can now unlock a new level of precision and efficiency in diagnosing Mendelian disorders. This webcast will showcase the latest innovations in variant interpretation and automation, exemplifying why the VarSeq Clinical Suite is the premier NGS analysis platform for germline and cancer testing.

VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG

Golden Helix

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.

Getting Started with VSWarehouse

Golden Helix

The ability to use predefined sets of genes to isolate clinically relevant variants is an important aspect of clinical variant analysis. Golden Helix’s VarSeq product houses the tools, namely our Gene Panel Manager and Match Genes set of algorithms, that enable users to create and manage reusable gene lists within projects, incorporate the ACMG Secondary Findings v3.0 gene list for the reporting of incidental findings, make use of well validated publicly available gene panels with published evidence of disease associations and create gene panels based on specific disorders or phenotypes of interest. These capabilities were covered in a webcast “Creating and Managing Reusable Gene Lists with VSClinical” by Dr. Nathan Fortier our Director of Research. In the upcoming webcast, we will dive deeper into these capabilities, implementing our gene panel tools from the user’s perspective by focusing on two clinical use cases where custom virtual gene panels are particularly useful. For the standard use case, users typically incorporate targeted gene panel-based data to hone in on any number of variants that fall within the scope of their targeted genes list. More recently, we have observed from the field application perspective, a trend among Golden Helix customers towards importing WES and WGS data followed by creating unique per sample gene panels. Therefore, the purpose of this webcast will be to showcase how simple it can be to construct and manage both styles of virtual gene panels within VarSeq in ways that will best suit the specific needs of your lab. We will share with you several clever shortcuts for users to implement filters on gene panels, to design and manage gene panels and calculate the coverage over these regions. We will also delve into the details of incorporating gene panel data into variant evaluation in VSClinical and bringing the relevant information into a final clinical report. Viewers tuning in to this webcast will be exposed to all the tools available in VarSeq for creating and managing their potential gene panel workflows.

Integrating Custom Gene Panels for Variant Innovations

Golden Helix

Earlier this year, we released VarSeq 2.3.0 which brought massive updates to our VSClinical AMP interface, such as enhanced capabilities for automation and analysis of structural variants in the cancer context. Naturally, we wanted to follow that up shortly with similar advancements to our VSClinical ACMG interface, and also make our customers doing germline variant analysis happy. Our latest software release, VarSeq 2.4.0, was therefore focused on the advancements in VSClinical ACMG, namely support for importing and clinically evaluating structural variants, long read sequencing, advanced automation with evaluation scripts in VSClinical ACMG and end-to-end automation of ACMG workflows with VSPipeline. These new and improved features were discussed in a great webcast by our VP of Product and Engineering, Gabe Rudy, last month. This upcoming webcast by our FAS team will be a user’s perspective on the new features in VarSeq 2.4.0 and VSClinical ACMG and how our tools can precisely and efficiently enable the full spectrum NGS analysis for Mendelian disorders.

VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective

Golden Helix

VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective

Golden Helix

A transition period regarding in vitro medical device (IVD) regulation in the European Union (EU) is upon us. The former IVDD regulations are phasing out and IVDR 2017/746 has already taken its place as the acting regulation for IVD manufacturers but also lab developed tests (LDTs) and health institutions. In our upcoming webcast we will talk about the roles and significance of IVDR and ISO 13485 certification for clinical labs and for Golden Helix as a medical device manufacturer. Join us as we will introduce VarSeq 2.6.1 complete with Dx Mode, which offers the use of VarSeq as CE marked medical device. Even more we will also present strategies to facilitate the transition of Golden Helix customers to operate in accordance with IVDR.

Introducing VarSeq Dx as a Medical Device in the European Union

Golden Helix

NGS tests in the clinic cover more use cases than ever and are increasingly complex to implement. This leads to an increase in time to validate and bring tests to production, impacting a lab’s ability to be economically viable and serve the needs of patients. Core to the complexity is the expansion of tests to include multiple types of biomarkers and variants, including CNVs, gene fusions, and genomic signatures. The bioinformatics demands of these pipelines require powerful tools with built-in capabilities to handle the diverse needs of modern NGS tests and to integrate and automate the disparate steps leading to clinical insight. Join us in this webinar as we explore the VarSeq suites’ capabilities as a fast, modular, and highly configurable solution for variant analysis and interpretation. We will cover: The bioinformatic diversity of comprehensive genetic tests with NGS Automation of FASTQ to clinical reports without losing control over the results of a test Leverage built-in and custom automation capabilities in the VSClinical cancer guideline workflow to reduce work and improve accuracy Reporting the relevant diagnostic and therapeutic findings for a patient based on the raw genomic data of modern NGS tests requires both human experience and advanced analysis software. We hope you can join us as we unpack how automation is a critical part of implementing NGS tests and furthering the application of precision medicine.

Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution

Golden Helix

With our recent launch of VarSeq 2.5.0, our ability to expedite somatic analysis for NGS labs is more accessible than ever before. Our recent webcasts have shown our range of updates, including our new oncogenicity classifier and carrier status workflows: Identifying Oncogenic Variants in VarSeq VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis In this user perspective webcast, we will highlight how the combination of our new oncogenicity classifier and the updates to our CancerKB database streamline the interpretation of oncogenic variants. In addition, as NGS labs progress from gene panels to WES analysis for ideal genomic signature generation, we will demonstrate how a VarSeq somatic workflow can scale with these increased scopes of data analysis with ease. Our user perspective webcast will cover: Application of virtual panels to WES tumor/normal workflows. Use of the oncogenicity classifier to streamline filter chains. Updates to our CancerKB database to include the CancerKB gene track. Including parallel germline secondary findings for the whole NGS workflow.

VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective

Golden Helix

Next Generation Sequencing allows for the detection of a wide variety of genomic alterations. This includes small mutations, copy number variants and complex rearrangements. However, it can be difficult to annotate, filter, and interpret these alterations. As part of our VarSeq 2.3.0 release, we have greatly simplified this process by allowing you to import, annotate, and filter mutations across all spectrums of genomic variation. This supports concurrent importation of small variants and CNVs as well as complex rearrangements. This release also includes strong support for structural variant annotation, filtering, and interpretation, including structural variant effect prediction. After filtering is complete, any clinically relevant structural variants can be interpreted with the VSClinical AMP Guidelines workflow and included in the final clinical report. Come join us for this webcast to discuss VarSeq’s enhanced import and annotation capabilities, including: Concurrent importation of variants CNVs and complex rearrangements Improved multi-threaded import which dramatically speeds up the importation of large VCFs Annotation of structural variants and prediction of effect Interpretation of structural variants in the VSClinical AMP Guidelines workflow Support for visualization and use of CRAM files as input for computing coverage statistics

VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation

Golden Helix

The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you to utilize your existing NGS data and perform the analysis all in one suite. Coupled with this innovative feature is the ability to annotate CNV events against a variety of databases, and by incorporating our VSClinical AMP workflow, we can now assess CNVs as potential biomarkers. Most importantly, Golden Helix CancerKB is an AMP workflow feature that provides expert-curated biomarker interpretations, including those for common somatic CNVs, that will streamline the analysis time and report generation. In this demonstration we will cover: Setting up the VS-CNV caller using BAM files from whole exome data Filtering down to high quality, high confidence CNV events Annotating CNVs using publicly curated catalogs and databases Adding clinically relevant CNVs to the VSClinical AMP workflow Utilizing Golden Helix CancerKB to obtain expert-curated interpretations Showing updated features and polishes to the software Together, VarSeq incorporates the ability to accurately call and annotate CNVs and evaluate germline and somatic mutations according to the ACMG and AMP guidelines, respectively. This webcast demonstration will provide insight into these best practice workflows and will hopefully show you how you can implement this top-quality software into your pipeline solution.

Clinical Validation of Copy Number Variants Using the AMP Guidelines

Golden Helix

Comprehensive genomic testing via next generation sequencing (NGS) is being increasingly adapted as part of cancer care in conjunction with molecular and immunohistochemical tests. Comprehensive genomic profiling potentially expands the number of targeted therapies that are available to patients, improves patient diagnosis and prognosis, and increases the number of clinical trials that are relevant to patients. However, with these advancements come challenges such as gaps in expertise resulting in inadequate efforts to interpret genomic data accurately and efficiently, poorly coordinated efforts to implement precision care, patients being diagnosed and treated despite inadequate access to relevant information and subsequent lack of patient exposure to all available treatment options. Golden Helix CancerKB v2.0 provides a means of closing the gap, whether you're a beginner who is trying to capture the vast amount of knowledge in the cancer field or an expert who has high sample volume AND needs to keep up with the ever-evolving knowledge of Tier II and III variants. In this webcast, we will discuss and apply Golden Helix CancerKB in the context of cancer precision medicine. Golden Helix CancerKB is systematically curated and reviewed by experts in the field and contains information about cancer genes, biomarkers, and treatments generated from several trusted cancer resources. With VarSeq 2.3.0’s added support for comprehensive cancer genomic profiling tests, Golden Helix CancerKB has expanded to include interpretations for genomic signatures, combination biomarkers, and more investigational (tier II) biomarkers, among several other additions that will be discussed. With the Golden Helix CancerKB database, users will experience a streamlined automatic matching of biomarkers to available drugs and trials which ultimately saves users massive amounts of time and effort while reducing the possibility for errors.

Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...

Golden Helix

Clinical variant analysis involves many steps and potentially requires the expertise and input from multiple individuals. For many, this process can be rather complex as it entails moving the data from user to user and possibly multiple platforms or internal bioinformatic pipelines. In general, this workflow can be broken down into three stages: - Quality control (QC) and processing of the data. This step involves importing the data into a tertiary analysis platform and validating that the variants and samples are high quality. - Variant evaluation using different genomic databases and annotation sources, which is then incorporated into a draft report. - Assessment and assurance that the previous steps were performed correctly and a sign-off on the report. Golden Helix offers VSClinical, a complete clinical workflow solution that simplifies and streamlines the clinical analysis process outlined above. VSClinical is a single testing paradigm that consolidates and automates the tertiary analysis workflow. With this software, users can perform variant and sample QC, create a variant evaluation using a plethora of public and licensed annotation sources and evaluate variants with the automated ACMG and AMP guidelines for SNVs, Indels, and CNVs. All this information can then be used to create a clinical report with our new word-based report templates. In this webcast, we plan to demonstrate the full clinical analysis workflow within VSClinical, focusing on the topics below: - How easy it is to perform the different stages of a tertiary analysis in VarSeq and VSClinical - The fluidity in transferring data between different users - Evaluating germline and somatic variants according to the ACMG and AMP guidelines - Creating and signing off on a clinical report with the new word-based templates

VSClinical: a complete clinical workflow solution

Golden Helix

Inter-individual variability in drug response poses a significant challenge for clinicians, with much of this variability resulting from inherited genetic differences. While the field of pharmacogenomics (PGx) can provide powerful insights into how genomic factors affect drug response, the implementation of PGx testing in the clinic is hampered by the difficulty of translating genetic test results into actionable recommendations. In this webcast, we will discuss VarSeq’s new PGx testing capabilities, including the ability to identify actionable pharmacogenomic diplotypes and generate clinical reports. In this webcast you will learn: -How to identify pharmacogenomic diplotypes and drug recommendations from NGS data. -How to incorporate externally called CNVs and SVs into your PGx annotations. -How to generate customizable PGx reports from these annotations.

Introducing VSPGx: Pharmacogenomics Testing in VarSeq

Golden Helix

In the rapidly evolving field of genomic analysis, staying current with the latest research, data sources, and test advancements is crucial. In this webinar, we review how VarSeq addresses the needs to stay on top of the latest with the release of VarSeq 2.6.0. This release features an exome-optimized workflow for LOH and CNV calling as well as the introduction of VSPGx to produce pharmacogenomic reports for gene panels as well as exomes and genomes. With the recent release of gnomAD v4, we have had many requests for the integration of this large update to the most population frequency source. With VarSeq 2.6.0, the latest version of gnomAD has been integrated into VSClinical and the updated tracks spans beyond variants to cover CNVs and gene scores to update all your workflows to the latest data. In this webcast, we will cover. Improved VS-CNV performance and updated exome analysis workflows. Pharmacogenomics in action: Utilizing VSPGx for exome and genome assessments. gnomAD v4 in practice: Updated automated and manual variant interpretation workflows. Join us for an insightful session on the latest VarSeq 2.6.0 features, bringing you the most up-to-date data and workflows for your genomic analysis.

VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis

Golden Helix

VarSeq is a tertiary analysis platform that allows users to filter and annotate NGS sequencing data to identify clinically relevant variants. Following this workflow, VSClinical can then be used to automate both germline and somatic variant analysis in accordance with the ACMG and AMP guidelines by using a variety of functional prediction models and clinical and reviewer-based annotations. Once variant or biomarker interpretations are completed, they can be rendered in a customizable clinical report and stored in an internal assessment catalog as an internal variant database repository. Together, implementation of VSClinical will promote increased lab throughput as well as accuracy and compliance with the ACMG and AMP guidelines, which in turn can save time and money. To show the capabilities of our software, this webcast will provide a demonstration of how to use VarSeq and VSClinical for the evaluation of both germline and somatic variants in accordance with the ACMG and AMP Guidelines. In this webcast, we will cover: - Filter logics for germline and somatic variants and selecting them into the VSClinical interface - Capabilities of functional prediction and splice site algorithms for edge case variants - The functionality of changing the clinically relevant transcript on variant interpretation - Rendering a clinical report with germline and somatic variants with the inclusion of clinical trials

Next-Generation Sequencing Analysis in VSClinical

Golden Helix

One major hurdle facing medicine is the need to quickly identify and assess the genetic components contributing to rare diseases. It has been estimated that nearly 350 million people suffer from rare diseases, 140 million of which are children, of whom ~30% do not live past their fifth birthday1,2. The specific issue to overcome is reducing morbidity by facilitating rapid diagnosis and treatment. Fortunately, the cost of whole genome sequencing has dropped below the $1000 mark, which not only makes the NGS approach more affordable but has become the status quo method of comprehensive diagnosis for these rare disorders. Currently, there are limited options in the market when it comes to quality software that can scale to this size of data and handle variant processing and evaluation in a timely fashion. Fortunately, Golden Helix has sought to set the market standard for top-quality NGS analysis with our bioinformatic software VarSeq. The focus of this webcast will be to explore example workflows tailored for rare disorders and elaborate on how best to expedite the NGS pipeline process with our command-line tool VSPipeline. During the webcast, we will address the following: Customizing clinically validated NGS workflows with VarSeq for both single sample and trios Demonstrating the automation of ACMG-based guideline review in the VSClinical variant interpretation hub and rendering of customized clinical reports Expediting the NGS workflow via Golden Helix command-line tool VSPipeline We look forward to you joining us for our presentation, where we can demonstrate the value of our products when building your next-gen workflows. Ultimately, we wish to diminish the intimidation of genome workflow design and leave our future customers feeling confident that there is capable software to suit their needs. Bick D, Jones M, Taylor SL, et al. Case for genome sequencing in infants and children with rare, undiagnosed or genetic disease. J Med Genet 2019; 56:783-791. Owen M, Lefebvre S, Hansen C, et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13: 4057. https://doi.org/10.1038/s41467-022-31446-6

Single Sample and Family Based Genome Analysis With VarSeq

Golden Helix

Similar to VSWarehouse; a scalable, rapid genomic repository solution (20)

VSWarehouse: Tracking Changing Variant Evidence and Classifications

ACMG-Based Variant Classification with VSClinical

Family-Based Workflows in VarSeq and VSClinical

Evaluating Cloud vs On-Premises for NGS Clinical Workflows

VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG

Getting Started with VSWarehouse

Integrating Custom Gene Panels for Variant Innovations

VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective

Introducing VarSeq Dx as a Medical Device in the European Union

Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution

VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective

VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation

Clinical Validation of Copy Number Variants Using the AMP Guidelines

Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...

VSClinical: a complete clinical workflow solution

Introducing VSPGx: Pharmacogenomics Testing in VarSeq

VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis

Next-Generation Sequencing Analysis in VSClinical

Single Sample and Family Based Genome Analysis With VarSeq

More from Golden Helix

Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analyses. However, standard commercial exome kits are limited to targeting exon coding regions, leaving significant gaps in coverage between genes which could hinder comprehensive CNV detection. Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Twist Exome 2.0 Plus Comprehensive Exome Spike-in capture panel with added "backbone" probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25kb, 50kb, and 100kb intervals. In this webcast, we discuss the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV in identifying known CNVs using the Coriell CNVPANEL01 reference set. This webcast reviews: -The sensitivity rate for the detection of known CNV events at all three probe densities. -The impact of best-practice quality metrics and filters on sensitivity. -How VarSeq’s CNV annotation capabilities can be leveraged to identify likely pathogenic CNVs. -The interpretation of clinically relevant CNVs using VSClinical.

Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...

Golden Helix

From gene panels to whole genome, from short to long-read sequencing, the VarSeq suite is the solution for NGS analysis and reporting in a modern clinical lab. VarSeq handles the spectrum of variant types (SNV, Indel, CNV, Fusions) and provides automated classification and reporting capabilities following the ACMG and AMP guidelines. With our new PacBio partnership, we are more adaptable than ever with creating a spectrum of custom workflows to suit our unique user needs. This webcast will review: -Data analysis scaling from Gene Panel to Genome analysis with VarSeq and VSWarehouse. -Analysis and annotation of SNVs, Indels, CNVs, and fusions. -A close look at a PacBio long-read trio analysis. Come join us for this showcase in modern VarSeq analysis capabilities.

From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...

Golden Helix

Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. The latest SVS release introduces a significant leap in capabilities, with a focus on advanced Polygenic Risk Score (PRS) calculations. PRS has become a fundamental tool in genomic research, enabling the identification of correlations between genotypic variants and phenotypes across large populations. This enhancement is particularly relevant for researchers working on large cohorts and meta-analysis. Please join us as we explore: -SVS Workflow Review: A review of the extensive capabilities of SVS to meaningful insights from large cohorts and association test result datasets -Computing Polygenic Risk Scores: An overview of the PRS capabilities in SVS, including Clumping and Thresholding and creation of multiple PRS models -Evaluating and Applying PRS: Evaluating PRS models in-sample and out-of-sample and applying PRS models to perform trait prediction -Future Implications: Brief exploration of how these advancements in SVS could influence future genomic research. This webcast will explore how SVS facilitates the creation of multiple PRS models from large-scale genomic data, such as those obtained from extensive cohort studies or comprehensive meta-analyses. Join us to discover how these latest updates in SVS are supporting large-scale genomic research.

Enhance Genomic Research with Polygenic Risk Score Calculations in SVS

Golden Helix

Over the past 50 years, partners with potential genetic risks have sought advanced genetic testing to guide family planning decisions. Carrier screening is a valuable tool in genetics and reproductive medicine that helps individuals and families make informed choices about family planning and reduce the risk of passing autosomal recessive or X-linked genetic disorders to their children. Several carrier screening panels are available for Next-Generation Sequencing platforms, ranging from those targeting prevalent disorders to expanded ones covering various inherited conditions. Since NGS offers an affordable, high-throughput solution, carrier screening has become a common practice in healthcare systems. We are excited to announce that VarSeq and VSClinical now support a multi-sample carrier screening workflow. VarSeq 2.5.0 unlocks the ability to: -Filter variants between samples and identify genes in which a variant from each partner sample is present. -Apply the ACMG Carrier Screening gene panel or generate customized carrier screening panels to include in your analysis. -Evaluate partnered samples side-by-side in a single VSClinical evaluation. -Generate a combined sample clinical report that includes reproductive risk calculations for the most prevalent autosomal recessive and X-linked diseases.

VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis

Golden Helix

The interpretation of somatic variants can be a challenging process. While AMP Guidelines provide detailed rules for accessing the clinical evidence associated with a specific variation, they do not specify criteria for determining if a variant is likely to be a driver mutation, which generates functional changes that enhance tumor cell proliferation. In this webcast, we will discuss a new VarSeq algorithm for estimating the oncogenicity of a variant. This will include a deep dive into our oncogenicity scoring system and a discussion of the various criteria used to distinguish driver mutations from benign variations and variants of uncertain significance. What you will learn in this webcast: -How to use the scoring algorithm to identify variants with evidence of oncogenicity -Which criteria are used to assess a variant's oncogenicity -How to evaluate the oncogenicity of a variant in VSClinical

Identifying Oncogenic Variants in VarSeq

Golden 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.

Best Practices for Validating a Next-Gen Sequencing Workflow

Golden Helix

2023 Innovation Awards Winner, Dr. Muthukumaran

Golden Helix

There is a strong motivation for labs to bring most, if not all, of their next-gen sequencing pipeline in-house. This is especially relevant for clinical applications where there is a need to validate any routine diagnostics when seeking to provide genetic results to patients. The entirety of the NGS pipeline is highly automatable and comprised of multiple stages but from the geneticist's point of view, the tertiary stage requires the lengthiest review. This stage is where the geneticist sifts through the massive collection of genetic variants to find and report on those most relevant to the patient or population. Unfortunately, the tertiary stage can be a fairly sophisticated process and there aren’t many tools on the market that handle it comprehensively and simply. Many of the tools that are available may have severe limitations on the scale of genomic data they can process or limitations on the types of NGS assays that can be designed. Moreover, their license model may be on an individual sample basis and present cost-benefit hurdles for the user, especially when sample load will inevitably increase. Fortunately, none of these assay or cost-based issues are relevant with Golden Helix products. The goal of this webcast is to expose our viewers to the versatility that GHI VarSeq provides when constructing your dream NGS assay. This demonstration will provide examples of germline and somatic workflows for both single and multi-sample analysis for a variety of different disorders. Please join us and learn more about the analytical possibilities you can achieve when using the VarSeq software.

The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq

Golden Helix

Our past webcast explored the current approaches for screening and diagnosis of genetic disorders in prenatal testing. While the methods available at the time were robust, they were severely limited, creating a need for a higher diagnostic yield and more efficient analysis for a wider range of genetic tests. The solution proposed was to improve and simplify prenatal screening and diagnosis with whole exome sequencing (WES). During that webcast, we highlighted the advantages of WES over traditional methods such as karyotyping and chromosomal microarray, including improved accuracy, granularity, and cost-effectiveness. We also emphasized the potential of WES to expand diagnosis for many other adverse maternal-fetal complications beyond the large aneuploidy events previously covered. However, there was still an intimidation factor when it came to the massive data output from the exome. Fortunately, Golden Helix provided the necessary tools to build and standardize these genetic assays, simplifying the analytical process while leveraging increased diagnostic output. We explored our VarSeq software to demonstrate some example workflows of cases positive for Trisomy 21, an exon loss in DMD related to Duchenne Muscular Dystrophy, and detection of a single base change resulting in a LOF variant in RUNX1 relevant to hereditary leukemia. Our goal was to expose our viewers to the methods of conquering this vast NGS-based data and play a role in dissolving any feeling of intimidation. Overall, exome sequencing has the potential to vastly improve diagnostic outcomes and widen discoveries in the research related to prenatal testing, and Golden Helix products are designed to facilitate this process.

Prenatal Genetic Screening with VarSeq

Golden Helix

VarSeq 2.3.0 facilitates the evaluation of a multitude of somatic genomic variations with a more refined user interface to streamline variant evaluation. Our recent webcasts have shown the full range of these newly developed upgrades: VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP Now, we are showing it all in action from the user’s perspective. This webcast will provide a comprehensive demonstration of performing somatic variation analysis and reporting. We will review how to use workflow automation to expedite the NGS project creation process and report rendering. We will also demonstrate the streamlined capture of knowledge during variant evaluation by leveraging our clinical expert-curated interpretations with the Golden Helix Cancer Knowledge Base (CancerKB). We hope you will join us to see VarSeq 2.3.0 from a user’s perspective, covering: -Somatic variant workflows: necessary algorithms and filtering strategies -Import of all relevant biomarker and genomic signatures data from TSO-500 -Review content and value of clinically curated interpretations and treatments with CancerKB -Interpretation of structural variants in the VSClinical AMP Guidelines workflow -Workflow automation with VSPipeline

A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0

Golden Helix

Precision medicine for cancer is rapidly accelerating because of the development and approval of targeted molecular therapies. These therapies require new genomic biomarkers as an indication for use, and require evaluating additional mutation types that are available in comprehensive genomic profiling assays as well as the small variants detected by Next-Generation Sequencing gene panels. We are excited to announce VarSeq 2.3.0 which will update the VSClinical AMP workflow to meet the growing needs of labs conducting comprehensive genomic profiling (CGP) of tumors. This includes built-in support for the Illumina TruSight Oncology 500 (TSO-500) kit as well as similar kits from other vendors. The VSClinical AMP workflow has also gained native support for the bioinformatic outputs of CGP kits. Join us to learn about comprehensive genomic profiling in cancer, specifically: Evaluation and clinical reporting of genomic signatures such as Microsatellite (MSI), Tumor mutation burden (TMB), PD-L1, Homologous recombination deficiency (HRD) statuses, and more. Built-in TSO-500 import and expandable import capabilities for new genomic data types through the new advanced workflow scripting system. Golden Helix CancerKB updates with report-ready genomic-signature interpretations written for approved therapies as well as gene interpretations for all 500 genes of the TSO-500 panel. In addition, CancerKB scopes have been extended to reference multiple relevant biomarkers in a single interpretation, capture approved therapies at the tumor type level, and include interpretations for clinically relevant negative findings. Expanded clinical trial support to include international trials and the ability to search within proximity of European postal codes. VSClinical is accessing all active studies in AACT/ClinicalTrials.gov wherein users can search and select trials based on relevant drugs, biomarkers, and the geographic distance to the patient or testing site. VarSeq 2.3.0 will deliver powerful capabilities for genomic profiling in cancer, enabling a new level of personalized and effective care for your patients. We look forward to demonstrating these updates and Golden Helix’s continued innovation making the VarSeq Clinical Suite the NGS analysis platform of choice for germline and cancer testing.

VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP

Golden Helix

Somatic analysis is a complex and precise process that is constantly evolving. As the volume of available data and the accessibility of sequencing technology increase, so too does the value of a versatile, well-vetted, and efficient workflow solution. In this webcast, we will take a deep dive into the current state of our AMP interpretation software and explore various ways to optimize workflows. For anyone from grizzled VarSeq veterans to those seeing our software for the first time and labs of any size, we will provide a practical overview of our somatic analysis capabilities and how those capabilities scale with improving technology. Throughout this webcast we will be discussing the following: - Universal principles of somatic workflows, providing baseline recommendations - Specific tumor-normal and somatic-only use cases - VSClinical AMP interpretation hub and some variants of interest - Opportunities for automation and how to decrease time to report for increased throughput Join us as we show off the versatility and scalability of our AMP interpretation capabilities!

User perspective for somatic variant analysis in VSClinical AMP

Golden Helix

The automation of clinical NGS workflows provides a number of important benefits for labs. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In turn, these benefits create higher profitability from a P&L perspective. Golden Helix software is designed to meet these needs by automating the full analysis workflow from sequencer to clinical report on a fixed annual subscription model. We are looking forward to discussing the best practices of maximizing profitability in your NGS testing lab and how Golden Helix supports these efforts. Join us in this webinar as we cover how to develop repeatable cancer and germline interpretation workflows that scale from panels to whole exomes and genomes.

Maximizing Profitability in your NGS Testing Lab

Golden Helix

VarSeq has become renowned for the accuracy of its CNV Caller, and the ease with which VSClinical takes the user through CNV evaluation. Cited in many publications, this well-validated tool brings our customers the ability to run both variant and CNV interpretations in one program, on data ranging from Gene Panels to whole genomes. What is less well known about CNV analysis through VarSeq, is that our users are not only limited to CNVs called through our software. VarSeq CNV is able to import CNVs in several file formats (VCFs, text, or tsv) generated by a wide variety of secondary callers, allowing the user to analyze their externally derived data. In this webcast, we will take you through the basics of CNV analysis with both the VarSeq CNV caller and from several common external CNV callers. Join us in this webinar as we cover: Leveraging the Copy Number Probability and Segregation Algorithm to add power to a CNV Trio workflow. Importing externally called CNVs. Expediting the path to analysis with CNV specific templates. Utilizing the auto-recommendations to efficiently analyze the pathogenicity of several CNV calls and generate clinical reports.

Handling a Variety of CNV Caller Inputs with VarSeq

Golden Helix

As our users have come to know, VarSeq serves as a hub for variant annotation and the full interpretation/classification of germline (ACMG) and somatic (AMP) variants. Whether direct annotation or backend variant evidence is being presented to the user via VSClinical for the interpretation process, users greatly benefit from the hosted variant databases being available directly from VarSeq. Our team has automated much of the curation process and hosts the ongoing updates to these tracks so that users no longer suffer manual review of each database via the web or manual curation efforts. Useful databases include ClinVar and ClinGen for classification submissions, gnomAD exomes/genomes for filtering out common variants in the population, RefSeq for gene impact and sequence ontology assessment, and OMIM for phenotypic information. Obviously, there is a large collection of databases out there, and not all of them make it into our automated queue. However, GHI supports the utilization of custom databases in our software. This webcast will expose features of custom database curation/utilization in VarSeq to optimize your NGS workflows even further. During the presentation, we will discuss many different approaches with custom annotations, including: Interval Tracks: Bed files defining target regions for coverage calculations and CNV detection. Assessment catalogs: record keeping of variant classification/interpretations in VSClinical. Frequency catalogs: approaches to capture all variant allele frequencies at a project level and cohort level with VSWarehouse.

VarSeq Custom Database Curation Capabilities.pdf

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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.

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The Healthy Ageing and Prevention Index is an online tool created by ILC that ranks countries on six metrics including, life span, health span, work span, income, environmental performance, and happiness. The Index helps us understand how well countries have adapted to longevity and inform decision makers on what must be done to maximise the economic benefits that comes with living well for longer. Alongside the 77th World Health Assembly in Geneva on 28 May 2024, we launched the second version of our Index, allowing us to track progress and give new insights into what needs to be done to keep populations healthier for longer. The speakers included: Professor Orazio Schillaci, Minister of Health, Italy Dr Hans Groth, Chairman of the Board, World Demographic & Ageing Forum Professor Ilona Kickbusch, Founder and Chair, Global Health Centre, Geneva Graduate Institute and co-chair, World Health Summit Council Dr Natasha Azzopardi Muscat, Director, Country Health Policies and Systems Division, World Health Organisation EURO Dr Marta Lomazzi, Executive Manager, World Federation of Public Health Associations Dr Shyam Bishen, Head, Centre for Health and Healthcare and Member of the Executive Committee, World Economic Forum Dr Karin Tegmark Wisell, Director General, Public Health Agency of Sweden

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Pediatric nurses play a vital role in the health and well-being of children. Their responsibilities are wide-ranging, and their objectives can be categorized into several key areas: 1. Direct Patient Care: Objective: Provide comprehensive and compassionate care to infants, children, and adolescents in various healthcare settings (hospitals, clinics, etc.). This includes tasks like: Monitoring vital signs and physical condition. Administering medications and treatments. Performing procedures as directed by doctors. Assisting with daily living activities (bathing, feeding). Providing emotional support and pain management. 2. Health Promotion and Education: Objective: Promote healthy behaviors and educate children, families, and communities about preventive healthcare. This includes tasks like: Administering vaccinations. Providing education on nutrition, hygiene, and development. Offering breastfeeding and childbirth support. Counseling families on safety and injury prevention. 3. Collaboration and Advocacy: Objective: Collaborate effectively with doctors, social workers, therapists, and other healthcare professionals to ensure coordinated care for children. Objective: Advocate for the rights and best interests of their patients, especially when children cannot speak for themselves. This includes tasks like: Communicating effectively with healthcare teams. Identifying and addressing potential risks to child welfare. Educating families about their child's condition and treatment options. 4. Professional Development and Research: Objective: Stay up-to-date on the latest advancements in pediatric healthcare through continuing education and research. Objective: Contribute to improving the quality of care for children by participating in research initiatives. This includes tasks like: Attending workshops and conferences on pediatric nursing. Participating in clinical trials related to child health. Implementing evidence-based practices into their daily routines. By fulfilling these objectives, pediatric nurses play a crucial role in ensuring the optimal health and well-being of children throughout all stages of their development.

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Benefits of Salivary Testing with Dentulu Salivary Test Kit Salivary testing has revolutionized diagnostics, offering non-invasive and highly informative insights into oral and systemic health. The Dentulu saliva test kit exemplifies these advancements. Early Detection of Diseases Periodontal Disease: Saliva testing for periodontal disease detects pathogenic bacteria before symptoms appear, allowing for timely intervention and preventing severe complications. Oral Cancer: Salivary tests identify biomarkers for oral cancer at an early stage, improving treatment success rates and patient prognosis. Non-Invasive and Comfortable Comfort: Collecting a saliva sample is painless, reducing patient anxiety and making it ideal for all ages. Convenience: Dentulu’s saliva testing kit allows at-home sample collection, facilitating regular monitoring without clinic visits. Comprehensive Analysis Microbial Profiling: The saliva test for bacteria identifies specific pathogens, enabling targeted treatment plans. Genetic Markers: The DNA saliva test kit identifies genetic predispositions, aiding in personalized preventive measures. Conclusion Dentulu’s saliva test kit offers early disease detection, comprehensive health analysis, and enhanced patient compliance, making it a valuable tool in modern healthcare. <a href="https://www.dentulu.com/blog/how-salivary-testing-is-revolutionizing-early-disease-detection/"></a> <a href="https://www.dentulu.com/saliva-testing.html></a> <a href ="https://www.dentulu.com/"></a>

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Stewardship is the act of taking good care of something. Antimicrobial stewardship is a coordinated program that promotes the appropriate use of antimicrobials (including antibiotics), improves patient outcomes, reduces microbial resistance, and decreases the spread of infections caused by multidrug-resistant organisms. WHO launched the Global Antimicrobial Resistance and Use Surveillance System (GLASS) in 2015 to fill knowledge gaps and inform strategies at all levels. ACCORDING TO apic.org, Antimicrobial stewardship is a coordinated program that promotes the appropriate use of antimicrobials (including antibiotics), improves patient outcomes, reduces microbial resistance, and decreases the spread of infections caused by multidrug-resistant organisms. ACCORDING TO pewtrusts.org, Antibiotic stewardship refers to efforts in doctors’ offices, hospitals, long term care facilities, and other health care settings to ensure that antibiotics are used only when necessary and appropriate According to WHO, Antimicrobial stewardship is a systematic approach to educate and support health care professionals to follow evidence-based guidelines for prescribing and administering antimicrobials In 1996, John McGowan and Dale Gerding first applied the term antimicrobial stewardship, where they suggested a causal association between antimicrobial agent use and resistance. They also focused on the urgency of large-scale controlled trials of antimicrobial-use regulation employing sophisticated epidemiologic methods, molecular typing, and precise resistance mechanism analysis. Antimicrobial Stewardship(AMS) refers to the optimal selection, dosing, and duration of antimicrobial treatment resulting in the best clinical outcome with minimal side effects to the patients and minimal impact on subsequent resistance. According to the 2019 report, in the US, more than 2.8 million antibiotic-resistant infections occur each year, and more than 35000 people die. In addition to this, it also mentioned that 223,900 cases of Clostridoides difficile occurred in 2017, of which 12800 people died. The report did not include viruses or parasites VISION Being proactive Supporting optimal animal and human health Exploring ways to reduce overall use of antimicrobials Using the drugs that prevent and treat disease by killing microscopic organisms in a responsible way GOAL to prevent the generation and spread of antimicrobial resistance (AMR). Doing so will preserve the effectiveness of these drugs in animals and humans for years to come. being to preserve human and animal health and the effectiveness of antimicrobial medications. to implement a multidisciplinary approach in assembling a stewardship team to include an infectious disease physician, a clinical pharmacist with infectious diseases training, infection preventionist, and a close collaboration with the staff in the clinical microbiology laboratory to prevent antimicrobial overuse, misuse and abuse. to minimize the developme

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When a patient uses a bedpan, promote comfort and normalcy and respect the patient’s privacy as much as possible. Be sure to maintain a professional manner. In addition, provide skin care and perineal hygiene after bedpan use Regular bedpans have a rounded, smooth upper end and a tapered, open lower end. The upper end fits under the patient’s buttocks toward the sacrum, with the open end toward the foot of the bed . A special bedpan called a fracture bedpan is frequently used for patients with fractures of the femur or lower spine Fracture bedpan - used for patients with fractures of the femur or lower spine. The fracture pan has a shallow, narrow upper end with a flat wide rim, and a deeper, open lower end. The upper end fits under the patient’s buttocks toward the sacrum, with the deeper, open lower end toward the foot of the bed. Ordinary Bedpan EQUIPMENTS Bedpan (regular or fracture) Toilet tissue Disposable clean gloves Additional PPE, as indicated Cover for bedpan or urinal (disposable waterproof pad or cover) ASSESSMENT Assess the patient’s normal elimination habits. Determine why the patient needs to use a bedpan (e.g., a medical order for strict bed rest or immobilization). Assess the patient’s degree of limitation and ability to help with activity. Assess for activity limitations, such as hip surgery or spinal injury, which would contraindicate certain actions by the patient. Check for the presence of drains, dressings, intravenous fluid infusion sites/equipment, traction, or any other devices that could interfere with the patient’s ability to help with the procedure or that could become dislodged. Assess the characteristics of the urine and the patient’s skin Assisting With Use of a Bedpan When the Patient Has Limited Movement Patients who are unable to lift themselves onto the bedpan or who have activity limitations that prohibit the required actions can be assisted onto the bedpan in an alternate manner using these actions

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Male patients confined to bed usually prefer to use the urinal for voiding. The use of a urinal in the standing position facilitates emptying of the bladder If the patient is unable to stand, the urinal may be used in bed. Patients may also use a urinal in the bathroom to facilitate measurement of urinary output. Provide skin care and perineal hygiene after urinal use and maintain a professional manner EQUIPMENT Urinal with end cover (usually attached) Toilet tissue Clean gloves Additional PPE, as indicated ASSESSMENT Assess the patient’s normal elimination habits. Determine why the patient needs to use a urinal, such as a physician’s order for strict bed rest or immobilization. Assess the patient’s degree of limitation and ability to help with activity Assess for activity limitations, such as hip surgery or spinal injury, which would contraindicate certain actions by the patient. Check for the presence of drains, dressings, intravenous fluid infusion sites/equipment, traction, or any other devices that could interfere with the patient’s ability to help with the procedure or that could become dislodged. Assess the characteristics of the urine and the patient’s skin. Document the patient’s tolerance of the activity. Record the amount of urine voided on the intake and output record, if appropriate. Document any other assessments, such as unusual urine characteristics or alterations in the patient’s skin. SPECIAL CONSIDERATION Urinal should not be left in place for extended periods because pressure and irritation to the patient’s skin can result. If patient is unable to use alone or with assistance, consider other interventions, such as commode or external condom catheter. It may be necessary to assist patients who have difficulty holding the urinal in place, such as those with limited upper extremity movement or alteration in mentation, to prevent spillage of urine. The urinal may also be used standing or sitting at the bedside or in the patient’s bathroom, if patient is able to do so.

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VSWarehouse; a scalable, rapid genomic repository solution

1. VSWarehouse; a scalable, rapid genomic repository solution Darby Kammeraad Field Application Scientist Manager 20 Most Promising Biotech Technology Providers Top 10 Analytics Solution Providers Hype Cycle for Life sciences

2. Questions & Answers

3. VSWarehouse; a scalable, rapid genomic repository solution Darby Kammeraad Field Application Scientist Manager 20 Most Promising Biotech Technology Providers Top 10 Analytics Solution Providers Hype Cycle for Life sciences

4. NIH Grant Funding Acknowledgments • Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under: • Award Number R43GM128485-01 • Award Number R43GM128485-02 • Award Number 2R44 GM125432-01 • Award Number 2R44 GM125432-02 • Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005 • PI is Dr. Andreas Scherer, CEO Golden Helix. • The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

5. Who Are We? Golden Helix is a global bioinformatics company founded in 1998 Filtering and Annotation ACMG Guidelines Clinical Reports CNV Analysis Pipeline: Run Workflows Variant Warehouse Centralized Annotations Hosted Reports Sharing and Integration CNV Analysis GWAS | Genomic Prediction Large-N Population Studies RNA-Seq Large-N CNV-Analysis

6. Cited in 1,000s of Peer-Reviewed Publications

7. Over 400 Customers Globally

8. SIMPLE, SUBSCRIPTION- BASED BUSINESS MODEL o Yearly fee o Unlimited training & support SOFTWARE IS VETTED o 20,000+ users at 400+ organizations o Quality & feedback DEEPLY ENGRAINED IN SCIENTIFIC COMMUNITY o Give back to the community o Contribute content and support INNOVATIVE SOFTWARE SOLUTIONS o Cited in 1,000s of publications When you choose Golden Helix, you receive more than just the software

10. VarSeq Suite Simple Flexible Scalable Variant annotation filtering, and interpretation Powerful GUI with rich visualizations Repeatable workflows

11. • Archive full VCFs for Sample Cohort o Optimized repository infrastructure for rapid queried through millions of variants • Centralized Genomic Data Hosting o Integrated with other systems • Query Variant Warehouse o Have I seen this variant in my cohort? o Has the classification changed with new evidence in ClinVar? o How do I ensure consistency of CNV/variant interpretations across all users? VSWarehouse - Variant Warehouse Server

12. • From VarSeq to VSWarehouse  Upload full cohort data  Upload variant classification/interpretations  Upload clinical reports • From VSWarehouse to VarSeq  Annotate with cohort data o Variant frequencies  Annotate with classified variants  Access congruent Assessment Catalogs & Reports • VSWarehouse Browser  Query all genomic data o Reports, catalogs, projects  Evidence updates with ClinVar  Manage access permissions Integration with VarSeq

13. VSWarehouse – Centralized Collaboration Project A Project B VSWarehouse Server Group A Group B Collaborators

14. • Part I – Exploring VSWarehouse Browser o General variant search o Filtering/query o Classification changes in ClinVar • Part II – VarSeq & VSWarehouse o Filtering out common variants Example Project

15. Scalable Variant Warehouse for VarSeq Project Demonstration >

16. NIH Grant Funding Acknowledgments • Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under: • Award Number R43GM128485-01 • Award Number R43GM128485-02 • Award Number 2R44 GM125432-01 • Award Number 2R44 GM125432-02 • Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005 • PI is Dr. Andreas Scherer, CEO Golden Helix. • The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

17. Questions & Answers

18. Visit Golden Helix in booth 46!

19. Questions & Answers

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