Custom Family Workflows
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VarSeq contains default workflows for Trio analysis which include filter chains for identifying de Novo and Compound Heterozygous variants, but what if you have data for a full Quad or even just a few siblings? How could your VarSeq workflow be adjusted to handle this custom family structure? In this presentation we will demonstrate how to customize your VarSeq workflow to handle the following family scenarios: Full Quad (mother, father and 2 affected children) Siblings with different affection status (mother, father, 1 affected and 1 unaffected child) No parents (2 affected siblings)
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Guillermo Martinez has over 30 years of experience in healthcare laboratory management, including serving as Technical Director for two large testing laboratories. He has a background in process improvement using Lean Six Sigma tools and has coordinated numerous research studies evaluating new testing technologies. Martinez is also actively involved in professional organizations and has authored several publications related to transfusion medicine and laboratory science.
Open innovation contributions from RSC resulting from the Open Phacts project
Open innovation contributions from RSC resulting from the Open Phacts projectUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The NIH Data Commons must treat the data it will contain not unlike the mortar and stones of a road. To help our fellow scientists travelers use the road, we must engineer for heavy traffic and diverse destinations. There are many steps to architecting a robust and persistent road. First, the data must be sourced and manipulated into common data models. This requires versioned access to the data, equivalency determination of identifiers within the data or minting of new ones for the data and/or within it, manipulating the data according to common data models (e.g. a genotype-to-pehnotype association in one source may relate a variant to a disease, where in another it may be a set of alleles associated with a set of phenotypes, each source models the data differently). Inclusion of the data in the Commons must meet all licensing restrictions, which are varied and usually poorly declared, as well as security, HIPAA, and ethics requirements. Software tools are needed to perform the Enhance-Transform-Load (ETL) process on a regular cycle to keep the data current, and to assess changes and quality assurance over time. For records that disappear, there needs to be a way to keep an archive of them. Once in the Commons, the data requires a map to navigate the roads: where do you want to go? Indexing and search across the data requires having the data be self-reporting - loading ontologies used in the data for indexing and providing faceted query over these and other attributes, sophisticated text mining tools, relevance ranking, and equivalency and similarity determination from amongst different providers. Once found, the users need vehicles to drive upon the road. These are their workspaces, the place where they design and implement the operations they need in order to get where they want to go. Unimaginable scientific emeralds are to be found at the end of the road, as the sum of all the data, if well integrated and made computationally reusable, has proven to be well beyond the sum of its parts in getting us where we want to go.
CNV Annotations: a crucial step in your variant analysis
Since the development of our NGS-based CNV solutions for VarSeq and SVS, we've generated a long list of content demonstrating simple workflows to help isolate clinically relevant events for a given sample. However, it's just as important to talk about the exclusionary filters that help remove any extraneous CNVs from the analysis.
Golden Helix stands alone in our delivery of multiple methods for filtering down to top-quality, rare, and clinically relevant variants. This webcast will focus on the application of the various CNV annotations, discussing their purpose and usability in quickly removing CNVs with high-population frequency, duplicated regions inherent to the human genome, benign events, and events known in healthy individuals.
Please join us in an exploration of VarSeq's unique CNV annotation capabilities to see how users can overcome the challenges of NGS-based CNV detection.
What will you learn in this webcast?
Initial assessment of sample and CNV event quality
General review and understanding of various CNV annotations in VarSeq
The application of CNV annotations to eliminate common and benign CNVs
VSWarehouse: Tracking Changing Variant Evidence and Classifications
Over the years, VarSeq has evolved into a powerfully efficient next-gen sequencing variant analysis platform. Some of the recent advances Golden Helix has made to this software have been to implement the standard ACMG and AMP guidelines for variant classification and interpretation. The guidelines are composed of many criteria impacting any variant final classification. These criteria consider topics such as frequency of the variant among the population, functional predictions, hotspot pathogenic rich regions in the gene, as well as known clinical submissions from other labs. The reality with this guideline review is that variant evidence can changeover time. Among the long list of databases needed to automate this guideline process, many databases have massive updates or are frequently updated perhaps on a month-to-month basis. So, it follows that any classification can be altered once discoveries for these variants are made. A problem that arises is, how to manage changing classifications, retroactively review previous patient outcomes and updatevariant classifications accordingly. Fortunately, Golden Helix has solved this dilemma with the use of our VSWarehouse genomic repository.
In this webcast, we are going to explore the value and application of VSWarehouse. Our example variants will showcase a situation where variants of uncertain significance ultimately reach a pathogenic classification based on updates to ClinVar. This change will be presented not only in VarSeq with listings of previous samples but also shown directly from the VSWarehouse browser in a ClinVar classification tracker. We will also look at an alternative situation where the classification may change to benign for some previously reported variants which would require follow-up with the patient. The importance of a tool like the ClinVar tracker in VSWarehouse cannot be understated as it is a simple way to comprehensively review the backlog of changing variant classifications when users must update their locked down validated NGS pipeline. Please join us in the upcoming webcast to explore how these features in VarSeq and VSWarehouse work to allow users thorough accountability in updating historical patient results with new variant evidence
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
The document describes funding that supported research conducted by Golden Helix. It lists several National Institute of General Medical Sciences grant numbers that supported the work. The principal investigator for the grants is named as Dr. Andreas Scherer, CEO of Golden Helix. It is noted that the content of any research supported by this funding is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.
ACMG-Based Variant Classification with VSClinical
Golden Helix is a global bioinformatics company founded in 1998 that provides software for variant annotation, filtering, and interpretation. Their flagship products are VarSeq Suite and VSClinical. VarSeq Suite allows for powerful variant filtering and annotation using curated public databases and premium annotations. VSClinical streamlines variant classification using American College of Medical Genetics and Genomics guidelines through a four-phased workflow involving variant filtering, evidence assessment, classification, and reporting. It provides consistent results and reduces learning curves for users. Golden Helix has over 400 customers globally and their software is cited in thousands of peer-reviewed publications.
Canadian health census to lod
The document discusses transforming Canadian health census data into linked open data (LOD). The goals are to acquire and refine public health census data, transform it into the RDF format, integrate semantic vocabularies, and configure a linked open data explorer and SPARQL endpoint to allow for querying of the data. Methodologies discussed include data acquisition, manipulation to transform unstructured data into a relational format, using RDF tools to transform the data, and exposing and integrating the data through a Pubby explorer and Snorql endpoint. Examples of SPARQL queries on the transformed data are provided.
Whole Genome Trait Association in SVS
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. As Next-Generation Sequencing of whole genomes becomes more affordable, large cohorts of Whole Genome Sequencing (WGS) samples are available to search for additional trait association signals that were not found in array-based testing. In fact, recent papers have shown that WGS analysis using advanced GREML (Genomic Relatedness Restricted Maximum Likelihood) techniques is able to outperform micro-array based GWAS methods in the analysis of complex traits and proportion of the trait heritability explained.
Our latest update release of SVS has expanded the exiting maximum likelihood and GRM methods to support these new techniques. We have also enhanced various other association testing and prediction methodologies. This webcast showcases:
- Newly supported analysis workflow for whole genome variants using LD binning and enhanced GBLUP analysis
- Enhanced gender correction using REML
- Additional capabilities for genomic prediction and phenotype prediction
We are continually improving our products based on our customer’s feedback. We hope you enjoy this recording highlighting the exciting new features and select enhancements we have made.
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
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.
Resource Identification Initiative
Presentation on the Resource Identification Pilot Project, an initiative to develop a machine-processable citation system for key research resources used in scientific studies
AMP-Based Variant Classification with VSClinical
The document discusses Golden Helix's VSClinical software and its capabilities for analyzing biomarkers and variants according to AMP and ACMG guidelines. VSClinical provides a four-phased workflow to 1) filter variants, 2) assess evidence, 3) develop classifications, and 4) include interpretations in clinical reports. It leverages Golden Helix's CancerKB knowledgebase to accelerate variant interpretation and standardized reporting. The document demonstrates VSClinical's analysis and reporting of variants from a myeloid gene panel according to AMP guidelines.
Advanced VSClinical Reports with Scripting and Custom Integrations
Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines for the evaluation of variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since VSClinical was introduced, we have provided a powerful Word-based templating system that allows labs to customize reports to include their specific content and branding.
Although powerful, this capability has been limited to customizing the contents of a Word file. Sometimes, the next logical step for the VSClinical analysis result is not a Word file, but some other file or target system: A database, LIMS, EMR, or even just a custom structured text file.
Join us in this webinar, as we discuss the next version of VarSeq, which will introduce a powerful scripting and custom integration engine built into VSClinical Reports. We will cover:
Capabilities and outputs of the workflows of VSClinical ACMG and Cancer
Content of VSClinical reports, including sample-QC, coverage statistics, custom gene panels, and data providence
The shipped report templates that range from gene panels to exome trios and comprehensive cancer testing
The new custom script-based reports and example workflows it enables
The tools enabling a powerful developer experience when building custom outputs and integrations
The VarSeq Suite holds customization and extendibility as core values, allowing the powerful capabilities of variant analysis to be truly customized to the needs of a specific laboratory and NGS test. The new scripting and integration capabilities build on this tradition for the VSClinical workflows. We hope you can join us as we explore this topic in-depth in this webinar.
An Exploration of Clinical Workflows in VarSeq
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
Next-Generation Sequencing Analysis in VSClinical
VarSeq is a tertiary analysis platform that allows users to filter and annotate NGS sequencing data to identify clinically relevant variants. Following this workflow, VSClinical can then be used to automate both germline and somatic variant analysis in accordance with the ACMG and AMP guidelines by using a variety of functional prediction models and clinical and reviewer-based annotations. Once variant or biomarker interpretations are completed, they can be rendered in a customizable clinical report and stored in an internal assessment catalog as an internal variant database repository. Together, implementation of VSClinical will promote increased lab throughput as well as accuracy and compliance with the ACMG and AMP guidelines, which in turn can save time and money. To show the capabilities of our software, this webcast will provide a demonstration of how to use VarSeq and VSClinical for the evaluation of both germline and somatic variants in accordance with the ACMG and AMP Guidelines.
In this webcast, we will cover:
- Filter logics for germline and somatic variants and selecting them into the VSClinical interface
- Capabilities of functional prediction and splice site algorithms for edge case variants
- The functionality of changing the clinically relevant transcript on variant interpretation
- Rendering a clinical report with germline and somatic variants with the inclusion of clinical trials
Annotation capabilities
VarSeq provides powerful annotation capabilities for variant analysis including gene tracks, assemblies, variant functions, frequency tracks, functional predictions, and transcript annotations. It integrates information from over 20 public databases and sources and updates annotations monthly to provide the most current clinically relevant information for researchers. By centralizing variant annotations from disparate sources, VarSeq saves customers significant time and resources compared to manual curation of this data.
Resume_Bill_Martinez
Guillermo Martinez has over 30 years of experience in healthcare laboratory management, including serving as Technical Director for two large testing laboratories. He has a background in process improvement using Lean Six Sigma tools and has coordinated numerous research studies evaluating new testing technologies. Martinez is also actively involved in professional organizations and has authored several publications related to transfusion medicine and laboratory science.
Open innovation contributions from RSC resulting from the Open Phacts project
Open innovation contributions from RSC resulting from the Open Phacts projectUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we developed our existing platforms, created new and innovative widgets and data platforms to handle chemistry data, extended existing chemistry ontologies and embraced the semantic web open standards. As a result RSC served as the centralized chemistry data hub for the project. With the conclusion of the Open PHACTS project we will report on our experiences resulting from our participation in the project and provide an overview of what tools, capabilities and data have been released into the community as a result of our participation and how this may influence future projects. This will include the Open PHACTS open chemistry data dump including the chemistry related data in chemistry and semantic web consumable formats as well as some of the resulting chemistry software released to the community. The Open PHACTS project resulted in significant contributions to the chemistry community as well as the supporting pharmaceutical companies and biomedical community. What's hot (19)
Golden Helix's End-to-End Solution for Clinical Labs
Golden Helix's End-to-End Solution for Clinical Labs
Creating & Managing Reusable Gene Lists with VSClinical
Creating & Managing Reusable Gene Lists with VSClinical
Building (and traveling) the data-brick road: A report from the front lines ...
Building (and traveling) the data-brick road: A report from the front lines ...
CNV Annotations: a crucial step in your variant analysis
CNV Annotations: a crucial step in your variant analysis
VSWarehouse: Tracking Changing Variant Evidence and Classifications
VSWarehouse: Tracking Changing Variant Evidence and Classifications
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline Workflow
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq
Advanced VSClinical Reports with Scripting and Custom Integrations
Advanced VSClinical Reports with Scripting and Custom Integrations
Open innovation contributions from RSC resulting from the Open Phacts project
Open innovation contributions from RSC resulting from the Open Phacts project
Similar to Custom Family Workflows
Two Clinical Workflows
This document discusses two clinical workflows for analyzing genetic variants from raw data to a clinical report. It describes using VarSeq software to filter variants from gene panel or exome/genome sequencing data, review and annotate variants of interest, and generate a customized report. It also covers using repeatable VarSeq workflows and the VSPipeline tool to automate high-throughput analysis and generate standardized deliverables for each sample.
Using VarSeq to Improve Variant Analysis Research Workflows
Many questions must be answered when analyzing DNA sequence variants: How do I determine which variants are potentially deleterious? Is the sequencing quality sufficient? How do I prioritize the results? Which annotation sources may help answer my research question?
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.
The presentation will include interactive demonstrations using VarSeq to analyze variants found by exome sequencing of an extended family with a complex disease. We will review strategies for assessing variant quality, applying genomic annotations, incorporating custom annotation sources, and creating variant filters in VarSeq. We will also demonstrate the PhoRank gene ranking algorithm and its application for prioritizing variants.
Using VarSeq to Improve Variant Analysis Research Workflows
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.
Best Practices for Validating a Next-Gen Sequencing Workflow
Validating an NGS workflow is an iterative process that begins with collaboration with personnel and planning protocols for the entire workflow from sample preparation, sequencing and variant calling, all the way to data analysis and reporting. At Golden Helix, while we do not provide pre-validated black-box workflows, we provide our customers with support to validate workflows in a transparent manner, and assist them in reaching production deadlines. This webcast will be led by members of our Field Application Scientist team, and we will explore some of the best practices for NGS workflow validation that we have observed and helped to implement based on real-world examples from our customer base. Key topics for discussion will include:
Sample preparation and collection of adequate case/control data
Designing a robust workflow with special considerations for single versus family analyses and phenotypic considerations
Generating the desired output for clinical or other reports
Real world NGS workflow validation strategies
Tune in for tips and strategies that you can deploy when designing and validating your NGS workflow.
Computational Resources In Infectious Disease
This document summarizes bioinformatics tools that can be used for analysis of high-throughput sequencing data for molecular diagnostics. It discusses databases for virulence factors and antimicrobial resistance as well as tools for assembly, annotation, pan-genome analysis, visualization, and commercial solutions. The presentation emphasizes that there is no single best tool and different approaches are needed for different questions. Collaboration with other researchers is recommended.
Enhancing the Quality of ImmPort Data
Presentation to ImmPort Science Meeting, February 27, 2014 on the proper treatment of value sets in the Immport Immunology Database and Analysis Portal
Spark Summit EU talk by Erwin Datema and Roeland van Ham
The document discusses KeyGene's use of Apache Spark for high-throughput genomics data analysis. KeyGene is a crop innovation company that analyzes genomic data from thousands of plants to improve crop traits like yield and quality. They previously used conventional HPC clusters for genomics pipelines but found Spark enabled more interactive analysis. KeyGene developed a "Sparkified" genomics pipeline using tools like BWA, GATK and their own Guacamole variant caller. This allowed interactive variant selection and GWAS using Spark SQL queries, demonstrating Spark is well-suited for interactive plant genomics analysis.
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"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeq
1) The document discusses a genetic data warehousing solution called VSWarehouse from Golden Helix that allows users to store, query, and analyze large genomic datasets.
2) VSWarehouse uses a column-based storage approach that is more scalable than traditional row-based databases and allows efficient querying and joining of variant call and sample data.
3) Golden Helix is launching an early adopter program for VSWarehouse, offering interested customers the chance to influence the product roadmap in exchange for a discounted license and commitment through March 2016.
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
In the rapidly evolving field of genomic analysis, staying current with the latest research, data sources, and test advancements is crucial. In this webinar, we review how VarSeq addresses the needs to stay on top of the latest with the release of VarSeq 2.6.0.
This release features an exome-optimized workflow for LOH and CNV calling as well as the introduction of VSPGx to produce pharmacogenomic reports for gene panels as well as exomes and genomes. With the recent release of gnomAD v4, we have had many requests for the integration of this large update to the most population frequency source. With VarSeq 2.6.0, the latest version of gnomAD has been integrated into VSClinical and the updated tracks spans beyond variants to cover CNVs and gene scores to update all your workflows to the latest data.
In this webcast, we will cover.
Improved VS-CNV performance and updated exome analysis workflows.
Pharmacogenomics in action: Utilizing VSPGx for exome and genome assessments.
gnomAD v4 in practice: Updated automated and manual variant interpretation workflows.
Join us for an insightful session on the latest VarSeq 2.6.0 features, bringing you the most up-to-date data and workflows for your genomic analysis.
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
The document provides information about Golden Helix's VarSeq 2.4.0 software and its VSClinical ACMG workflow module. It summarizes a presentation given on the topic, including details about Golden Helix as a company, the content covered in the presentation, and examples that will be demonstrated including analysis of variants, copy number variants, and structural variants from PacBio long read sequencing data using VSClinical.
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
The document provides information about Golden Helix's VarSeq 2.4.0 software and its VSClinical ACMG workflow module. It summarizes a presentation given on the topic, including details about Golden Helix as a company, the content covered in the presentation, and examples that will be demonstrated including analysis of variants, copy number variants, and structural variants from PacBio long read sequencing data using VSClinical.
Building Secure Analysis and Storage Systems with Golden Helix
Genetic testing labs deal with personal data in categories with the highest level of security requirements: personal identity and medical records. Given the liability and risk associated with a breach of this secure information, it is not surprising that many labs and institutes that aggregate genomic data prefer if not require on-premise analysis and storage solutions.
Golden Helix is in a unique position to provide completely on-premise analysis solutions with a history of building analysis software from the ground-up on first principles and a focus on providing integrated, turn-key solutions. This allows for a licensing model based on training and supporting users, not tracking per-sample usage of cloud resources. As the regulatory environment around the world strengthens the privacy rights of individuals and the outcry around data breaches raises the stakes for building a secure system, we have developed a number of best practices for building secure, offline genomic analysis pipelines. Watch as we cover:
- Building a FASTQ to clinical reports pipeline behind a firewall
- On-premise analysis, warehouse and data servers independent of the internet
- Single sign-on based on local credential systems and without internet access
- Storage and network considerations for the analysis of patient-linked data
- Choose when to update and validate new pipelines, data sources and software versions
We hope you enjoy as we review the capabilities and best practices in building the most secure environment for hosting the analytics behind your precision medicine tests.
Expanding Your Research Capabilities Using Targeted NGS
Target enrichment enables researchers to focus their next generation sequencing (NGS) efforts on regions of interest, allowing them to obtain more sequencing data relevant to their study. In-solution target capture is a method of enrichment using oligonucleotide probes directed to specific regions within a genome. Target capture can be used to enrich multiple samples simultaneously, reducing the cost per sample, while using individually synthesized probes allows researchers to construct gene panels that can be optimized over time.
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The document discusses the Genome in a Bottle Consortium's efforts to develop reference materials and reference methods to help validate whole genome sequencing for clinical applications. This includes developing well-characterized reference genomes and reference data from these genomes to enable evaluation of variant calling accuracy and help standardize performance metrics. The consortium is working to generate integrated variant calls from multiple sequencing platforms and technologies for different reference genomes to serve as benchmarks for evaluation.
Production Bioinformatics, emphasis on Production
Production bioinformatics at Sema4 can be thought of as data ops - a peer to the lab ops organization. We operate 24/7 to deliver correct and timely results on NGS and other data for thousands of samples per week. This deck introduces the Prod BI organization and systems architecture with a focus on what it takes to run bioinformatics in production rather than for R&D or pure research.
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The document discusses the Genome in a Bottle Consortium's efforts to generate reference materials and data to evaluate the accuracy of human genome sequencing and variant calling. Specifically:
- The consortium is developing reference samples with well-characterized genomes to test sequencing platforms and bioinformatics methods.
- An initial sample, NA12878, has been extensively sequenced and analyzed to generate high-confidence variant calls across 77% of the genome.
- Efforts are ongoing to expand the reference data to additional samples from different populations and integrate data from multiple sequencing technologies.
- The goal is to enable standardized evaluation, benchmarking and regulatory oversight of clinical genome sequencing.
Cool Informatics Tools and Services for Biomedical Research
This document provides an overview of bioinformatics tools and services for analyzing big data in biomedical research. It discusses traditional bioinformatics tools, analyzing genomic data from microarrays and next-generation sequencing without and with code, interpreting results using protein interaction networks and pathways, tools for data storage, cleaning and visualization, and making research reproducible. Galaxy, R, and programming are presented as useful for automated, reproducible analysis of large genomic datasets.
MutaDATABASE
The MutaDATABASE project aims to create a centralized and standardized database of human gene mutations called MutaDATABASE. It will collect all known human gene mutations related to monogenic diseases from existing databases and laboratories. The goal is for MutaDATABASE to become the most comprehensive mutation database by making submission of new mutations easy and encouraging participation. Key aspects include standardized formats, central access, free sharing of mutation data, and supporting software and groups to facilitate data sharing and review.
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Using VarSeq to Improve Variant Analysis Research Workflows
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Introducing VSWarehouse - A Scalable Genetic Data Warehouse for VarSeq
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VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
VarSeq 2.4.0: VSClinical ACMG Workflow from the User Perspective
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More from Golden Helix
Introducing VarSeq Dx as a Medical Device in the European Union
A transition period regarding in vitro medical device (IVD) regulation in the European Union (EU) is upon us. The former IVDD regulations are phasing out and IVDR 2017/746 has already taken its place as the acting regulation for IVD manufacturers but also lab developed tests (LDTs) and health institutions. In our upcoming webcast we will talk about the roles and significance of IVDR and ISO 13485 certification for clinical labs and for Golden Helix as a medical device manufacturer.
Join us as we will introduce VarSeq 2.6.1 complete with Dx Mode, which offers the use of VarSeq as CE marked medical device. Even more we will also present strategies to facilitate the transition of Golden Helix customers to operate in accordance with IVDR.
Introducing VSPGx: Pharmacogenomics Testing in VarSeq
Inter-individual variability in drug response poses a significant challenge for clinicians, with much of this variability resulting from inherited genetic differences. While the field of pharmacogenomics (PGx) can provide powerful insights into how genomic factors affect drug response, the implementation of PGx testing in the clinic is hampered by the difficulty of translating genetic test results into actionable recommendations. In this webcast, we will discuss VarSeq’s new PGx testing capabilities, including the ability to identify actionable pharmacogenomic diplotypes and generate clinical reports.
In this webcast you will learn:
-How to identify pharmacogenomic diplotypes and drug recommendations from NGS data.
-How to incorporate externally called CNVs and SVs into your PGx annotations.
-How to generate customizable PGx reports from these annotations.
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analyses. However, standard commercial exome kits are limited to targeting exon coding regions, leaving significant gaps in coverage between genes which could hinder comprehensive CNV detection.
Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Twist Exome 2.0 Plus Comprehensive Exome Spike-in capture panel with added "backbone" probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25kb, 50kb, and 100kb intervals. In this webcast, we discuss the combined efficacy of the backbone-probe enhanced exome capture kit and VS-CNV in identifying known CNVs using the Coriell CNVPANEL01 reference set.
This webcast reviews:
-The sensitivity rate for the detection of known CNV events at all three probe densities.
-The impact of best-practice quality metrics and filters on sensitivity.
-How VarSeq’s CNV annotation capabilities can be leveraged to identify likely pathogenic CNVs.
-The interpretation of clinically relevant CNVs using VSClinical.
From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
From gene panels to whole genome, from short to long-read sequencing, the VarSeq suite is the solution for NGS analysis and reporting in a modern clinical lab. VarSeq handles the spectrum of variant types (SNV, Indel, CNV, Fusions) and provides automated classification and reporting capabilities following the ACMG and AMP guidelines. With our new PacBio partnership, we are more adaptable than ever with creating a spectrum of custom workflows to suit our unique user needs.
This webcast will review:
-Data analysis scaling from Gene Panel to Genome analysis with VarSeq and VSWarehouse.
-Analysis and annotation of SNVs, Indels, CNVs, and fusions.
-A close look at a PacBio long-read trio analysis.
Come join us for this showcase in modern VarSeq analysis capabilities.
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. The latest SVS release introduces a significant leap in capabilities, with a focus on advanced Polygenic Risk Score (PRS) calculations. PRS has become a fundamental tool in genomic research, enabling the identification of correlations between genotypic variants and phenotypes across large populations.
This enhancement is particularly relevant for researchers working on large cohorts and meta-analysis. Please join us as we explore:
-SVS Workflow Review: A review of the extensive capabilities of SVS to meaningful insights from large cohorts and association test result datasets
-Computing Polygenic Risk Scores: An overview of the PRS capabilities in SVS, including Clumping and Thresholding and creation of multiple PRS models
-Evaluating and Applying PRS: Evaluating PRS models in-sample and out-of-sample and applying PRS models to perform trait prediction
-Future Implications: Brief exploration of how these advancements in SVS could influence future genomic research.
This webcast will explore how SVS facilitates the creation of multiple PRS models from large-scale genomic data, such as those obtained from extensive cohort studies or comprehensive meta-analyses. Join us to discover how these latest updates in SVS are supporting large-scale genomic research.
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
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: Empowering Family Planning through Carrier Screening Analysis
Golden Helix introduced new capabilities in VarSeq 2.5.0 to support carrier screening analysis through NGS data. Key features include the ability to import partnered samples, detect shared carrier variants between samples at the gene level using a couples carrier screening workflow, and generate clinical reports that calculate reproductive risks and include variant interpretations. The software is designed to scale from gene panels to whole exomes/genomes. A demo showed how these new features streamline the carrier screening analysis process from data import and filtering to clinical reporting.
Identifying Oncogenic Variants in VarSeq
The interpretation of somatic variants can be a challenging process. While AMP Guidelines provide detailed rules for accessing the clinical evidence associated with a specific variation, they do not specify criteria for determining if a variant is likely to be a driver mutation, which generates functional changes that enhance tumor cell proliferation. In this webcast, we will discuss a new VarSeq algorithm for estimating the oncogenicity of a variant. This will include a deep dive into our oncogenicity scoring system and a discussion of the various criteria used to distinguish driver mutations from benign variations and variants of uncertain significance.
What you will learn in this webcast:
-How to use the scoring algorithm to identify variants with evidence of oncogenicity
-Which criteria are used to assess a variant's oncogenicity
-How to evaluate the oncogenicity of a variant in VSClinical
2023 Innovation Awards Winner, Dr. Muthukumaran
Expanded carrier screening in an infertile/affected Couple for determining carrier status for genetic mutations - VarSeq Couple Carrier Workflow
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
Mendelian disorders can be caused by various classes of genetic mutations, from small variants to CNVs and even Structural Variants. With the introduction of VarSeq 2.4.0, we are excited to unveil the latest advancements in VSClinical ACMG, focusing on the integration of Structural Variants and the enhanced automation capabilities that streamline your analysis process.
Join us in this webcast as we dive into the following topics:
Integration of Structural Variants: Learn how VarSeq 2.4.0 enables you to import and incorporate Structural Variants into your VSClinical ACMG evaluations and reports, providing a comprehensive understanding of the genetic landscape.
Advanced Automation in the ACMG Interface: Discover how evaluation scripts can be employed to automate the VSClinical ACMG interface, allowing you to perform custom actions or eliminate manual steps, thus increasing efficiency and reducing the risk of errors.
End-to-End Automation: Explore how VSPipeline can fully automate your analysis process, from raw VCF to report, ensuring a streamlined and consistent workflow that saves time and resources.
Harnessing the Power of VSClinical: Gain insights into how VarSeq 2.4.0 empowers you to tackle complex genomic data, enabling faster and more accurate identification of Mendelian disorders and facilitating personalized patient care.
With the advanced capabilities of VarSeq 2.4.0 and VSClinical, you can now unlock a new level of precision and efficiency in diagnosing Mendelian disorders. This webcast will showcase the latest innovations in variant interpretation and automation, exemplifying why the VarSeq Clinical Suite is the premier NGS analysis platform for germline and cancer testing.
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
There is a strong motivation for labs to bring most, if not all, of their next-gen sequencing pipeline in-house. This is especially relevant for clinical applications where there is a need to validate any routine diagnostics when seeking to provide genetic results to patients. The entirety of the NGS pipeline is highly automatable and comprised of multiple stages but from the geneticist's point of view, the tertiary stage requires the lengthiest review. This stage is where the geneticist sifts through the massive collection of genetic variants to find and report on those most relevant to the patient or population. Unfortunately, the tertiary stage can be a fairly sophisticated process and there aren’t many tools on the market that handle it comprehensively and simply. Many of the tools that are available may have severe limitations on the scale of genomic data they can process or limitations on the types of NGS assays that can be designed. Moreover, their license model may be on an individual sample basis and present cost-benefit hurdles for the user, especially when sample load will inevitably increase. Fortunately, none of these assay or cost-based issues are relevant with Golden Helix products.
The goal of this webcast is to expose our viewers to the versatility that GHI VarSeq provides when constructing your dream NGS assay. This demonstration will provide examples of germline and somatic workflows for both single and multi-sample analysis for a variety of different disorders. Please join us and learn more about the analytical possibilities you can achieve when using the VarSeq software.
Prenatal Genetic Screening with VarSeq
Our past webcast explored the current approaches for screening and diagnosis of genetic disorders in prenatal testing. While the methods available at the time were robust, they were severely limited, creating a need for a higher diagnostic yield and more efficient analysis for a wider range of genetic tests. The solution proposed was to improve and simplify prenatal screening and diagnosis with whole exome sequencing (WES).
During that webcast, we highlighted the advantages of WES over traditional methods such as karyotyping and chromosomal microarray, including improved accuracy, granularity, and cost-effectiveness. We also emphasized the potential of WES to expand diagnosis for many other adverse maternal-fetal complications beyond the large aneuploidy events previously covered. However, there was still an intimidation factor when it came to the massive data output from the exome. Fortunately, Golden Helix provided the necessary tools to build and standardize these genetic assays, simplifying the analytical process while leveraging increased diagnostic output. We explored our VarSeq software to demonstrate some example workflows of cases positive for Trisomy 21, an exon loss in DMD related to Duchenne Muscular Dystrophy, and detection of a single base change resulting in a LOF variant in RUNX1 relevant to hereditary leukemia.
Our goal was to expose our viewers to the methods of conquering this vast NGS-based data and play a role in dissolving any feeling of intimidation. Overall, exome sequencing has the potential to vastly improve diagnostic outcomes and widen discoveries in the research related to prenatal testing, and Golden Helix products are designed to facilitate this process.
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
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.
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
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.
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
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
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
Next Generation Sequencing allows for the detection of a wide variety of genomic alterations. This includes small mutations, copy number variants and complex rearrangements. However, it can be difficult to annotate, filter, and interpret these alterations.
As part of our VarSeq 2.3.0 release, we have greatly simplified this process by allowing you to import, annotate, and filter mutations across all spectrums of genomic variation. This supports concurrent importation of small variants and CNVs as well as complex rearrangements. This release also includes strong support for structural variant annotation, filtering, and interpretation, including structural variant effect prediction. After filtering is complete, any clinically relevant structural variants can be interpreted with the VSClinical AMP Guidelines workflow and included in the final clinical report.
Come join us for this webcast to discuss VarSeq’s enhanced import and annotation capabilities, including:
Concurrent importation of variants CNVs and complex rearrangements
Improved multi-threaded import which dramatically speeds up the importation of large VCFs
Annotation of structural variants and prediction of effect
Interpretation of structural variants in the VSClinical AMP Guidelines workflow
Support for visualization and use of CRAM files as input for computing coverage statistics
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Precision medicine for cancer is rapidly accelerating because of the development and approval of targeted molecular therapies. These therapies require new genomic biomarkers as an indication for use, and require evaluating additional mutation types that are available in comprehensive genomic profiling assays as well as the small variants detected by Next-Generation Sequencing gene panels.
We are excited to announce VarSeq 2.3.0 which will update the VSClinical AMP workflow to meet the growing needs of labs conducting comprehensive genomic profiling (CGP) of tumors. This includes built-in support for the Illumina TruSight Oncology 500 (TSO-500) kit as well as similar kits from other vendors. The VSClinical AMP workflow has also gained native support for the bioinformatic outputs of CGP kits. Join us to learn about comprehensive genomic profiling in cancer, specifically:
Evaluation and clinical reporting of genomic signatures such as Microsatellite (MSI), Tumor mutation burden (TMB), PD-L1, Homologous recombination deficiency (HRD) statuses, and more.
Built-in TSO-500 import and expandable import capabilities for new genomic data types through the new advanced workflow scripting system.
Golden Helix CancerKB updates with report-ready genomic-signature interpretations written for approved therapies as well as gene interpretations for all 500 genes of the TSO-500 panel. In addition, CancerKB scopes have been extended to reference multiple relevant biomarkers in a single interpretation, capture approved therapies at the tumor type level, and include interpretations for clinically relevant negative findings.
Expanded clinical trial support to include international trials and the ability to search within proximity of European postal codes. VSClinical is accessing all active studies in AACT/ClinicalTrials.gov wherein users can search and select trials based on relevant drugs, biomarkers, and the geographic distance to the patient or testing site.
VarSeq 2.3.0 will deliver powerful capabilities for genomic profiling in cancer, enabling a new level of personalized and effective care for your patients. We look forward to demonstrating these updates and Golden Helix’s continued innovation making the VarSeq Clinical Suite the NGS analysis platform of choice for germline and cancer testing.
Single Sample and Family Based Genome Analysis With VarSeq
One major hurdle facing medicine is the need to quickly identify and assess the genetic components contributing to rare diseases. It has been estimated that nearly 350 million people suffer from rare diseases, 140 million of which are children, of whom ~30% do not live past their fifth birthday1,2. The specific issue to overcome is reducing morbidity by facilitating rapid diagnosis and treatment. Fortunately, the cost of whole genome sequencing has dropped below the $1000 mark, which not only makes the NGS approach more affordable but has become the status quo method of comprehensive diagnosis for these rare disorders. Currently, there are limited options in the market when it comes to quality software that can scale to this size of data and handle variant processing and evaluation in a timely fashion. Fortunately, Golden Helix has sought to set the market standard for top-quality NGS analysis with our bioinformatic software VarSeq. The focus of this webcast will be to explore example workflows tailored for rare disorders and elaborate on how best to expedite the NGS pipeline process with our command-line tool VSPipeline.
During the webcast, we will address the following:
Customizing clinically validated NGS workflows with VarSeq for both single sample and trios
Demonstrating the automation of ACMG-based guideline review in the VSClinical variant interpretation hub and rendering of customized clinical reports
Expediting the NGS workflow via Golden Helix command-line tool VSPipeline
We look forward to you joining us for our presentation, where we can demonstrate the value of our products when building your next-gen workflows. Ultimately, we wish to diminish the intimidation of genome workflow design and leave our future customers feeling confident that there is capable software to suit their needs.
Bick D, Jones M, Taylor SL, et al. Case for genome sequencing in infants and children with rare, undiagnosed or genetic disease. J Med Genet 2019; 56:783-791.
Owen M, Lefebvre S, Hansen C, et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13: 4057. https://doi.org/10.1038/s41467-022-31446-6
User perspective for somatic variant analysis in VSClinical AMP
Somatic analysis is a complex and precise process that is constantly evolving. As the volume of available data and the accessibility of sequencing technology increase, so too does the value of a versatile, well-vetted, and efficient workflow solution. In this webcast, we will take a deep dive into the current state of our AMP interpretation software and explore various ways to optimize workflows. For anyone from grizzled VarSeq veterans to those seeing our software for the first time and labs of any size, we will provide a practical overview of our somatic analysis capabilities and how those capabilities scale with improving technology.
Throughout this webcast we will be discussing the following:
- Universal principles of somatic workflows, providing baseline recommendations
- Specific tumor-normal and somatic-only use cases
- VSClinical AMP interpretation hub and some variants of interest
- Opportunities for automation and how to decrease time to report for increased throughput
Join us as we show off the versatility and scalability of our AMP interpretation capabilities!
Maximizing Profitability in your NGS Testing Lab
The automation of clinical NGS workflows provides a number of important benefits for labs. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In turn, these benefits create higher profitability from a P&L perspective.
Golden Helix software is designed to meet these needs by automating the full analysis workflow from sequencer to clinical report on a fixed annual subscription model. We are looking forward to discussing the best practices of maximizing profitability in your NGS testing lab and how Golden Helix supports these efforts.
Join us in this webinar as we cover how to develop repeatable cancer and germline interpretation workflows that scale from panels to whole exomes and genomes.
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Introducing VarSeq Dx as a Medical Device in the European Union
Introducing VarSeq Dx as a Medical Device in the European Union
Introducing VSPGx: Pharmacogenomics Testing in VarSeq
Introducing VSPGx: Pharmacogenomics Testing in VarSeq
Analyzing Performance of the Twist Exome with CNV Backbone at Various Probe D...
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From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short ...
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Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
Enhance Genomic Research with Polygenic Risk Score Calculations in SVS
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
VarSeq 2.5.0: VSClinical AMP Workflow from the User Perspective
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
VarSeq 2.4.0: Structural Variants and Advanced Automation in VSClinical ACMG
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeq
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with ...
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0
VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation
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
VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP
Single Sample and Family Based Genome Analysis With VarSeq
Single Sample and Family Based Genome Analysis With VarSeq
User perspective for somatic variant analysis in VSClinical AMP
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Custom Family Workflows
- 1. Custom Family Workflows May 11th, 2016 Jami Bartole Senior Field Application Scientist
- 2. Use the Questions pane in your GoToWebinar window Questions during the presentation
- 3. Agenda Quad Workflow Two Affected Siblings Workflow 2 3 4 Trio plus Unaffected Sibling Workflow Overview of Golden Helix and VarSeq1
- 4. Golden Helix – Who We Are Golden Helix is a global bioinformatics company founded in 1998. We are cited in over 1000 peer-reviewed publications
- 5. Over 350 customers globally
- 6. Golden Helix – Who We Are When you choose a Golden Helix solution, you get more than just software REPUTATION TRUST EXPERIENCE INDUSTRY FOCUS THOUGHT LEADERSHIP COMMUNITY TRAINING SUPPORT RESPONSIVENESS TRANSPARENCY INNOVATION and SPEED CUSTOMIZATIONS
- 7. VarSeq Suite Organize Samples into Projects Projects as Variant Frequency Annotations Centralized VSReports Hosting Scalable Technology Multiple Interfaces VCF Import Variant and Gene Annotations Various Algorithms Filter Variants Flag Variants Customized Reports (HTML, PDF, etc.) VSReports VSPipeline Automate Workflow High-Throughput Analysis
- 8. Sample Data for our Custom Family Family was simulated from the 1000 Genomes Vietnamese (KHV) related samples using the VN049 trio and the VN056 sibling pair. Family formed with two affected daughters and one unaffected son. BAM files and VCF files available for all five samples - Downloaded Illumina Exome Alignment BAM files from the 1000 Genomes Phase 3 Project - GATK was used for variant calling
- 9. Phenotype for the Affected Samples • HED may be inherited in one of 3 patterns: X-linked recessive (95%), autosomal recessive or autosomal dominant (5%) • Changes or mutations in the EDA, EDAR, EDARADD, and WNT10A genes are most commonly associated with HED. These genes tell the body to make proteins that are needed early in life (before birth and shortly after) for the normal development of sweat glands, teeth, hair, skin, and other mucous glands. • These four genes account for 90% of hypohidrotic/anhidrotic ectodermal dysplasia cases References: • http://nfed.org/index.php/about_ed/hypohidrotic-ectodermal-dysplasia • http://rarediseases.org/rare-diseases/hypohidrotic-ectodermal-dysplasia/#affected-populations • http://www.ncbi.nlm.nih.gov/pubmed/17354266
- 10. Agenda Quad Workflow Two Affected Siblings Workflow 2 3 4 Trio plus Unaffected Sibling Workflow Overview of Golden Helix and VarSeq1
- 11. Quad Analysis Workflow Mother, Father and Two Affected Siblings • Using Variant Sets to look at the combined set of de Novo candidate variants between the two daughters. • Using a custom Filter Chain to identify common variants between the two affected daughters. • de Novo Candidates • Compound Heterozygous Candidates • Prioritize variants using PhoRank to be included in a custom Clinical Report!
- 13. Agenda Quad Workflow Two Affected Siblings Workflow 2 3 4 Trio plus Unaffected Sibling Workflow Overview of Golden Helix and VarSeq1
- 14. Trio + Unaffected Sibling Workflow Mother, Father, Affected Daughter and Unaffected Son • Custom template creating separate sample specific filter cards for each child • Using Count Allele algorithm to restrict the number of heterozygous calls for each variant • Inverting filter cards to remove variants present in unaffected sibling
- 16. Agenda Quad Workflow Two Affected Siblings Workflow 2 3 4 Trio plus Unaffected Sibling Workflow Overview of Golden Helix and VarSeq1
- 17. Affected Sibling Pair Workflow Two Affected Daughters • Using Genotype Zygosity Algorithm to find shared “de Novo” candidate variants • Using Count Alleles by Gene Algorithm to find Shared “Compound Het” candidate regions • Using Custom template to set sample specific filters • Prioritize variants using CADD annotation (Coming SOON to a VarSeq near you!) • CADD provides pre-computed scores for all possible 8.6 billion single-letter substitutions, as well as 20 million previously observed indels. For novel indels, the score is estimated using scores from flanking or deleted bases
- 19. Summary • Quad Workflow • Used Variant Sets to create a multi-sample VCF file, which includes de Novo Candidate variants present in either affected sample • Setting sample specific filter cards created a custom filter chain for de Novo and Compound Heterozygous Gene candidates in common between the two affected samples • Prioritized variants using PhoRank to be added to customized Clinical Report. • Trio plus Unaffected Sibling Workflow • Used the ability to invert filter cards to exclude de Novo variants in the unaffected sample • Used Count Alleles algorithm to restrict the number of heterozygous calls for each variant position, which excluded hets present in the unaffected sample • Two Affected Siblings Workflow • Used Genotype Zygosity to identify possible de Novo variants • Used Count Alleles by Gene to identify possible Compound Het genes • Looked at prioritizing variants based on new CADD annotation.
- 20. Questions or more info: Email info@goldenhelix.com Request an evaluation of the software at www.goldenhelix.com