Although VarSeq is intentionally designed to be a clinical NGS pipeline tool able to run a handful or even single samples through, we have many users who run large cohort style studies with the tool as well. One common use is to compare case/control data to isolate variants shared among affected individuals and exclude those in unaffected. One incredibly powerful… Read more »
Since the initial release of the copy number variant algorithms in VarSeq, our team has created a variety of content to help users get started with building their copy number variant projects. In our webcast library, you can find a few of our recent webcasts in 2019 covering CNV workflows and validation: Clinical Validation of Copy Number Variants Using the… Read more »
As many of our users know, VarSeq comes shipped with various project templates that are designed to give users a baseline workflow to get started with their projects. These templates are tailored for various applications including tumor-normal, trios, cancer and hereditary gene panels, and ACMG Guidelines workflows. The templates contain application-specific annotation sources and algorithms that will automatically load into… Read more »
We have recently added a tutorial to help introduce customers to the ease and utility of the AMP Guidelines incorporated in VarSeq’s VSClinical package. The AMP Guidelines allow users to sort through available clinical evidence in a streamlined fashion to arrive at final classification and interpretation and then transfer that information into a clinical report. And the AMP Guidelines also… Read more »
VarSeq 2.2.0 was released today and this a stable release full of upgrades and polishes. Some of the newer features include the ability to store and include AMP Cancer assessment catalogs on VSWarehouse, quicker accessibility to common annotations plotted in GenomeBrowse, and the addition of all of our standard templates for the GRCh38 genome assembly. Many of the polishes were… Read more »
When using VarSeq; annotations, application settings, and assessment catalogs are all stored locally. Sometimes these resources can grow to large space grabbing directories, causing you to either purchase additional storage devices or getting rid of previously downloaded resources you might need down the road. But there’s hope! You can set where you want all of your data stored to be… Read more »
Smoothing Hurdles into Speed Bumps when creating Annotation Sources Although most researchers assume that getting the pile of VCF sequence files is the largest hurdle in moving towards an analysis, there still exists the looming step of normalizing the variant calls in annotation sources to make variant comparison easier. In this ever-refining field of study, VarSeq continually works to increase… Read more »
In the previous two articles, we explored the different steps of a clinical workflow. The first post covered the automated analysis that creates a VarSeq project. While the second post covered the interpretation steps and generation of a clinical report. These posts illustrated the ease with which these complex tasks can be carried out. Today we’ll dig a little bit… Read more »
In the previous blog post, we covered the automated steps to create a VarSeq project. Today we will examine the active analysis steps. These are the steps that require human interpretation to analyze the clinically relevant variants. A lab tech can take the first pass at the output in the generated VarSeq project. They can perform the quality control and… Read more »
Automating a clinical workflow creates a stable and repeatable clinical analysis. Automation reduces the potential to introduce human error, helps in regulatory compliance, and improves the precision of the clinical results. It is important to know that if you run a sample through your clinical pipeline, you are going to get the same results today as you will in 6… Read more »
The Department of Clinical Genetics at Odense University Hospital offers a variety of genetic analyses for families of syndromic children and other inherited conditions, averaging 4,000 genetic analyses per year. In 2016, the lab decided to introduce whole exome sequencing to their offerings to take over a lot of the work they were currently conducting via gene panel analysis. They… Read more »
The Beginning of Your Tertiary Analysis VarSeq is designed to be your NGS tertiary analysis solution providing users simple but in-depth means of exploring gene panel, exome, and whole genome variants. For those not accustomed to the VarSeq software, the main import file for variant analysis is the VCF. Those who are familiar with the VCF know that there can… Read more »
The PhoRank tool in VarSeq is further explored in this post by looking at the sample-specific capability. VarSeq PhoRank Part: 1 Variant Phorank Gene Ranking showed how the PhoRank algorithm could be applied to all the variants in a VarSeq project, regardless of the number of (or difference in) samples. There is another PhoRank algorithm in VarSeq that allows the… Read more »
One of the main goals of clinical genomic labs is to identify problematic variants in affected individuals. One tool to assist in this search is the phenotype driven variant ontological re-ranking tool in VarSeq called PhoRank. A common situation facing clinicians is sorting through thousands of variants provided by an individual’s exome data (or possibly the individual’s nuclear family exome… Read more »
We love when our viewers send questions in during the webcast but unfortunately we can’t answer all of them during the time allotted! If you asked a question see below for answers, or if after viewing, you have any questions that weren’t asked, please feel free to send those over to support@goldenhelix.com. Does this work for FFPE derived DNA or ctDNA?… Read more »
2017 was a busy year regarding the development of our CNV tools. Since the release of the CNV caller, we have produced quite a bit of content tailored to assist our users with getting started. Here are some links: Robarts Research Institute CNV analysis on patients with familial hypercholesterolemia CNV annotations Common CNV questions CNV calling with shallow whole genome… Read more »
The recent release of VSClinical gives users the ability to evaluate variants based on the 33 criteria according to the American College of Medical Genetic and Genomics (ACMG) guidelines. This feature leverages a variety of variant sequencing evidence including population data, functional data, and computational predictions while providing rich visualizations and auto recommendations to help answer challenging criteria. This highly… Read more »
In our previous webcast, we discussed the splice site algorithms for clinical genomics within VSClinical. We took it a step further in yesterday’s webcast and looked at the functional predictions and conservation scores. We had a great turnout for this event with lots of great questions from the attendees. I’d like to recap our Q&A for anyone else who might… Read more »
Ready to take your analysis to the next level? Our Small-Lab VarSeq PowerPack enables users to move their analysis from FASTQ to clinical reporting through one streamlined pipeline. Here’s what’s included: VarSeq VarSeq is an intuitive, integrated software solution for tertiary analysis. With VarSeq you can automate your workflows and analyze variants for gene panels, exomes, and whole genomes. VS-CNV… Read more »
I hope you were able to join us for last week’s webcast where we invited first-place abstract competition winner Michael Iacocca to present on his submission “Using NGS to detect CNVs in familial hypercholesterolemia”. Today, I’d like to announce our second-place winner, Nicole Weaver, Clinical Geneticist at Cincinnati Children’s Hospital. Nicole adopted VarSeq into her research pipeline in 2015 and… Read more »
