Reading scientific articles that our customers have recently published is one of my favorite things here at Golden Helix. It is fascinating to learn about the research and to see the various ways our software gets put to the test.Since we are rolling out our most extensive VarSeq update yet, I thought it would be a great time to look… Read more »
Curious about how coverage statistics can be used in conjunction with VarSeq? Evaluating the coverage over target regions or whole genomes is essential whether you are working with variant or CNV analysis. VarSeq has had the capability to compute sample level coverage statistics for some time now, but in the 2.2.2 release of VarSeq, there are some new features that… Read more »
Webcast Recap In the recent webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”, Gabe and I took viewers through an evaluation with CNVs and SNVs according to the ACMG Guidelines where we generated and customized a clinical report. Along the way, we highlighted many new features that will soon be available in the upcoming VarSeq release…. Read more »
In this blog post, I will be analyzing a loss-of-function splice variant in MTHFR using VarSeq. In the search for clinically relevant variants contributing to rare disorders, efficient filtering strategies are an important step in eliminating disinteresting variants. However, any applied filters must also ensure no interesting variants inadvertently get filtered out. Golden Helix provides the tools to complete this… Read more »
In our previous webcast, Evaluating CNVs with VSClinical’s New ACMG Guidelines, we focused on a CNV deletion (12:27715515-29628122×1) in which the patient had a known disorder called Brachydactyly type E. The CNV was isolated using our VS-CNV caller and applied to the ACMG CNV guidelines using the intuitive steps of VSClinical. If you missed the webcast, you can watch the… Read more »
In a recent webcast, users were exposed to some new features upcoming in the next release of VarSeq. In this update, we will use an example de Novo CNV in a cardiomyopathy panel in VarSeq. There is a long list of new tools and polishes to the software but one major upgrade is the inclusion of the ACMG and ClinGen… Read more »
Typically, researchers are looking for rare variants in their next generation sequencing datasets. However, most of the nonsynonymous variants have unknown significance because there is an inherent difficulty in validating large numbers of rare variants or even detecting rare variants with high statistical power. In lieu of this issue, computational tools are needed as they accurately predict the pathogenicity of… Read more »
A common discussion with our customers includes the challenges with the tertiary stage of analyzing next-gen sequencing data. This is the stage where all data from gene panels, exome, or whole genome scale pass through filters to quickly isolate the clinically relevant variant contributing to a patient disorder. Golden Helix has recognized these challenges in the scale of data and… Read more »
In this blog update, I’ll be walking you through some of the advanced plotting capabilities with GenomeBrowse. The strategy with any next-gen sequencing analysis is to filter down to interesting variants for either research or clinical conclusion. Golden Helix produces powerful software specifically tailored for this efficient and comprehensive search for interesting and clinically relevant variants. One additional advantage of… Read more »
In our recent webcast announcing the upcoming release of VarSeq VSClinical and the implementation of the ACMG guidelines for NGS CNVs, we had a number of live questions we didn’t get a chance to cover at the end of the presentation. I will follow up on those questions in this blog post. But first, if you didn’t get a chance to join us for… Read more »
In the 1990s the genetic industry voiced a request for a variant catalog that incorporates associated variant information such as phenotypic and metabolic pathways. The call was answered by NCBI, which created dbSNP; dbSNP became publicly available in 1998 and around 1.5 million variants. Fast forward to the present and dbSNP now contains over 2 billion SNPs spanning human, rat,… Read more »
The potential of genetic testing to impact a patient’s life has been greatly accelerated by the sharing of variant interpretations done by clinical labs in public repositories such as ClinVar. This is not an inevitable outcome, but the persistent work and advocacy of people like Dr. Heidi Rehm and organizations like ClinGen. We recently participated in a survey and vetting… Read more »
SVS 8.9.0 was released on August 19th and features a new GBLUP by Bin feature and a new utility to find the LD scores of markers and categorize them into bins, along with several mixed-model upgrades and many other upgrades, fixes, and polishes. The two new features LD Score Computation and Binning and Compute GBLUP Using Bins, while they can… Read more »
Our software solutions and partners have brought dramatic improvements to the secondary and tertiary analysis stages of variant evaluation. Regarding secondary analysis, we’ve discussed increased efficiencies in speed and overall accuracy in the variant calling process with Sentieon. On the tertiary side, we have explored numerous workflows in VarSeq highlighting filtration to clinically relevant variants, as well as the automated… Read more »
The detection and interpretation of Copy Number Variants (CNVs) is vital for the clinical evaluation of individuals with a wide range of disorders. Golden Helix has remained at the forefront of CNVs in Next-Gen Sequencing (NGS) data since 2016 with the release of VS-CNV, our solution that allows you to both detect and analyze CNVs directly from NGS data. Earlier… Read more »
It doesn’t take much effort to find articles discussing the value of Next-Generation Sequencing (NGS). There is a consistent tone amongst authors that implementing NGS pipelines are critical for clinical efficiency in both hereditary disorders and somatic. However, NGS strategies do not come without their own challenges. Challenges include not only the detection and calling of high quality/probability variants from… Read more »
In the search for disease causing mutations it is important to determine if the variant has been previously observed in humans and at what frequency. With the advent of increasing genomic information, there is now a variety of different databases and annotation sources that can be utilized. For some, this could be a tedious task that leads only to implementing… Read more »
The world has been making a shift to use GRCh38 human genome reference coordinates, but the transition has not been fast. Many of the mainstay human catalog projects are changing to use native GRCh38 catalogs, or are remapping their current data to GRCh38 coordinates. While this seems to be the advancing goal, it is leaving researchers and analysts with the… Read more »
Thank you to everyone who joined our webcast, “Whole Genome Trait Association in SVS.” If you missed the live event and are interested in knowing what we talked about, you may access the recorded event below: Our Live Q&A generated a lot of great questions. Unfortunately, we were unable to answer them all, but we have compiled some of the… Read more »
Introduction: Malignant Rhabdoid tumors (MRT) are among the most aggressive and lethal forms of infant and child cancer (1). These tumors are characterized by an unusual combination of mixed cellular elements similar to but not typical of teratomas and can originate at any anatomic location. When MRTs are present in the brain, they are called atypical teratoid/rhabdoid tumors (AT/RT), which… Read more »
