Our previous webcast demonstrated some of the new functionalities of VSClinical, including the ability to add ACMG frequency sources for the ACMG BA1, BS1, and PM2 criteria. This new feature was spurred by the feedback from our users, which requested supporting frequency tracks other than gnomAD Exomes and 1kG Phase3. Now, users can implement population catalogs to VSClinical such as… Read more »
In the webcast, Evaluation of Copy Number Variants with VSClinical’s New ACMG Guideline Workflow, we discussed how VSClinical implements Section 4 of the ACMG guidelines. Specifically, we focused on integrating literature and publications to assess the pathogenicity of a CNV event when there was a lack of dosage sensitivity information. One of the primary pieces of evidence for evaluating genes… Read more »
Golden Helix is excited to release an upcoming VSClinical feature that allows users to analyze next-generation sequencing (NGS) CNV event reporting with ACMG guidelines. This feature will be the first in the NGS workspace to allow this capability and if you are curious about the functionalities you can get a sneak peek by looking at some of our most recent… Read more »
Our previous webcast from VP Gabe Rudy in September exposed us to some fundamentals of this years’ updated Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). This recent webcast was dedicated to breaking down these new guidelines… Read more »
VSClinical is a feature to evaluate clinically relevant variants according to the ACMG or AMP guidelines. This feature can also be used to identify if a variant has been observed previously or evaluate a manually inserted variant. Take, for example, the scenario where a colleague is interested to see if you have seen any variants associated with Bechet syndrome, which… 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 »
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 »
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 »
Golden Helix software provides huge analytic gain in handling large-scale genomic data. For example, a number of VarSeq users run cohort projects of whole genome level data processing hundreds of millions of variants at a time. However, many of our users are running gene panel level data for custom panels related to cancer (both hereditary and somatic), autism, cardiac, and… 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 »
Abstract Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses a variety of metrics to classify a given somatic mutation… Read more »
Our Support Team curates a variety of tutorials to help orient new users to the capabilities of VarSeq. We are happy to announce the team’s new release of the trio tutorial that places emphasis on using the ACMG guidelines. This tutorial gives insight into the proper setup of pedigree structure as well as detailed descriptions of the filter containers and… Read more »
Customizing VSClinical ACMG Guidelines Workflow Part 2 In the first part of this series, we covered how VarSeq provides customization of the clinical analysis workflow process. VSClinical’s various customization parameters within the ACMG Guidelines workflow includes the choice of how the internal knowledge base of previous variant interpretations are stored and what considerations go into this choice. In this blog, we… Read more »
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… Read more »
Clinical labs offer a unique and sophisticated product that is performed repeatedly with high standards of quality. VarSeq was developed to provide labs with the customization required for clinical genetic tests in a repeatable workflow. On top of this, VSClinical offers additional parameters and choices that can be made when designing the test workflow. In this blog series, we will… Read more »
Our tutorials are a popular resource for prospective users. We have added a tutorial to help introduce customers to the ease and utility of the ACMG Guidelines incorporated in VSClinical. The ACMG Guidelines are a collection of 33 criteria that are used to determine a variant’s level of pathogenicity. VSClinical and VarSeq make it easy for users to sort and… 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 »
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… Read more »
Before examining the clinical evidence associated with a specific mutation, a clinician must establish that the variant is likely to be a driver mutation which generates functional changes that enhance tumor cell proliferation. Our recent blog series “Following the AMP Guidelines with VSClinical” briefly mentioned how the oncogenicity scoring system in VSClinical could be used to automate and assist the… Read more »
VSClinical users can interpret and report genomic mutations in cancer following the AMP guidelines which we’re demonstrating in this “Following the AMP Guidelines with VSClinical” blog series. Part I introduced the hands-on analysis steps involved in creating a high-quality clinical report for targeted Next-Generation Sequencing (NGS) assays. We reviewed sample and variant quality, including the depth of coverage over the target regions by the sequencing performed for each sample. Now, we are ready to… Read more »
