Tag Archives: VSClinical

VSClinical Updates & a Tour of Cancer Annotations – Webcast Q&A

         November 8, 2018

This webcast generated a lot of great questions about the content covered in the video above. I have summarized our Q&A session below and included some questions I didn’t have time to answer during the live event. If you have any further questions, reach out to us at info@goldenhelix.com! Q: Can I upload my existing classifications into a consortium source?… Read more »

VSClinical and VSWarehouse – Leveraging Consistent Clinical Interpretations

         October 22, 2018
VSWarehouse Updates

Part 1 of this blog series was focused on new capabilities in Warehouse to store your CNV results. We explored some approaches of how to utilize assessment catalogs of cohort and known pathogenic events. What makes Warehouse so useful in this application is that the catalog is accessed from one central location and ensures every user is leveraging the same… Read more »

VSClinical: The details you should know

         July 19, 2018
ClinVar

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 »

Functional Predictions & Conservation Scores in VSClinical

         May 17, 2018

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 »

Clinical Variant Interpretation: Part VII

         May 3, 2018
VSClinical algorithm

Automating the ACMG Guidelines and Providing Scoring Recommendations As we discussed in our recent webcast on VSClinical, the process of scoring the ACMG guidelines requires evaluating evidence for the connection between a variant and the disorder or condition being evaluated by the genetic test for an individual. These lines of evidence cover clinical presentation, gene function, bioinformatic annotations and in-silico… Read more »

Clinical Variant Interpretation: Part VI

         May 1, 2018
VSClinical algorithm

Functional Predictions and Conservation Scores in VSClinical Several algorithms have been developed to predict the impact of amino acid substitutions on protein function and quantify conservation of nucleotide positions. These methods provide vital supporting evidence to clinicians when interpreting variants in accordance with the ACMG guidelines. The two most popular functional prediction algorithms are SIFT and PolyPhen2, while the most… Read more »

Clinical Variant Interpretation: Part V

         April 26, 2018
VSClinical algorithm

Revisiting the Five Splice Site Algorithms used in Clinical Genetics Interpretation of variants in accordance with the ACMG guidelines requires that variants near canonical splice boundaries be evaluated for their potential to disrupt gene splicing [1]. The five most common tools for splice site detection are NNSplice, MaxEntScan, GeneSplicer, HumanSplicingFinder, and SpliceSiteFinder-like. Because these algorithms have been made easily accessible… Read more »

Clinical Variant Interpretation: Part IV

         April 24, 2018
VSClinical algorithm

In the last installment of this series, I covered the basics of variant interpretation and how it fits into the genomic testing process. Now we can cover in more detail how VSClinical works, what algorithms and annotation sources power the recommendations and how the ACMG criteria are organized into useful categories. VSClinical is built to make the process of evaluating… Read more »

VSClinical Webcast Q&A

         April 20, 2018

This week we launched VSClincial with our first webcast to show our powerful new way to perform variant interpretation following the ACMG guidelines. Our audience asked a lot of great questions on the new product and I’d like to highlight a few here. Can VSClinical run on a laptop and/or a locked down environment? Like all of Golden Helix products, you have… Read more »

Clinical Variant Interpretation: Part III

         April 19, 2018
VCF file format

Yesterday we launched VSClincial with our first webcast in what will be a series about this powerful new way to perform variant interpretation following the ACMG guidelines. In this post, I wanted to cover the motivation for VSClinical and how we curated and presented the 33 criteria from the ACMG Guidelines into an intuitive workflow with various bioinformatic evidence and… Read more »

Clinical Variant Interpretation Based on ACMG Guidelines – Part II

         April 17, 2018
VarSeq annotations

We just came back from ACMG in North Carolina where we launched our new product VSClinical. The reception has been terrific and our booth has never been as frequented. We had record level visitors and demo presentations. So, what is all that buzz about this new product? Why do people care so much and how does it help a clinical… Read more »

Clinical Variant Interpretation Based on ACMG Guidelines – Part I

         April 9, 2018
VSClinical

The clinical interpretation of variants is time-consuming and requires attention to details. Clinicians are being asked to thoroughly review any variants that could potentially cause disease. There are guidelines for the interpretation of variants relating to hereditary risk, germline diagnostics, and molecular oncology panels, such as those issued by the American College of Medical Genetics (ACMG), which are nationally and internationally… Read more »