Tag Archives: VSClinical

Limited-Time Offer for VSClinical’s Cancer Add-On

         June 27, 2019

We are upgrading all VSClinical +Cancer Add-On purchases to a 15-months license! One license of VSClinical +AMP Guidelines – $17,995* Additional Users: $8,995* The individualized nature of tumors requires genomic testing for providing the best outcomes for patients. Next-Gen Sequencing enables the detection of small mutations, copy number changes, and common fusions affordably and with high precision. However, the interpretation… Read more »

Clinical Variant Analysis for Cancer: Part IV

         June 25, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Somatic variants can manifest in different ways: Single Nucleotide Variants Indels Fusions and Copy Number Variations There is a difference between the interpretation of germline and somatic variants. The former is exclusively focused on establishing the level of pathogenicity vis a vis a particular disease. In contrast… Read more »

Clinical Variant Analysis for Cancer: Part III

         June 18, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants As described in my eBook “Genetic Testing for Cancer,” any bioinformatic pipeline for cancer ultimately calls variants based on the aligned reads that the sequencer generated. Variant calling is the process of reviewing a sequence alignment, typically in the form of a BAM file, to identify loci… Read more »

Clinical Variant Analysis for Cancer: Part II

         June 13, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Analogous to the ACMG guidelines for germline mutations, the Association for Molecular Pathologists (AMP) has issued guidelines to assess and report on somatic variants. The key paper in this area was published by Li et. al (2017) with the title “Standards and Guidelines for the Interpretation and… Read more »

Clinical Variant Analysis for Cancer: Part I

         June 11, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Precision Medicine uses genetic information from individual patients. This may include the following areas: Diagnosis Treatment Prevention Specifically, in the cancer space, data derived from Next-Gen Sequencing (NGS) is used to diagnose and prognose diseases, select a targeted therapy and potentially evaluate the suitability of a patient… Read more »

New eBook Release: Clinical Variant Analysis for Cancer

         June 6, 2019

Applying AMP Guidelines to Analyze Somatic Variants Today, I am thrilled to share with you the launch of a brand new eBook titled “Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants”. We would happy to send you a complimentary copy which can be requested on our website here. The clinical utilization of Next-Gen Sequencing data… Read more »

Variant Interpretation with VSClinical: Evaluation of an X-linked recessive mutation

         May 21, 2019

Overview VSClinical enables users to evaluate variants according to the ACMG guidelines in a high-throughput fashion and obtain consistent results and accurate variant interpretations. This feature is tightly integrated into our VarSeq platform as well, and when paired together, users can evaluate NGS data and obtain clinical reports all in one suite. Coupled with the ability to find novel or… Read more »

VSClinical Best Practice Workflows: Part III

         November 20, 2018

This blog will conclude our VSClinical Best Practice Workflow series and focuses on one of our new reports: VSClinical ACMG Gene Panel Template. This template is valuable because it automatically enters your variant interpretation from the ACMG Guidelines into the report and eliminates the need for manual submission. I would like to explain how to properly implement this report into… Read more »

VSClinical Best Practice Workflows: Part II

         November 15, 2018

In part one of this series, we discussed how the ACMG Classifier can be implemented in your filter chain to support a best practice workflow. To continue our discussion on best practices of VSClinical, this blog will shed light on other attributes of VSClinical that can add support to your evaluation. Specifically, we will explore how VSClinical can help users… Read more »

VSClinical Best Practice Workflows: Part I

         November 13, 2018

VSClinical is our most recent product that allows users to evaluate variants according to the ACMG guidelines. As with any tertiary analysis, there is a need to implement best practices into your workflow and using VSClinical for the ACMG guidelines is no exception. That said, we have put together a Best Practices Blog Series, with the purpose of discussing some… Read more »

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 »