Tag Archives: ACMG guidelines

Importing External Assessment Catalogs for use in VSClinical ACMG and VSClinical AMP

         July 13, 2023

When doing clinical variant analysis, it is often essential to keep track of the variants that are encountered in each sample, their pathogenic or oncogenic classifications, which individual created or saved an interpretation, and when. For this purpose, VarSeq prompts VSClinical users to create default assessment catalogs in which to store variants and other events. However, we are aware that… Read more »

ESHG 2023 Insights

         June 22, 2023

We had a great time in Glasgow, connecting with many current customers and prospective customers at our booth. The in-depth conversations were engaging and offered beneficial insights for our team and the attendees. Thank you all for visiting our booth for a demo as well as attending our Corporate Satellite talk. Below are a few themes that we noticed throughout… Read more »

VarSeq 2.4.0 Has Been Released!

         May 24, 2023

Greetings VarSeq users! VarSeq 2.4.0 has officially been released. VarSeq 2.4.0 is a significant release that focuses on enhancing the VSClinical ACMG workflow by introducing new features and noteworthy improvements. The major highlights of the release are: 1. Welcoming structural variant support to the VSClinical ACMG workflow 2. ACMG workflow automation has been enhanced via the application of evaluation scripts… Read more »

ACMG STRIKES BACK

         May 4, 2023

Use the force of evaluation scripts to automate and customize your VSClinical ACMG workflow in VarSeq 2.4.0. VarSeq 2.3.0 came packed with new features! Most notably, VarSeq variant analysis expanded to support the import and annotation of structural variant files, and the AMP cancer workflow in VSClinical gained new functionality with the addition of evaluation scripts which help automate and… Read more »

ACMG 2023 Insights: Exploring Whole Exome Sequencing, Hereditary Cancer, and Prenatal Genetics

         March 28, 2023

Our team at Golden Helix remains committed to advancing genomics and personalized medicine. We actively participate in industry conferences to stay current with the latest developments, such as the recent ACMG 2023 in Salt Lake City, Utah. This event facilitated valuable insights and discussions on several topics. Three key areas of focus included:   Whole Exome Sequencing: Whole Exome Sequencing (WES)… Read more »

We Are Headed to ACMG 2023!

         March 7, 2023

Discover the Latest Advances in Variant Classification and Interpretation Tools at Golden Helix’s Booth at ACMG 2023 We are excited to announce that Golden Helix will be attending the American College of Medical Genetics and Genomics (ACMG) 2023 conference in March! We can’t wait to connect with leading healthcare professionals and researchers in the field of genetics at this premier… Read more »

Maximizing Cancer Care with Golden Helix CancerKB 2.0: Unveiling the Latest in Precision Medicine

         January 26, 2023
Maximizing Cancer Care with Golden Helix CancerKB 2.0 Unveiling the Latest in Precision Medicine icon

Our recent webcast, Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with Golden Helix CancerKB 2.0, was an opportunity to unveil Golden Helix CancerKB v2.0. Our latest VarSeq release was designed to address the changing landscape of cancer genomics, and in this webcast, we discussed the application of our very own Golden Helix CancerKB in the context of… Read more »

Webcast Recap: Somatic Variant Analysis in VarSeq 2.3.0

         December 22, 2022
Webcast Recap: Somatic Variant Analysis in VarSeq 2.3.0

Our FAS team would like to thank everyone who attended our December 2022 webcast, A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0. This webcast allowed three members of our FAS team to give their unique insights concerning the improvements to our new VarSeq 2.3.0 release, which will be recapped here. Starting with template creation, our Technical Field Application Scientist,… Read more »

Webcast Recap: VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation

         November 22, 2022

Thank you to everyone who joined us for our webcast on the upcoming VarSeq features supporting the full spectrum of genomic variation! Traditionally, NGS cancer testing started with small gene panels that looked at a small set of the most common genes to identify small mutations, such as BRAF V600E. However, there are many classes of mutation that cannot be… Read more »

ACMG Auto Classifier: Variant Site or Sample Classifier?

         November 1, 2022

The ACMG classification guidelines for variant pathogenicity are as ubiquitous as they are complicated to implement. They play a consistent and evolving role in the standard workflows of many experts in the next-generation sequencing field, both in the clinical and research space. Furthermore, they can be effectively applied in both somatic and germline workflows. Hence, consistent and auditable methods for… Read more »

Customer Publications – October 2022

         October 31, 2022

The month of VarSeq must be October. This month we saw incredible research and clinical application being utilized with the VarSeq suite. Whole exome sequencing and variant filtering and annotation, CNV calling for oncology research, and pathogenicity classification using the ACMG guidelines. VarSeq was able to be a front-runner this month, showing the full range of capabilities. Germline RB1 Mutation… Read more »

Streamlining Variant Analysis for Large Genetic Cohorts: Part 1

         September 27, 2022

Large genetic cohorts require substantial effort to analyze. Genetic researchers are increasingly turning to whole exome and whole genome sequencing analyses for their clinical diagnostics and research. However, with that approach comes the challenge of making sense of these massive datasets. This is especially challenging when looking for tools that can streamline variant analysis for large genetic cohorts and include… Read more »

Impressions from ACMG 2022

         March 31, 2022

This year’s ACMG conference in Nashville, TN, marked a positive turning point after two years of virtual meetings in our community. The conference was well attended and found an outstanding balance between on-site meetings and virtual talks. From the Golden Helix perspective, it was wonderful to connect with customers and partners at the event. We were very humbled by the… Read more »

Reporting Secondary Germline Variants in VSClinical AMP

         March 2, 2022
Reporting Secondary Germline Variants in VSClinical AMP

Tumor profiling via next generation sequencing (NGS) often reveals secondary germline variants that may constitute important incidental findings. In May 2021, the American College of Medical Genetics and Genomics (ACMG) released an updated policy statement for reporting incidental findings in exome and genome sequencing data along with a corresponding list of genes. These recommendations state that laboratories should report pathogenic… Read more »

Integrating Custom Gene Panels for Variant Annotations Q&A Follow Up

         February 16, 2022
Integrating Custom Gene Panels for Variant Annotations

Thanks to all those who attended the recent webcast by Dr. Rana Smalling, “Integrating Custom Gene Panels for Variant Annotations”. If you were unable to attend or would like to recap, here is a link to watch the broadcast. We covered a lot of content regarding virtual gene panels, and there were several questions submitted during our Q&A session that… Read more »

Using ACMG Secondary Findings v3.0 List in VarSeq and VSClinical

         December 21, 2021

As the number of genes on a gene panel increases, there is the possibility of picking up variants of medical significance that are not related to the primary indication for the test. Especially with large gene panels, exomes, and genomes, it is medically and ethically important to report variants that may be actionable to the patient. These include variants implicating… Read more »

VarSeq 2.2.4 Release

         November 30, 2021
varseq2.2.4

We are very excited to announce that just last week, we released VarSeq 2.2.4! In the past few months, we have been building the excitement for the 2.2.4 version of VarSeq with several webcasts in which we describe some of the headlining features in detail such as the new support for Gene Panels and Gene Lists, PhoRank Clinical, and Customized… Read more »

Breaking Down ACMG CNV Guidelines in VSClinical

         November 25, 2021

In February 2020, the American College of Medical Genetics (ACMG) and the Clinical Genome Resource (ClinGen) published a joint consensus on standards for the interpretation and reporting of copy number variants (CNVs) ranging from large CNVs spanning multiple genes to small intragenic events1. The guidelines consist of over 80 different criteria which are arranged into five distinct sections. These extensive… Read more »

Reviewing Clinical Studies for Novel Splice Variants in VSClinical

         October 12, 2021
DNA spliced site

In order to thoroughly assess a variant’s pathogenicity, it is important to take into account the variant’s effect on splicing. While the interpretation of variants that disrupt the pairs of bases at the beginning of a splice site is fairly straightforward, variants resulting in the introduction of a novel splice site are more difficult to interpret. In this blog post,… Read more »

VSClinical Customer Publications for August 2021

         August 31, 2021
customer

Welcome to the August edition of our customer publications blog post! Each month we spotlight a few recently published articles by our incredible Golden Helix customers. With users spanning both research and clinical spaces, the topics vary widely across many fields. This month, we will be highlighting VSClinical users and the guided workflow. Host Genetics and Antiviral Immune Responses in… Read more »