Customer VarSeq Publications in January 2022

         January 31, 2022
Jan 2022 VarSeq Customer Publications

2022 has started off with a significant number of customers publishing their research. We saw several customers utilizing various softwares within our suite, but the most prominent being VarSeq. VarSeq is an intuitive, integrated software solution for tertiary analysis. With VarSeq you can automate your workflows and perform variant analysis for gene panels, exomes, and whole genomes. Understanding genomic data… Read more »

Large Scale PCA Analysis in SVS – Webcast Q&A Follow Up

         January 26, 2022
Large Scale PCA Analysis in SVS - Webcast Q&A Follow Up

Thank you to those who attended our recent webcast by Gabe Rudy, Large Scale PCA Analysis in SVS. For those who could not attend, you can find a link to the recording here. While this webcast discussed methods for principal components analysis (PCA) in SVS, including the new capability for performing principal components analysis on large sample sizes, it also… Read more »

How to Create Your Own CNV Frequency Catalog

         January 20, 2022
cnv frequency catalog

Global population frequency catalogs like 1kG Phase 3, gnomAD, DGV, and others are excellent resources for identifying rare variants in your copy number variant (CNV) analysis. However, they are not exhaustive, and the reality is a lot of variants that are missing from global population frequency catalogs are still common variants. At the same time, CNVs that are identified by… Read more »

Highlights from Advanced Report Customization in VSClinical Webcast: Somatic Reports

         January 6, 2022
advanced somatic report customization in vsclinical

In our previous blog, we covered the highlights of our Advanced Report Customization in VSClinical webcast in the context of germline clinical reports. Now, we bring you the next of the series: somatic clinical reports. In the recent webcast, Advanced Report Customization, we covered a range of somatic-focused clinical reports, demonstrating how easy it is to create AMP guideline-based clinical… Read more »

What to Expect in 2022

         January 3, 2022

Happy New Year to all! I hope that you were able to enjoy quality time over the holidays with family and friends. It is time to begin discussing our plans for the new year again, but I would first like to review a few highlights from 2021 that laid the foundation for Golden Helix’s future. Golden Helix had a resoundingly… Read more »

Customer Publications in November and December 2021

         December 30, 2021

The articles we saw this November and December cited a wide range of applications of our product suite. The following publications feature usage of our SNP & Variation Suite, VSClinical, and VarSeq products. We see them being utilized to identify loci associated with facial eczema in New Zealand sheep, somatic mutation response impact, and assisting in estimating breast cancer risk… Read more »

SVS 8.9.1 Release

         December 28, 2021
svs 8.9.1 release

We would like to announce that a new version of SVS has been released! The headlining feature of the SVS 8.9.1 release was new functionality for Large Data Principle Component Analysis. A detailed description of this new feature can be explored in this recent blog post: Finding a Few Principal Components Quickly from Data with Thousands of Samples. However, there… 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 »

Consideration when using CADD in your NGS Workflow

         December 15, 2021

VarSeq serves as a streamlined approach to handle the rare variant analysis typically carried out for your next-generation sequencing data. Our team at Golden Helix seeks to simplify this process by automating the curation of staple databases needed for filtering and evaluation of clinically relevant variants. The goal we seek to accomplish with our software is to provide ease in… Read more »

Highlights from Advanced Report Customization in VSClinical Webcast: Germline Reports

         December 14, 2021
germline clinical report blog

When it comes to clinical variant analysis for germline variants using ACMG guidelines, we understand that the clinical report is essentially the receipt for your services for the patient. In our recent webcast, Advanced Report Customization in VSClinical, we displayed several examples of report templates to show off the range of possibilities our users have to format their clinical report…. Read more »

VS-CNV Command-Line CNV Tool

         December 9, 2021

If you stay current on the developments of Golden Helix features, you are aware of the substantial evolution of our copy number detection and evaluation capabilities in VarSeq. The process of CNV detection and evaluation is typically handled through the VarSeq graphic user interface. However, in some cases, users benefit from running this process via the command-line interface. Fortunately, Golden… Read more »

Alternate Allele Frequency and VCF File Format

         December 7, 2021

VCF file format comes with a lot of interesting quality assurance and statistics fields that can be used for filtering in VarSeq. Open your files in a text editor to see all the fields that are available in your files, each field will have a header line with a description of its content. See the VCF Specifications to help with… Read more »

2022 Innovation Awards

         December 1, 2021

We at Golden Helix love seeing our software and solutions out in action. Whether it is to find a clinical solution or to assist in academic research, seeing YOU use our tools to the best of their ability gets us excited to continue developing industry-leading software. For the 2022 Innovation Awards we would like to see all the creative and… 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 »

Highlights From Our CancerKB Webcast

         November 24, 2021

Thank you to everyone who attended Using Golden Helix CancerKB to Accelerate NGS Cancer Testing! I had a great time showing off CancerKB and how it can enhance NGS analysis in cancer, I certainly hope you enjoyed it! If you were unable to make the live session, we have added the on-demand recording to our site, or we would be… Read more »

Top FAS Tricks You Wish You Knew When Getting Started with VSClinical

         November 18, 2021
vsclinical top things to know

As a newer member of the Golden Helix FAS Team I, like many of our customers, went through a phase of learning the ins, outs, and shortcuts of clicking around the program. In an effort to expedite new users coming up to speed, or to teach some tricks to experienced users, I’ve compiled a list of the top things I… Read more »

Validating Your CNV Workflow

         November 16, 2021
VS-CNV Blog Validation

The VarSeq CNV calling algorithm, VS-CNV, is a powerful tool for calling CNVs from the NGS coverage data stored in your BAM files. However, before this algorithm can be deployed in a clinical setting, it must be tuned and validated using data that is representative of your lab’s NGS workflow. In the past, this validation process could be difficult, as… Read more »