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 »
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 »
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 »
In this blog post, I am very excited to talk about The Broad Institute’s release of the latest version of gnomAD, v 3.1.2, which is now available for use as an annotation source in your SVS or VarSeq projects. For VarSeq users, I also want to point out that gnomAD v3.1.2 can also be used as a population frequency in… Read more »
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 »
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 »
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 »
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 »
I’m sure everyone’s favorite winter activity is getting cozy next to a fire, with a nice cup of tea, and reading the VarSeq instruction manual, right? Of course all VarSeq users have read the manual, but if you have not had the chance to review this captivating read, let me entice all of you to do so by announcing that… Read more »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
Thank you to everyone who attended Using Golden Helix CancerKB to Accelerate NGS Cancer Testing! I had a great time showing off Golden Helix 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… Read more »
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 »
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 »
As a lab or group scales the number of NGS samples analyzed, it is important to automate the sample analysis pipeline from the sequencer to the point where it is ready for a variant scientist or lab personnel to follow the interpretation workflow and draft a clinical report. VSPipeline leverages the core VarSeq capability to create reproducible test-specific workflows through… Read more »
