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 »
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 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 »
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 »
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 »
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 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 »
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 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 »
As we move towards the end of the year, our FAS Team is excited to announce our short blog series highlighting some of the Customization Features in our up-and-coming VarSeq release! The goal of this blog series is to show examples of how generating a clinical report can be customized to accommodate a wide range of functionality. Our December webcast,… Read more »
The customer-published articles this October cite the range of Golden Helix’s VarSeq annotation range and capability. The following publications feature everything from annotating an Italian nobleman mummy, assisting in identifying mutations in primary congenital and juvenile glaucoma, new mutations associated with muscular dystrophinopathy, and germline variants associated with head and neck cancer. In each of these cases, VarSeq was utilized… Read more »
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 »
Merging variant records, VCFs, across samples is important when performing trio or family analysis as it ensures that hereditary relationships can be properly inferred. There are many ways to represent a single variant. Insertions and deletions may be right or left aligned, prefixes and suffixes can be added, and adjacent variants in the same sample may be combined or split… Read more »
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 »
Clinical diagnostic efforts in next-generation sequencing are commonly defined at a gene panel level. The validation process of adding new genes to any diagnostic panel is ongoing, but labs typically construct and validate their clinical workflows for the current status of verified genes. This is not limited to primary finding results but can also include any incidental findings among the… Read more »
Clinical labs often maintain gene panels, which are lists of genes with evidence of disease association. These panels are used to prioritize variants and limit interpretations to a predefined set of test-specific genes. In general, gene panels should be stored independently of any specific project or interpretation, as it is common for an individual gene panel to be generally applicable… Read more »
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects (1). We have covered this annotation in-depth in other blog posts, but this resource contains over 125,000 exome sequences and around 16,000 whole genome… Read more »
