Advances in high-throughput sequencing have allowed us to be able to detect structural variants such as copy number variants in addition to small variants such as SNVs and indels. We provide users with an industry-leading CNV calling algorithm to detect CNVs directly from their next-generation sequencing data including whole genome, whole exome, and gene panel datasets, and also import CNVs… Read more »
In the era where cloud-based solutions are the default for the modern office, it may not be obvious why many laboratories and testing centers choose to host their data and analysis pipelines on-premises or on self-managed cloud services. In the recent webcast Evaluating Cloud vs On-Premises for NGS Clinical Workflows, I explored the topic of how to make infrastructure decisions… Read more »
The overall objective of Trio Analysis is to leverage inheritance data to determine the ancestry of variants in the proband, whether that be through transmission from the mother and father, or of de novo origin. We have previously covered family based analysis in this blog post and this webcast, but both of these sources have been based on variants brought… Read more »
While the interpretation of germline variants generally focuses on the pathogenicity of a variant for a specific disease, the interpretation of somatic variants is centered around each variant’s impact on clinical care. As a result, clinical trials play an important role in assessing the clinical significance of somatic biomarkers, with the AMP Guidelines assigning a higher level of evidence to… Read more »
Curated databases are a real time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to the ACMG guidelines and somatic variants according to the AMP… Read more »
For this month’s Customer Success blog, I decided to revisit some of my favorite studies that had previously been featured in years past. At the time we first highlighted the below publications, some of them were in pre-print and have since been accepted and published. What they all have in common is the implementation of our VSClinical software, which saved… Read more »
An under-utilized use of VarSeq is the ability of mining raw variant data in GenomeBrowse for relevant literature. By bringing in various public and private annotation sources, GenomeBrowse allows the user to interface with raw variant data in a compressed and manageable view. This blog will show you how to leverage these sources to power up your search for variant… Read more »
I’d like to take a moment to announce the release of updated gene tracks for the GRCh38 genome assembly! Gene annotation tracks are essential to all VarSeq projects and workflows. Whether your favorite gene track is Ensembl or RefSeq, both sources have been updated and released and can be used for variant annotation. These gene tracks are used to annotate… Read more »
When doing next-generation sequencing (NGS) analysis in VarSeq, the fundamental goal is to develop efficient ways to filter through your NGS data. If you are just getting started with Varseq, a pre-designed project template can really come in handy for variant filtering! This blog series will cover a number of template design recommendations for variant filtering on data types ranging… Read more »
We at Golden Helix thoroughly enjoy seeing our software being utilized to solve problems and assist in the diagnosis of hereditary diseases. It is gratifying to be notified of customer publications in which they are doing precisely this. While there have been numerous publications this month showcasing Golden Helix software being applied, below are a few that stuck out specifically…. Read more »
Although best known for its auto-generation of custom reports, VarSeq comes with a slew of options for exporting your data. In this blog, we will review some of the lesser-known methods for exporting your data into usable formats. These four export options can all be found under the Export tab at the upper left corner of your VarSeq interface (Figure… Read more »
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 »
VarSeq software again takes center stage in our recent publications for February. It is our great honor to be a part of the groundbreaking discoveries highlighted below as well as the many others too numerous to include in this blog post! We are happy to contribute to scientific findings from all our analysis platforms, but we are especially proud of… Read more »
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 »
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 »
