Researchers and clinicians alike utilize our software to progress diagnostic capabilities across the globe. Our tools are continuously validated, and below is a showcase of a few articles this month that demonstrate the range of uses. This is our final customer publications blog of 2022; I would like to say thank you to all of our current partners and customers,… Read more »
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 »
Variant normalization is essentially reducing the representation of a variant to its canonical representation. Variant normalization ensures that the way a variant is represented is parsimonious and left-aligned and can also refer to splitting variants into their allelic primitives. VarSeq normalizes variants by default, but we offer users the option to forego one or more aspects of variant normalization. This… Read more »
This November’s published articles citing Golden Helix software serve as a testament to our broad application and utility in NGS data analysis. We are always proud of our customers and the contributions they make to scientific discovery. Their continued work and research are motivators for us to continue delivering the best products we can. This month we are featuring two… Read more »
The last blog in this series covered streamlining variant analysis for large genetic cohorts, namely case-control studies, on a single-project basis. The reality when dealing with big data is that you often do not handle a high volume project all at once. Therefore, we will follow up on the topic of cohort analysis by discussing Golden Helix’s solution for streamlining… Read more »
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 »
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 »
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 »
There are a number of conferences coming up on our schedule in the next few weeks. It’s a great opportunity check out the latest developments at Golden Helix and see exciting technologies in action. These conferences are a wonderful opportunity to discuss new discoveries in genomics. We will be there with our clinical NGS analysis software, the VarSeq suite, to… Read more »
This past month has produced some very interesting and diverse publications, all of which are using the VarSeq suite of products for whole exome & whole genome sequencing strategies. This month had it all: investigations of an understudied population in pharmacogenomic testing, the first-ever find with implications for Maine coon cats, and a puzzling case with a unique family displaying… Read more »
Thank you to those who attended our webcast on the user perspective of our automated AMP guidelines! Furthermore, let me express our appreciation for those particularly engaged users who posed some very thoughtful questions. While we weren’t able to answer all of them live, I hope to shed some light on some pertinent details of somatic analysis here. Let’s start… Read more »
First, thank you to everyone who joined us for our recent webcast, Handling a Variety of CNV Caller Inputs with VarSeq. Also, we would like to thank those that Tweeted #CNVsupport @GoldenHelix or emailed us (mmarks@goldenhelix.com) to throw in their questions. This was a successful trial run, and we would like to continue engaging with our users through these outlets…. Read more »
Oftentimes, the endpoint of a clinical variant analysis is a standardized, clinical report. As such, we ship a number of default templates with VSClinical for users to report their findings. But these templates are just a starting point! Our platform allows users to fully customize their reports to adhere to lab-specific preferences. We have shared a plethora of how-to’s on… 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 »
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 »
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 »
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 »
