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 many reasons a user may wish to focus in on specific variants as part of variant annotation and filtration workflow. You may be looking for the occurrence of specific SNPs in a cohort or perhaps looking for variants known to be associated with specific forms of cancer. For both of these use cases, VarSeq provides a Match String… Read more »
Every month we compile customer publications that reference us, and every time I am excited to see the amazing work being done around the world. From pediatric heart conditions to rare diseases, or a Thai clinical study on dilated cardiomyopathy, it is always a pleasure to see the Golden Helix Software suite helping research and clinical genetics. Below are a… Read more »
Large genetic cohorts require substantial effort to analyze. Genetic researchers are increasingly turning to whole exome and whole genome sequencing analyses for their clinical diagnostics and research. However, with that approach comes the challenge of making sense of these massive datasets. This is especially challenging when looking for tools that can streamline variant analysis for large genetic cohorts and include… Read more »
The ability to analyze copy number variants (CNVs) is an important aspect of any clinical or research workflow. While calling CNVs can be a challenging engineering problem, we are thrilled by our capacity to detect, analyze, and catalog CNVs all in the same place with VarSeq-CNV. In this blog, we will dive into the particulars of detecting CNVs with gene… 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 »
Large-scale next-generation sequencing studies are becoming increasingly popular clinical and research tools. One enduring challenge for interpretion of these large amounts of data has been predicting the functional impact of genetic variants. Access to efficient computational tools for predicting the functional impact of variants is crucial to prioritizing the most potentially relevant variants in a dataset in a time-efficient manner…. Read more »
July brought about several customers having success with utilizing our VarSeq software. We saw publicized research regarding Axenfield-Reiger syndrome, Septo-Optic Dysplasia, and association of TGFBI variants. This range of customer usage displays the vast capabilities of VarSeq and the applications it can work with. Axenfeld-Rieger syndrome: more than meets the eye Background: Axenfeld-Rieger syndrome (ARS) is characterised by typical anterior segment… Read more »
Let’s say you are the director of a large lab, which is running tens or hundreds of standard NGS sample analyses per week. You have a number of employees with varying levels of analysis background, and you want to be sure everyone is running the analysis the same way. You are also concerned about updating catalogs that could create differences… 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 »
Below is a list of highlighted peer-reviewed publications from this month. The Golden Helix team consistently enjoys seeing our software applications hard at work in the field, whether it is clinical whole-exome sequencing, targeted CNV identification, or genotype-phenotype correlations. Enjoy reading below how our suite of VarSeq, VSClinical, and VS-CNV continues to contribute to the progression of genetics research. Looking… Read more »
As we look back on May, I wanted to highlight a range of applications that our VarSeq suite is capable of and show the success of our partners. In these publications, our VarSeq suite is utilized for the analysis of whole-exome, clinical variant classification and association, and assisting in an NGS panel for clinical oncology use. VarSeq’s range and capability… Read more »
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 »
