A Great Return to ESHG 2022

         June 22, 2022

The Golden Helix team just returned from ESHG 2022 in Vienna, Austria. It was a great opportunity to speak with colleagues, customers, and partners face-to-face which many of us greatly missed. It has been three years since the last ESHG occurred in this format. Here are  three takeaways from this year’s show: Strong bias to action: Some NGS initiatives that… Read more »

Customizing Your Clinical Reports: Reordering the Variant List

         June 7, 2022

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 »

Customer Publications May 2022

         May 31, 2022

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 »

Import CNVs from any secondary caller using VarSeq

         May 25, 2022

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 »

Questions from Webcast: Evaluating Cloud vs On-Premises for NGS Clinical Workflows

         May 23, 2022

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 »

CNV Probability and Inheritance Based on Coverage with VarSeq

         May 17, 2022

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 »

What’s Coming to VSClinical: Expanded Clinical Trial Search Results

         May 17, 2022
Expanding-Clinical-Trial-Search-in-VSClinical

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 »

Sentieon Updates: Now Supporting Long-Read Alignment and Calling

         May 9, 2022

Here at Golden Helix, we’ve sought to develop top-quality bioinformatic software to handle not only high-throughput clinical next-gen sequencing pipelines but also cater to research groups exploring their cohorts. Our tools fit in this NGS pipeline by importing the VCF and BAM files for downstream filtration, annotation, and classification/interpretation as well as clinical reporting. It was obvious early on and… Read more »

Mining Curated Databases for Literature in VSClinical

         April 29, 2022

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 »

Customer Success

         April 27, 2022
customer success april 2022

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 »

Mining VarSeq Curated Databases for Literature – Raw Data Search in Variant Table or GenomeBrowse

         April 21, 2022

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 »

Annotation Updates: RefSeq and Ensembl gene tracks for GRCh38

         April 20, 2022
Annotation Updates RefSeq and Ensembl Gene tracks for GRCh38

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 »

VarSeq Template Design Recommendations: Single Sample Variant Filtering

         April 6, 2022

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 »

Customer Publications March 2022

         March 31, 2022
customer publications march 2022

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 »

Impressions from ACMG 2022

         March 31, 2022

This year’s ACMG conference in Nashville, TN, marked a positive turning point after two years of virtual meetings in our community. The conference was well attended and found an outstanding balance between on-site meetings and virtual talks. From the Golden Helix perspective, it was wonderful to connect with customers and partners at the event. We were very humbled by the… Read more »

See you all at ACMG 2022!

         March 16, 2022

Everyone at Golden Helix is excited to be traveling once again to an eventful week in Nashville, Tennessee, for ACMG 2022! If you are attending the conference, we hope you will stop by our booth and say hello to the team: Andreas Scherer, Ph.D., Darby Kammeraad, Jennifer Dankoff, and myself, Casey Fullem. We are all excited to be having the… Read more »

Review of VarSeq Export Options

         March 10, 2022
varseq export options

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 »

Reporting Secondary Germline Variants in VSClinical AMP

         March 2, 2022
Reporting Secondary Germline Variants in VSClinical AMP

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 »