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 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 »
Our team is getting ready to head to Los Angeles, CA for the American Society of Human Genetics Annual Meeting (ASHG) 2022. We are looking forward to spending the week discussing genetics with new and familiar faces! If you are planning on attending, please stop by our booth and say hello! You will find the Golden Helix team in booth… 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 »
Manually converting FASTQs to VCFs, importing these into VarSeq, and building projects from scratch is adequate when you have only a handful of cases per week. But as you start ramping up production, the key to your lab’s success quickly becomes how quickly and efficiently you can get to the reporting of your analysis. This blog will explain how you… 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 »
Our team is excited to be in Vienna, Austria for the European Society of Human Genetics Annual Meeting (ESHG) 2022. We are looking forward to spending the week discussing genetics with new and familiar faces! If you are planning on attending, please stop by our booth and say hello! You will find the Golden Helix team in booth X5-476. Our… 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 »
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 »
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 »
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 »
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 »
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 »
Happy New Year to all! I hope that you were able to enjoy quality time over the holidays with family and friends. It is time to begin discussing our plans for the new year again, but I would first like to review a few highlights from 2021 that laid the foundation for Golden Helix’s future. Golden Helix had a resoundingly… Read more »
We would like to announce that a new version of SVS has been released! The headlining feature of the SVS 8.9.1 release was new functionality for Large Data Principle Component Analysis. A detailed description of this new feature can be explored in this recent blog post: Finding a Few Principal Components Quickly from Data with Thousands of Samples. However, there… 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 »
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 »
As a newer member of the Golden Helix FAS Team I, like many of our customers, went through a phase of learning the ins, outs, and shortcuts of clicking around the program. In an effort to expedite new users coming up to speed, or to teach some tricks to experienced users, I’ve compiled a list of the top things I… Read more »
Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines to evaluate variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since it was introduced, we have provided a powerful Word-based templating system to allow labs the ability to generate customized reports to include specific content… Read more »
