Author Archives: Darby Kammeraad

About Darby Kammeraad

Darby Kammeraad is a Senior Field Application Scientist at Golden Helix, joining the team in April of 2017. Darby graduated in 2016 with a master’s degree in Plant Sciences from Montana State University, where he also received his bachelor’s degree in Plant Biotechnology. Darby works on customer support and training. When not in the office, Darby is learning how to play guitar, hunting, fishing, snowboarding, traveling or working on a new recipe in the kitchen.

Consideration when using CADD in your NGS Workflow

         December 15, 2021

VarSeq serves as a streamlined approach to handle the rare variant analysis typically carried out for your next-generation sequencing data. Our team at Golden Helix seeks to simplify this process by automating the curation of staple databases needed for filtering and evaluation of clinically relevant variants. The goal we seek to accomplish with our software is to provide ease in… Read more »

VS-CNV Command-Line CNV Tool

         December 9, 2021

If you stay current on the developments of Golden Helix features, you are aware of the substantial evolution of our copy number detection and evaluation capabilities in VarSeq. The process of CNV detection and evaluation is typically handled through the VarSeq graphic user interface. However, in some cases, users benefit from running this process via the command-line interface. Fortunately, Golden… Read more »

Alternate Allele Frequency and VCF File Format

         December 7, 2021

VCF file format comes with a lot of interesting quality assurance and statistics fields that can be used for filtering in VarSeq. Open your files in a text editor to see all the fields that are available in your files, each field will have a header line with a description of its content. See the VCF Specifications to help with… Read more »

Five Annotation Sources You Should Know

         October 19, 2021
Golden Helix Annotation Blog Featured Image

In addition to Golden Helix providing easy-to-use genomic software, we also provide value to our users by automating the curation of public databases used in our tools. These annotation sources serve multiple purposes not only leveraging key fields in the filter chain but also automatically supplying evidence for the ACMG and AMP classifications reviewed in VSClinical. Supporting the curation of… Read more »

Efficient Gene Panel Utilization in VarSeq

         August 24, 2021

Clinical diagnostic efforts in next-generation sequencing are commonly defined at a gene panel level. The validation process of adding new genes to any diagnostic panel is ongoing, but labs typically construct and validate their clinical workflows for the current status of verified genes. This is not limited to primary finding results but can also include any incidental findings among the… Read more »

Golden Helix’s Next-Gen Sequencing Data Analysis Solutions Explained

         June 22, 2021
VSClinical algorithm

Next-gen sequencing (NGS) comprises many sophisticated steps that are often compressed into three major sections: library prep, sequencing, and data analysis. Obviously, the goal is to simplify each of these steps, but more often than not, there is a need for multiple tools to complete each one. Regarding the data analysis, Golden Helix seeks to provide simple yet comprehensive solutions… Read more »

Harmonizing Next-Generation Sequencing Data: VarSeq Liftover Tool

         June 15, 2021
genomeAsia

One of the inherent realities of next-generation sequencing is the ongoing updates to the human reference genome—one of the strongest recommendations to take the original sequencing data and remap to the latest genome assembly. However, there are several reasons why remapping may be impractical. So, an alternative solution is needed to convert the data running through an initial mapping to… Read more »

VarSeq NGS Workflow Design: Clinical vs. Research

         April 22, 2021
NGS Clinical Research

In many cases, VarSeq users design their next-gen sequencing workflows for a clinical application. One of the major values of using VarSeq is the standardization of sample analysis via project templates for filtering down to rare variants and isolate any clinically relevant variant. However, VarSeq also doubles as a robust research application as well. There are specific algorithms that can… Read more »

Webcast Recap: VSWarehouse: Tracking Changing Variant Evidence and Classifications

         March 11, 2021
VSWarehouse

Thank you to those who attended the recent webcast, “VSWarehouse: Tracking Changing Variant Evidence and Classifications”. For those who could not attend but wish to watch, here is a link to the recording. The webcast covered some general highlights of VSWarehouse value but also presented some specific capabilities covering the ClinVar classification tracker. Golden Helix provides complete solutions to handle… Read more »

New Mendel Error Algorithm in VarSeq

         March 2, 2021
mendel algorithm

In many cases, VarSeq users typically run single trio projects or perhaps an extended family project. Not only are all the inheritance model algorithms available in the VarSeq software to capture de novo, dominant, or recessively inherited variants but there are a number of quality control fields to help ensure the pedigree was set up properly. The last thing any… Read more »

New CNV Tools with VarSeq 2.2.2 Update

         February 16, 2021
copy number variant algorithm

Our latest release of the VarSeq software has had a major upgrade with the addition of the new CNV ACMG guidelines! Here are some recent webcasts we’ve given covering the new guideline tool: Family-Based Workflows in VarSeq and VSClinical A User’s Perspective: ACMG Guidelines for CNVs in VSClinical Not only does VarSeq 2.2.2 come with the new guideline tool, but… Read more »

New Annotation: GnomAD – Gene Constraints

         February 10, 2021
GnomAd screenshot

VarSeq recently received major upgrades in a wide range of areas, one of these areas includes adding annotations such as GnomAD. This includes new fundamental methods of CNV ACMG guideline processing but also a large number of small additions in annotations. One addition is the application of gnomADs – Gene Constraints. This provides various metrics for pathogenicity on a per… Read more »

VSClinical: Defining Sample Phenotypes

         January 20, 2021

Our recent release of VarSeq 2.2.2 comes with a long list of upgrades and new features. In this blog post, we will demonstrate how defining sample phenotypes are available in VSClinical. One noticeable change is the ACMG guideline variant evaluation in VSClinical. Not only has this interface added CNV guideline evaluation, simplified the reporting process with embedded Microsoft Word and… Read more »

Updated Annotations: RefSeq with MANE Select Transcripts

         December 17, 2020

Our upcoming release of VarSeq is one of the largest we’ve ever had with our software! It comes with an extensive list of polishes and new features like our recently mentioned ACMG CNV classifier and a redesigned reporting interface with updated templates. Additionally, this new release is also paired with some major upgrades to our list of new and supported… Read more »

Loss-of-Function Splice Variant in MTHFR

         November 26, 2020

In this blog post, I will be analyzing a loss-of-function splice variant in MTHFR using VarSeq. In the search for clinically relevant variants contributing to rare disorders, efficient filtering strategies are an important step in eliminating disinteresting variants. However, any applied filters must also ensure no interesting variants inadvertently get filtered out. Golden Helix provides the tools to complete this… Read more »

New Algorithm: Variants Matching Current Sample

         November 12, 2020
New Algorithm: Variants Matching Current Sample

Those of you who have been attending our recent webcasts have learned about our upcoming VarSeq release. A part of that release will be an additional algorithm that will annotate variants matching the current sample. If you are not familiar with these webcasts, here are several on-demand webcasts I recommend to get you familiar with these new features: Evaluating Copy… Read more »

Webcast Recap: A User’s Perspective: ACMG Guidelines for CNVs in VSClinical

         October 16, 2020

Our previous webcast from VP Gabe Rudy in September exposed us to some fundamentals of this years’ updated Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). This recent webcast was dedicated to breaking down these new guidelines… Read more »

VarSeq’s NGS Panel Workflow: COL4A2 Variant from an Intellectual Disability Panel

         October 1, 2020

A common discussion with our customers includes the challenges with the tertiary stage of analyzing next-gen sequencing data. This is the stage where all data from gene panels, exome, or whole genome scale pass through filters to quickly isolate the clinically relevant variant contributing to a patient disorder. Golden Helix has recognized these challenges in the scale of data and… Read more »

Advanced Plotting Capabilities with GenomeBrowse

         September 22, 2020

In this blog update, I’ll be walking you through some of the advanced plotting capabilities with GenomeBrowse. The strategy with any next-gen sequencing analysis is to filter down to interesting variants for either research or clinical conclusion. Golden Helix produces powerful software specifically tailored for this efficient and comprehensive search for interesting and clinically relevant variants. One additional advantage of… Read more »