Golden Helix Blog

VarSeq PhoRank Part 1: Variant PhoRank Gene Ranking

Dec 13, 2018

One of the main goals of clinical genomic labs is to identify problematic variants in affected individuals. One tool to assist in this search is the phenotype driven variant ontological re-ranking tool in VarSeq called PhoRank. A common situation facing clinicians is sorting through thousands of variants provided by an…

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Optimized Breeding Selection via Genomic Prediction

Dec 11, 2018

What is Genomic Prediction? Genomic prediction is an algorithm widely used to improve desirable phenotypic traits in agriculture. For example, the cattle industry uses genomic prediction to improve beef quality and palatability as well as improve dairy production (1,2). By using genomic prediction, researchers can minimize multiple expenses in breeding…

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Our Philosophy on Quality in Product Testing and Development

Dec 6, 2018

High product quality is a foundational characteristic of a useful and successful product. Quality testing, therefore, is a necessary, albeit an open-ended task. It can at times seem a limitless undertaking in the present using experience from the past to improve the future. Nonetheless, it is approached as a development…

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GRCh38 Liftover: Ensuring Top Quality Variant Analysis

Nov 27, 2018

In a recent webcast, our VP of Product and Engineering Gabe Rudy gave us insight into the current capability and benefits to lifting over to the GRCh38 assembly. Golden Helix fully supports this transition into the most recent reference assembly and have developed our tools on both the 38 and…

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SVS 8.8.3 Release

Nov 26, 2018

The SVS 8.8.3 release was created to incorporate some of the CNV, genome assembly control, and splice site capabilities that are present in VarSeq, as well as clean up and streamline the GWAS workflows (like when using Mixed Linear Model algorithms) for a better user experience. New Product Add-Ons for…

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VSClinical Best Practice Workflows: Part III

Nov 20, 2018

This blog will conclude our VSClinical Best Practice Workflow series and focuses on one of our new reports: VSClinical ACMG Gene Panel Template. This template is valuable because it automatically enters your variant interpretation from the ACMG Guidelines into the report and eliminates the need for manual submission. I would…

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VSClinical Best Practice Workflows: Part II

Nov 15, 2018

In part one of this series, we discussed how the ACMG Classifier can be implemented in your filter chain to support a best practice workflow. To continue our discussion on best practices of VSClinical, this blog will shed light on other attributes of VSClinical that can add support to your…

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VSClinical Best Practice Workflows: Part I

Nov 13, 2018

VSClinical is our most recent product that allows users to evaluate variants according to the ACMG guidelines. As with any tertiary analysis, there is a need to implement best practices into your workflow and using VSClinical for the ACMG guidelines is no exception. That said, we have put together a…

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Great Time at AMP 2018

Nov 6, 2018

We just got back from three busy days at the Molecular Pathology (AMP) conference in friendly San Antonio, Texas. Keeping up the Golden Helix conference momentum for the year, we had 3-4 in-booth demonstrations a day covering our CNV calling, variant interpretation, and data warehousing products for NGS-based genetic tests.…

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VarSeq Stable 2.1.0 Release Notes

Oct 31, 2018

VarSeq Stable 2.1.0 is Ready for Clinical Validation, See it in Action Next Week This week we are happy to see the general availability of VarSeq 2.1, the culmination of the last five months of work since we launched VSClinical. We have been blown away by the adoption of VSClinical,…

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We’re Headed to AMP 2018!

Oct 30, 2018

We’ve packed our bags and we’re off to The Lone Star State to take part in the Association for Molecular Pathology Annual Meeting and Expo (AMP 2018)! As first-time attendees, we’re looking forward to integrating ourselves in the AMP community and showcasing our clinical stack, including VSClinical released earlier this…

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Golden Helix Publication Features

Oct 24, 2018

Following a wonderful September with our 20th Anniversary and being awarded an NIH-SBIR Phase 2 Grant, October has been nothing short of exciting for us here at Golden Helix. We know that none of our success could happen without the continuous support all of you show us – so thank…

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Accessing your VSWarehouse Browser

Oct 23, 2018

In the first two parts of this blog, we presented examples of how to leverage Warehouse-stored VSClinical and CNV assessment catalogs in the VarSeq project. Now we are going to explore the Warehouse interface a bit more and show how to query on stored variant data. To access Warehouse from…

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VSClinical and VSWarehouse – Leveraging Consistent Clinical Interpretations

Oct 22, 2018

Part 1 of this blog series was focused on new capabilities in Warehouse to store your CNV results. We explored some approaches of how to utilize assessment catalogs of cohort and known pathogenic events. What makes Warehouse so useful in this application is that the catalog is accessed from one…

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Optimizing your CNV Analysis in VSWarehouse

Oct 16, 2018

We recently hosted a webcast covering the value and application of VSWarehouse through VarSeq. Not only is VSWarehouse a solution for storing your NGS data in a central repository, but it also provides a means to enhance the tertiary analysis done in VarSeq. VSWarehouse will store all your sample/variant data but also stores your catalogs of pathogenic variants, clinical reports, and has the capability…

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Storing your Copy Number Variant & ACMG Results in VSWarehouse – Webcast Q&A

Oct 11, 2018

This webcast generated some great questions! If you have any other questions for me that are not answered below, please feel free to ask those by emailing [email protected]. To what level does the Warehouse scale? We have tested multiple instances of Warehouse in-house and on the cloud and it scales…

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Headed to San Diego, CA for ASHG 2018

Oct 9, 2018

As we are beginning to welcome the crisp fall weather here in Montana, we cannot wait to make an escape to the warm, sunny weather of San Diego, CA for the American Society of Human Genetics Annual Meeting (ASHG 2018). We are looking forward to spending the week discussing with…

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Using the GRCh38 Reference Assembly for Clinical Interpretation in VSClinical – Webcast Recap

Oct 2, 2018

Even though GRCh37 is currently the most widely used human genome assembly, GRCh38 provides a more complete human reference genome, offers more accurate genomic analysis, and includes centromere and mitochondrial information. However, we’re getting ahead of ourselves. Perhaps start with how we got here. The Human Genome Project started this…

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Using the GRCh38 Reference Assembly for Clinical Interpretation in VSClinical: Webcast Q&A

Sep 27, 2018

This webcast generated some great questions! If you have any other questions for me that are not answered below, please feel free to ask those by emailing [email protected]. Does VSClinical come with support for the new reference genome? Yes! We worked hard to make everything work in VSClinical regardless of…

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Getting Started Guide for Sentieon – Part II

Sep 25, 2018

Creating Custom Scripts The first part of the Getting Started Guide for Sentieon described the steps for downloading the Sentieon tools, acquiring a license file, and running the example script/pipeline to generate the VCF and BAM files. This blog will cover some custom script changes users can make to add…

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