Golden Helix Blog

Accessing Report Templates and Simple Modifications

Sep 18, 2023

Your variants of interest have been identified, the SVs annotated, and the CNVs classified. Once the manifest has been imported (and here is a great blog on the subject), the last step is to bring all of this information into a report template! In this blog, we will go over…

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Choosing Bin Sizes for the VarSeq CNV Binned Caller

Sep 14, 2023

Detecting CNVs from whole genome data has a number of advantages but also unique challenges. Whole genomes offer a comprehensive and uniform picture of the entire genome, allowing a user to capture CNVs at a higher resolution than with data sequenced at a lesser scale. It also allows for the…

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Evaluation scripts in VSPipeline: We heard you like automation…

Sep 12, 2023

…so we added some automation to your automation so you can automate while you automate! Automation has been a hot topic recently and for all the right reasons. As we (proudly) watch our customers increase their sample and data volume, we are constantly seeking to provide tools to reduce click…

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Evaluate the use of Evaluation Scripts in your ACMG Workflow!

Sep 5, 2023

Recently, we have written a couple of blogs that were talking about the use of Evaluation Scripts in VSClinical workflows, in particular for the AMP workflow. Evaluation scripts were first introduced to VSClinical AMP in VarSeq 2.3.0 and VarSeq 2.4.0 welcomed evaluation scripts to the ACMG classification workflow. Evaluation scripts…

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Decoding DNA: Unraveling the Genetic Mysteries of Cancer Susceptibility

Aug 31, 2023

In an era where genetics is reshaping our understanding of diseases, recent customer research publications offer invaluable insights, particularly in the realm of cancer. A study titled “Co-Occurrence of Germline Genomic Variants and Copy Number Variations in Hereditary Breast and Colorectal Cancer Patients” dives into a rare phenotype bridging hereditary…

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VarSeq Assessment Catalogs for Beginners

Aug 29, 2023

Variant interpretation is a critical aspect of any clinical NGS workflow. VarSeq assessment catalogs are a tool used to save variants and associated variant information for easy tracking and retrieval of completed variant interpretations. As variant interpretations stack up and classifications are saved, storing in assessment catalogs makes it easy…

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Interpreting Fusions Variants in VCFs: A Handy Tool

Aug 22, 2023

When interpreting fusions in their VCF format, it is not easy immediately grasp which side of the positions are adjacent in the resulting fusion. When interpreting and troubleshooting fusion variants, I usually find myself reaching for the VCF spec. If you, like me, are looking to speed up this process…

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Webcast Recap: Best Practices for Validating a Next-Gen Sequencing Workflow

Aug 17, 2023

With the widespread adoption of next-generation sequencing for clinical and research applications comes the need for guidance and recommended standards and best practices for achieving accuracy and efficacy for each assay pipeline. The support team at Golden Helix has gotten a lot of hands-on experience in assisting users to build…

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Versatile NGS Exports with VSClinical’s Custom Scripts

Aug 10, 2023

Configuring a bioinformatic pipeline to reliably process genomic data — particularly at the tertiary analysis stage — is no small task. Doing so in an efficient, consistent way is an even grander challenge. Luckily, the VarSeq software suite provides a comprehensive toolbox for automation and integration. One of the first…

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Get More Out of Assessment Catalogs by Storing and Tracking Variant Artifacts

Aug 8, 2023

Assessment catalogs are a way for VarSeq users to save variants and variant information for clinically relevant variants, so when you come across this variant again in another sample, all of the work to analyze and classify the variant is already done! But there is more than meets to the…

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Using Text Manifests to Load in Sample Patient Information

Aug 3, 2023

The ability to import patient-level information into VarSeq and VSClinical can not only save time while evaluating a sample but can be a critical step in automating project creation through VSPipeline. Here we will review how to construct a basic text manifest and how to apply that manifest to a…

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Advancing Precision Medicine: A Spotlight on Golden Helix’s VarSeq in Genomic Research and Clinical Applications

Aug 1, 2023

The field of genomic research and precision medicine is rapidly evolving, bringing forth innovative diagnostic and treatment approaches. The cutting-edge techniques and technologies discussed in the following papers provide insight into how whole-exome sequencing (WES), whole-genome sequencing (WGS), and deep computational analysis are reshaping healthcare. Our spotlight is on recent…

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Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

Jul 25, 2023

While the analysis of gene fusions is crucial for understanding the genetic basis of cancer, the process of interpreting these mutations can be challenging. One important component of fusion interpretation is the identification of relevant publications. To aid researchers in the search for publications related to specific gene fusions, Felix…

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Optimizing the Capture of Tier II Evidence in VSClinical AMP

Jul 18, 2023

VarSeq 2.3.0 unleashed a whole new way to select, process, analyze, and report cancer variants through complete workflow automation, application of evaluation scripts, and enhanced annotation. Single nucleotide variants, copy number variants, structural variants, and genomic signatures could be added to a single patient evaluation, and Golden Helix CancerKB came…

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Importing External Assessment Catalogs for use in VSClinical ACMG and VSClinical AMP

Jul 13, 2023

When doing clinical variant analysis, it is often essential to keep track of the variants that are encountered in each sample, their pathogenic or oncogenic classifications, which individual created or saved an interpretation, and when. For this purpose, VarSeq prompts VSClinical users to create default assessment catalogs in which to…

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2023 Innovation Awards Winner: Dr. Muthukumaran

Jul 6, 2023

We would like to extend our heartfelt thanks to everyone who participated in our 2023 Innovation Awards Competition. Each year, we are profoundly inspired by the innovative applications and groundbreaking research conducted using Golden Helix software globally. With immense excitement, we are thrilled to announce this year’s winner! Dr. Muthukumaran…

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Moving the AppData Folder – A Look At Sharing Assessment Catalogs

Jul 3, 2023

Discover how to enhance collaboration in VSClinical by sharing variant scores and assessment catalogs through the strategic relocation of the AppData folder. A subtle but powerful utility of VSClinical concerns the ability to share variant scores between users on the same account. What I mean by that is, leveraging the…

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Unlocking Genetic Mysteries: Celebrating Customer Innovations with VarSeq Software

Jun 27, 2023

At Golden Helix, our community of customers and researchers is at the core of our commitment to advancing genomic research and precision medicine. We are thrilled to highlight some recent customer innovations that have made innovative use of our VarSeq software in their research. These studies, which span across diverse…

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Data Viewing with VarSeq: Plotting Tracks!

Jun 26, 2023

In recent weeks, GenomeBrowse capabilities have had a sudden resurgence of interest among our customers. To support this, the FAS team wanted to share with you several under-utilized GenomeBrowse plotting tricks. First, let’s cover plotting a BED file for easy track viewing. The first step is launching a GenomeBrowse window…

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ESHG 2023 Insights

Jun 22, 2023

We had a great time in Glasgow for ESHG 2023, connecting with many current customers and prospective customers at our booth. The in-depth conversations were engaging and offered beneficial insights for our team and the attendees. Thank you all for visiting our booth for a demo as well as attending…

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