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Defining HLA Diplotypes for Pharmacogenomics

Aug 14, 2025

In the dynamic field of pharmacogenomics (PGx), the human leukocyte antigen (HLA) system stands out as a critical factor in personalizing drug therapies, particularly in avoiding severe adverse reactions. However, as highlighted in a comprehensive review on the HLA system’s genetics and clinical testing, these genes are notoriously challenging to…

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Reduce, Reuse, Recycle: Creating Automatable Workflow Templates with VarSeq

Jun 10, 2025

Next-generation sequencing (NGS) data analysis often involves multiple steps from variant annotation, filtering, interpretation, visualization, and report generation. Repeating these steps manually for each new project can be error-prone and inefficient. In clinical and regulated environments, we recognize that consistency is critical. That’s why VarSeq offers robust support for workflow…

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Importing External PGx Calls for Extended Gene-Drug Reporting in VarSeq

May 27, 2025

Pharmacogenomic (PGx) analysis empowers researchers and clinicians to tailor drug therapies based on a patient’s genetic profile, but not all regions of the genome are easy to interpret. Genes like CYP2D6 and HLA-A are tricky when it comes to rendering diplotype calls. This is due to a number of factors…

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Automating Carrier Screening Analysis Using VarSeq

May 8, 2025

VarSeq, when used with VSPipeline, automates carrier screening analysis, allowing labs to run them in a parallelized, economical fashion.

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Variant Calling and CNV Import in PGx Genes using VSPGx

Apr 18, 2024

In this blog post, we will explore the nuances of variant calling and import in the context of VSPGx. We will discuss the importance of integrating must-call variant definitions into the calling processes and provide guidance on incorporating copy number variants (CNVs) and structural variations (SVs) into your PGx analysis…

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eBook Release: Pharmacogenetics

Feb 27, 2024

Welcome to our engaging journey through the fascinating world of pharmacogenetics! In this friendly guide, we’re going to explore how our unique genetic makeup influences the way we respond to medications. It’s all about making medicine more personalized and effective for everyone. This eBook, Pharmacogenetics takes you into the world…

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Decoding Complex Fusion Representations: A Deep Dive into VCF Breakend Notation and its Impact on Gene Analysis

Mar 14, 2023

Unlocking the intricacies of fusion representations is crucial for understanding the impact of complex genetic rearrangements on gene function and disease development. In the most recent release of VarSeq, we added support for the import of complex rearrangements from VCF files, which typically encode rearrangements using breakend notation. This powerful…

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4 Essential Support Resources for Golden Helix Software Users

Jan 5, 2023

Golden Helix provides extensive resources to help our users who are just getting started and address any issues they may encounter as they become more familiar with our software. Our resources are constantly updated and are tailored to the needs of our users. If you’re facing a problem, it’s likely…

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Highlights from our PhoRank 2.0 Webcast

Jun 10, 2021

Thank you to those who attended our recent webcast, “PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq”. For those who could not attend, you can find a link to the recording here. This webcast covered upcoming improvements to the PhoRank phenotype-based gene ranking algorithm based on literature published in the…

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Variant Filtration and Interpretation

Jun 3, 2021

I learned about Batten disease from a childhood friend’s Facebook post. Over the course of a few months, her 8-year-old, Eva, the oldest of 4 daughters – Emily, Lucy, and Carly – was rapidly going blind. Baffled, doctors ran a genetic panel that returned a devastating result – the diagnosis…

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VS-CNV Updates in VarSeq v2.2.3

May 18, 2021

Golden Helix has just released VarSeq v2.2.3. In this update, there are notable changes that can improve CNV calling capabilities covered in this webcast. The topics discussed included: Accounting for GC content Improvements to CNV quality flags Using target filtering Updates to the CNV sensitivity and precision settings This blog…

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Webcast Recap: High Precision Exome CNV Detection with VS-CNV

May 7, 2021

Thank you to those who attended the recent webcast, “High Precision Exome CNV Detection with VS-CNV”. For those who could not attend but wish to watch, here is a link to the recording. This webcast delved into the complex world of CNV calling for whole-exome samples, which presents unique challenges that…

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Lock in Annotation Source Versions to Increase Workflow Consistency

Feb 25, 2021

Next-generation sequencing generates an immense amount of data which is then subject to a multi-step process to establish a validated bioinformatic pipeline. From processing raw sequence data to the detection of genetic mutations, establishing a validated and consistent bioinformatic pipeline makes a huge difference in the quality of patient care…

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Customer Publications February 2021: The Heart Edition

Feb 23, 2021

Welcome to our Customer Publications for February 2021, dedicated to cardiac research. As we commemorate the 57th American Heart Month, it is important to remember why we are wearing red and using #OurHearts. Heart disease is the leading cause of death worldwide. The National Heart, Lung, and Blood Institute urges…

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New CNV Tools with VarSeq 2.2.2 Update

Feb 16, 2021

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…

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January 2021 Publications

Jan 28, 2021

New discoveries using NGS data analysis are never-ending and are pushing precision medicine to the forefront. In the January 2021 customer publication blog, I am focusing on our VarSeq software as investigators harness its power to perform a variety of investigational study designs. From cancer to inherited rare disease research,…

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New eBook Update: Precision Medicine – Third Edition

Jan 27, 2021

I am pleased to share with you the official release of my updated eBook, “Precision Medicine“. Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century, we take an understanding of the individual characteristics of a person to a new level. By…

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Webcast Recap: Evaluation of CNVs with VSClinical’s New ACMG Guideline Workflow

Nov 10, 2020

In the webcast, Evaluation of Copy Number Variants with VSClinical’s New ACMG Guideline Workflow, we discussed how VSClinical implements Section 4 of the ACMG guidelines. Specifically, we focused on integrating literature and publications to assess the pathogenicity of a CNV event when there was a lack of dosage sensitivity information.…

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Upcoming VS-CNV Update: CNV Event Reporting with ACMG Guidelines

Oct 22, 2020

Golden Helix is excited to release an upcoming VSClinical feature that allows users to analyze next-generation sequencing (NGS) CNV event reporting with ACMG guidelines. This feature will be the first in the NGS workspace to allow this capability and if you are curious about the functionalities you can get a…

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New eBook Update: Genetic Data Warehousing – Second Edition

Aug 17, 2020

We’re excited to share the release of a newly updated resource from our CEO, Andreas Scherer, Ph.D. This morning, we published the Second Edition of his eBook, Genetic Data Warehousing, offering an in-depth exploration of how data warehousing technologies are shaping the future of clinical genomics and precision medicine. This…

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