VSClinical AMP Matching of Interpretations In this blog post, we will delve into the intricacies of the VSClinical AMP interpretation workflow. At the heart of this process lies the task of annotating cancer biomarkers with the correct interpretations based on the classification of the tumor and the type and scope of the biomarker. This is a crucial step in understanding… Read more »
We are thrilled to announce that our company has been named the Best Global Bioinformatics Firm of 2023 by the Corporate Excellence Awards. This recognition is a testament to the hard work and dedication of our team, who are committed to delivering the highest quality bioinformatics solutions to our customers. At Golden Helix, we have always been committed to innovation… Read more »
Discover the latest advancements in cancer genomic profiling with the release of VarSeq 2.3.0 We are very excited to announce the release of VarSeq 2.3.0! This release was one of the largest VarSeq releases yet, as it includes a large refactor to the VSClinical AMP cancer module. A primary motivation for the release was focused on the availability and increased… Read more »
Unlocking the Potential of CRAM Files: The New VarSeq 2.3.0 Release for Enhanced Plotting, Coverage Analysis, and CNV Detection The CRAM (Compressed Reference-oriented Alignment Map) file format was conceived in 2011 as a more space-efficient way to store alignment data. It saves space over the previous standard BAM (Binary Alignment Map) by only storing the differences between each read and… Read more »
Learn about the latest cancer ontology software updates and how they can enhance your research and work. Cancer Ontology An important feature of the VSClinical AMP workflow is the ability to select the correct tumor type for a given evaluation. The selected tumor type is used to identify relevant clinical evidence, including drug sensitivities, resistances, and previous biomarker interpretations. This… Read more »
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 that others have encountered it as well, and we’ve included… Read more »
Happy New Year! I hope that you all were able to enjoy quality time with your loved ones over the holidays. Now that 2022 has come to a close, we would like to take the time to say thank you while looking back on a big year full of new experiences and accomplishments. During the pandemic, we’ve been using the… Read more »
Researchers and clinicians alike utilize our software to progress diagnostic capabilities across the globe. Our tools are continuously validated, and below is a showcase of a few articles this month that demonstrate the range of uses. This is our final customer publications blog of 2022; I would like to say thank you to all of our current partners and customers,… Read more »
Our FAS team would like to thank everyone who attended our December 2022 webcast, A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0. This webcast allowed three members of our FAS team to give their unique insights concerning the improvements to our new VarSeq 2.3.0 release, which will be recapped here. Starting with template creation, our Technical Field Application Scientist,… Read more »
Variant normalization is essentially reducing the representation of a variant to its canonical representation. Variant normalization ensures that the way a variant is represented is parsimonious and left-aligned and can also refer to splitting variants into their allelic primitives. VarSeq normalizes variants by default, but we offer users the option to forego one or more aspects of variant normalization. This… Read more »
This November 2022, published articles citing Golden Helix software serve as a testament to our broad application and utility in NGS data analysis. We are always proud of our customers and the contributions they make to scientific discovery. Their continued work and research are motivators for us to continue delivering the best products we can. This month we are featuring… Read more »
The last blog in this series covered streamlining variant analysis for large genetic cohorts, namely case-control studies, on a single-project basis. The reality when dealing with big data is that you often do not handle a high volume project all at once. Therefore, we will follow up on the topic of cohort analysis by discussing Golden Helix’s solution for streamlining… Read more »
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 »
Here at Golden Helix, we would like to take a moment and highlight some of our amazing and talented women in STEM! Below are short excerpts from some of our own Golden Helix employees and their experiences both in STEM and here at Golden Helix. Rana Smalling Field Application Scientist B.A. in Biological Sciences, Ph.D. in Biochemistry My experience in STEM started in… Read more »
We are honored to be awarded and recognized with this year’s BioTech Breakthrough Award, a prestigious accolade that highlights excellence and innovation across the biotechnology industry. At Golden Helix, we take immense pride in providing robust, user-friendly solutions that help researchers and clinicians translate complex genetic data into meaningful insights. This award is not just a win for our team—it’s… Read more »
The ACMG classification guidelines for variant pathogenicity are as ubiquitous as they are complicated to implement. They play a consistent and evolving role in the standard workflows of many experts in the next-generation sequencing field, both in the clinical and research space. Furthermore, they can be effectively applied in both somatic and germline workflows. Hence, consistent and auditable methods for… Read more »
The Golden Helix team is headed off to Phoenix, AZ for the Association for Molecular Pathology Annual Meeting & Expo (AMP) 2022. We are enthusiastically awaiting a week of genetics discussions with new and familiar faces. If you are attending, please stop by our booth and say hello! We will be exhibiting at booth 1432. Golden Helix President & CEO,… Read more »
October 2022 was VarSeq’s month, and 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 in Retinoblastoma Patients:… 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 »
There are many reasons a user may wish to focus in on specific variants as part of variant annotation and filtration workflow. You may be looking for the occurrence of specific SNPs in a cohort or perhaps looking for variants known to be associated with specific forms of cancer. For both of these use cases, VarSeq provides a Match String… Read more »
