Golden Helix Blog

Clinical Variant Analysis for Cancer: Part V

Jul 2, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Detecting cancer at an early stage can make it much more treatable. Developing tests and making them clinically actionable is crucial to beat this disease. This eBook covers the state-of-the-art gene panel tests for cancer, walking through…

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Limited-Time Offer for VSClinical’s Cancer Add-On

Jun 27, 2019

We are upgrading all VSClinical +Cancer Add-On purchases to a 15-months license! The individualized nature of tumors requires genomic testing for providing the best outcomes for patients. Next-Gen Sequencing enables the detection of small mutations, copy number changes, and common fusions affordably and with high precision. However, the interpretation of…

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Clinical Variant Analysis for Cancer: Part IV

Jun 25, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Somatic variants can manifest in different ways: There is a difference between the interpretation of germline and somatic variants. The former is exclusively focused on establishing the level of pathogenicity vis a vis a particular disease. In…

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Clinical Variant Analysis for Cancer: Part III

Jun 18, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants As described in my eBook “Genetic Testing for Cancer,” any bioinformatic pipeline for cancer ultimately calls variants based on the aligned reads that the sequencer generated. Variant calling is the process of reviewing a sequence alignment, typically…

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Clinical Variant Analysis for Cancer: Part II

Jun 13, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Analogous to the ACMG guidelines for germline mutations, the Association for Molecular Pathologists (AMP) has issued guidelines to assess and report on somatic variants, and AMP classification is a core component of any structured cancer variant workflow.…

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Clinical Variant Analysis for Cancer: Part I

Jun 11, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Precision Medicine uses genetic information from individual patients. This may include the following areas: Specifically, in the cancer space, NGS data analysis is used to diagnose and prognose diseases, select a targeted therapy and potentially evaluate the…

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New eBook Release: Clinical Variant Analysis for Cancer

Jun 6, 2019

Applying AMP Guidelines to Analyze Somatic Variants Today, I am thrilled to share with you the launch of a brand new eBook titled “Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants”. We would happy to send you a complimentary copy which can be requested on…

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Genetic Testing for Cancer – New Version Release

Jun 5, 2019

Yesterday, I released a new version of my eBook, “Genetic Testing for Cancer – Third Edition”. We would be happy to send you one! To download a complimentary copy, please submit a request on our site here. In 1914, the German cytologist Theodor Boveri coined the phrase “Cancer is a…

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Variant Interpretation with VSClinical: Evaluation of an X-linked Recessive Mutation

May 21, 2019

Overview VSClinical enables users to evaluate variants according to the ACMG guidelines in a high-throughput fashion and obtain consistent results and accurate variant interpretations. This feature is tightly integrated into our VarSeq platform as well, and when paired together, users can evaluate NGS data and obtain clinical reports all in…

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Variant Interpretation with VSClinical: Clinical Example for Congenital Indifference to Pain

May 16, 2019

VSClinical provides a rapid-fire way to investigate any variant’s impact by following the ACMG Guidelines process for classification. We will be demonstrating this by looking at interesting examples of rare disorders and showcasing some evaluation steps users may deploy in their analysis. Our first example in this blog series is…

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Top 5 Features of Sentieon

Apr 23, 2019

Sentieon develops bioinformatics secondary analysis tools to process genomic data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency. These features are what led to the partnership of Golden Helix and Sentieon to provide users with a comprehensive solution for NGS data analysis. This blog post gives…

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Automating Clinical Workflows: Part III

Apr 19, 2019

In the previous two articles, we explored the different steps of a clinical workflow. The first post covered the automated analysis that creates a VarSeq project. While the second post covered the interpretation steps and generation of a clinical reporting output. These posts illustrated the ease with which these complex…

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Automating Clinical Workflows: Part II

Apr 11, 2019

In the previous blog post, we covered the automated steps to create a VarSeq project. Today we will examine the active analysis steps. These are the steps that require human interpretation to analyze the clinically relevant variants. A lab tech can take the first pass at the output in the…

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Automating Clinical Workflows: Part I

Apr 3, 2019

Automating a clinical workflow creates a stable and repeatable clinical analysis, streamlining everything from variant filtering through clinical reporting. Automation reduces the potential to introduce human error, helps in regulatory compliance, and improves the precision of the clinical results. It is important to know that if you run a sample…

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2019 1st Place Abstract Competition Winner

Apr 2, 2019

Mark Trinder is our 2019 Abstract Competition 1st Place Winner. As we prepare for his upcoming webcast on April 10, 2019, we wanted to give our community a little bit of a background on him! Mark Trinder is an MD/Ph.D. student at the University of British Columbia, Canada working under…

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Golden Helix Receives NIH-SBIR Phase 2 Grant 2R44 GM128485-02

Mar 28, 2019

Golden Helix, Inc. has announced themselves as the recipient of an NIH SBIR Grant 2R44GM128485-02 entitled “Automated and Guided Workflows for Clinical Testing Using NGS Assays.” “With the help of this grant, we will take the clinical automation of NGS data to the next level, focusing on germline diseases and…

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On Our Way to ACMG 2019

Mar 28, 2019

Our team is looking forward to an eventful week at ACMG 2019 in Seattle, Washington! If you are attending the conference, we hope you’ll stop by our booth and say hello to the team: Andreas Scherer, Ph.D., Gabe Rudy, and myself, Shanna Finley! We would love the opportunity to connect…

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Clinical Variant Analysis: Part V

Mar 5, 2019

Examples of Clinical Variant Interpretation with VSClinical In this chapter, I’d like to go through a few examples for variants that have been classified with the help of VSClinical. This will give you a better understanding of how data sources are actually being represented in the software and how those…

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Clinical Variant Analysis: Part IV

Feb 28, 2019

Rules for Combining Various Classification Criteria Now that we have a solid understanding of how the various criteria are meant to be applied, it’s time to look at how the evidence collectively leads to the clinical categorization of a variant. Let’s go through the rule framework for combining the various…

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Clinical Variant Analysis: Part III

Feb 26, 2019

Clinical Variant Analysis – Classification Criteria of Benign Variants The classification of benign variants is overall simpler and more straightforward, with the majority of benign variants being eliminated through allele frequency in various population catalogs. BA1 If a variant is common in one or more population catalog, as indicated by…

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