Search Results for: annotation

Updated GRCh38 VarSeq Project Templates

         February 4, 2020

As many of our users know, VarSeq comes shipped with various project templates that are designed to give users a baseline workflow to get started with their projects. These templates are tailored for various applications including tumor-normal, trios, cancer and hereditary gene panels, and ACMG Guidelines workflows. The templates contain application-specific annotation sources and algorithms that will automatically load into… Read more »

Customizing Your VSClinical Workflow: Part II

         January 27, 2020

Customizing VSClinical ACMG Guidelines Workflow Part 2  In the first part of this series, we covered how VarSeq provides customization of the clinical analysis workflow process. VSClinical’s various customization parameters within the ACMG Guidelines workflow includes the choice of how the internal knowledge base of previous variant interpretations are stored and what considerations go into this choice. In this blog, we… Read more »

Cyber Security Strategies for NGS Testing Labs: Part I

         January 23, 2020

Hospitals and testing labs are undergoing a digital transformation like any other business in our time. They deal with personal data in categories with the highest level of security requirements: personal identity and medical records. The architecture chosen to store and analyze this data is critical to provide the best protection against a data breach incident. The liability and institutional… Read more »

Introducing Drugs & Trials for Cancer Diagnostics

         January 23, 2020

When interpreting a variant using the AMP/ASCO guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials, FDA approved therapies and peer-reviewed studies. Unfortunately, strong evidence linking… Read more »

Customizing Your VSClinical Workflow: Part I

         January 14, 2020

Clinical labs offer a unique and sophisticated product that is performed repeatedly with high standards of quality. VarSeq was developed to provide labs with the customization required for clinical genetic tests in a repeatable workflow. On top of this, VSClinical offers additional parameters and choices that can be made when designing the test workflow. In this blog series, we will… Read more »

Securing Your Genomic Testing with Golden Helix

         December 19, 2019

Genetic testing labs deal with personal data in categories with the highest level of security requirements: personal identity and medical records. Given the liability and risk associated with a breach of this secure information, it is not surprising that many labs and institutes that aggregate genomic data prefer, if not require, on-premise analysis and storage solutions.  Golden Helix is in… Read more »

Golden Helix’s End-to-End Architecture for Clinical Testing Labs

         December 19, 2019
Golden Helix's End-to-End Architecture

As clinical genetic tests have been adopted as a critical enabler of precision medicine, the number of tests offered by clinical labs and the volume of tested patients has grown by orders of magnitude in the past five years. The Gene Testing Registry, managed by the NIH, documented a rise from 13,000 to 60,000 tests offered in the US market… Read more »

Somatic Variant Calling with Sentieon: Customizations

         December 10, 2019
Sentieon

The first two blogs in this series covered Sentieon’s somatic variant calling from Tumor with Normal (Part I) and Tumor without Normal (Part II). In addition to providing multiple somatic variant calling processes, users also have access to high-sensitivity scripts and full support for the GRCh38 reference assembly. Without going into excessive detail, this final blog of the series will… Read more »

Reflecting on AMP 2019

         November 14, 2019

Our team has returned from the annual meeting of the Association of Molecular Pathology (AMP 2019), and, as always, I am grateful for all the wonderful experiences we are bringing back with us. The plenary sessions and talks were bountiful, and we were very impressed with the well-organized exhibition. Hats off to everyone involved in planning this great event! Innovation… Read more »

End of Year Bundles 2019

         November 12, 2019

It’s the most wonderful time of the year; our software specials are here! Now is the time to implement a Golden Helix solution to automate your workflows and analyze variants quick, easy, and affordably with our Year-End Bundles. Select packages which come once a year… these deals have been designed to fit your lab’s needs – and budget. Please note… Read more »

All New VSClinical AMP Workflow Tutorial

         November 5, 2019

We have recently added a tutorial to help introduce customers to the ease and utility of the AMP Guidelines incorporated in VarSeq’s VSClinical package. The AMP Guidelines allow users to sort through available clinical evidence in a streamlined fashion to arrive at final classification and interpretation and then transfer that information into a clinical report. And the AMP Guidelines also… Read more »

Somatic Variant Calling with Sentieon: Tumor-Normal Workflow

         October 31, 2019
Sentieon

As I mentioned in the first part of this series, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Utilization of a Tumor-Normal Workflow In addition to the fundamental process of alignment and variant calling, there are a few more steps that will improve the quality of your secondary analysis. Figure 1 (below)… Read more »

VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP Workflow

         October 25, 2019
VSWarehouse Updates

This month’s webcast delves into VSWarehouse with a focus on our new capability of storing somatic variant projects and catalogs built for the AMP Guidelines within VSClinical. If you didn’t have a chance to join us for the live event, please enjoy the video recording below. Previous webcasts have gone into great detail on the features and processing of somatic… Read more »

VarSeq 2.2.0 Release Notes

         October 23, 2019
ClinVar

VarSeq 2.2.0 was released today and this a stable release full of upgrades and polishes. Some of the newer features include the ability to store and include AMP Cancer assessment catalogs on VSWarehouse, quicker accessibility to common annotations plotted in GenomeBrowse, and the addition of all of our standard templates for the GRCh38 genome assembly. Many of the polishes were… Read more »

Reflecting on ASHG 2019

         October 22, 2019

As our team returns from another successful ASHG conference, I would like to reflect on the great memories, connections, and future plans that were made at this meeting. First, I will start by thanking everyone involved with the superb planning and execution of the conference. We are thankful to have this opportunity to connect with our customers, partners, and friends… Read more »

Copy Number Variants Using AMP Guidelines

         October 10, 2019

The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you… Read more »

Variant Interpretation with VSClinical: RET-KIF5b Gene Fusion

         September 24, 2019

Gene Fusion Background Gene fusions are hybrid genes that result from translocations, interstitial deletions, or chromosomal inversions that can lead to constitutive gene activation and result in increased or abnormal protein production. Increased or abnormal protein production subsequently can play an important role in tumorigenesis and thus identifying and evaluating this type of biomarker is important in the cancer workspace…. Read more »

Automating & Standardizing Your NGS Workflow: Part IV

         September 10, 2019

We have covered a lot of ground in this Automating & Standardizing Your Workflows blog series. First, we saw how to perform secondary analysis with Sentieon to generate the necessary VCF and BAM files for tertiary analysis in Part I. The implementation of VSPipeline allowed for rapid import and project generation for a predefined cancer gene panel project template in… Read more »

Following the AMP Guidelines with VSClinical: Part II

         September 5, 2019

VSClinical  users can interpret and report genomic mutations in cancer following the AMP guidelines which we’re demonstrating in this “Following the AMP Guidelines with VSClinical” blog series. Part I introduced the hands-on analysis steps involved in creating a high-quality clinical report for targeted Next-Generation Sequencing (NGS) assays. We reviewed sample and variant quality, including the depth of coverage over the target regions by the sequencing performed for each sample. Now, we are ready to… Read more »