Category Archives: Learn more about GHI software

Powerful Cohort Analysis with VarSeq’s Count Alleles Algorithm

Although VarSeq is intentionally designed to be a clinical NGS pipeline tool able to run a handful or even single samples through, we have many users who run large cohort style studies with the tool as well. One common use is to compare case/control data to isolate variants shared among affected individuals and exclude those in unaffected. One incredibly powerful… Read more »

Cyber Security Strategies for NGS Testing Labs: Part IV

Golden Helix is in a unique position to provide a secure on-premise analysis solution. This capability is based on two enablers. First, we build our software solutions from scratch and from the ground-up with the assumption that it should run on any operating system and potentially behind firewalls or even without internet access. Second, we provide these solutions on a licensing model based on training and supporting users, not… Read more »

Cyber Security Strategies for NGS Testing Labs: Part III

There is no shortage of actors in cyberspace who can be a potential threat to an organization. The list ranges from high schoolers who want to put newly acquired skills to the test, employees or partners who have access to the company network, to professional hackers who intend to hold data hostage or plan to resell information. On the highest-end, some state-financed actors extend their… Read more »

Cyber Security Strategies for NGS Testing Labs: Part II

Data and security breaches are a fact of life. Organizations are aware of the threats and putting their best efforts up to prevent them as much as possible. Industries across the entire spectrum have been exposed in recent years. I will go through a few examples to show how pervasive this issue has become.  Target  One prominent data breach occurred in… Read more »

Cyber Security Strategies for NGS Testing Labs: Part I

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 »

New eBook Release: Cyber Security Strategies for NGS Testing Labs

I am delighted to be starting the year with releasing a new eBook, “Cyber Security Strategies for NGS Testing Labs”. The field of Precision Medicine is at the forefront of changing the face of healthcare. It changes how we diagnose patients and provides new treatment options that did not exist just a few years ago. It is data-driven by nature. As a… Read more »

The New VSClinical ACMG Guidelines Tutorial

Our tutorials are a popular resource for prospective users. We have added a tutorial to help introduce customers to the ease and utility of the ACMG Guidelines incorporated in VSClinical. The ACMG Guidelines are a collection of 33 criteria that are used to determine a variant’s level of pathogenicity. VSClinical and VarSeq make it easy for users to sort and… Read more »

All New VSClinical AMP Workflow Tutorial

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 »

Variant Interpretation with VSClinical: Evaluation of an X-linked recessive mutation

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 one suite. Coupled with the ability to find novel or… Read more »

VarSeq PhoRank Part: 2 Sample PhoRank Gene Ranking

The PhoRank tool in VarSeq is further explored in this post by looking at the sample-specific capability. VarSeq PhoRank Part: 1 Variant Phorank Gene Ranking showed how the PhoRank algorithm could be applied to all the variants in a VarSeq project, regardless of the number of (or difference in) samples. There is another PhoRank algorithm in VarSeq that allows the… Read more »

VarSeq PhoRank Part 1: Variant PhoRank Gene Ranking

One of the main goals of clinical genomic labs is to identify problematic variants in affected individuals. One tool to assist in this search is the phenotype driven variant ontological re-ranking tool in VarSeq called PhoRank. A common situation facing clinicians is sorting through thousands of variants provided by an individual’s exome data (or possibly the individual’s nuclear family exome… Read more »

All Things VSClinical

      Delaina Hawkins    August 21, 2018    No Comments on All Things VSClinical

Featured in many of our recent blog posts, webcasts and tradeshow discussions, chances are you have heard about our newest tool, VSClinical, by now. Can you blame us though?! Allowing users to automate the clinical interpretation of variants based on ACMG guidelines – it is hard not to talk about it! But, in case you have not, this post serves as… Read more »

NGS-Based Clinical Testing eBook

      Andreas Scherer    February 16, 2017    1 Comment on NGS-Based Clinical Testing eBook

This generation of scientists, clinicians and bioinformaticians have already elevated the standards for diagnosis, prediction and care, ultimately improving patient outcome for millions of people by leveraging genomic information. This trend is only going to continue. Next-gen sequencing has made its way into the clinic. Golden Helix supports the adoption of Precision Medicine by building products, such as our VarSeq… Read more »

NGS-Based Clinical Testing: Part VI

reporting incidental genetic findings

With a properly defined wet-lab and bioinformatics process, we are able to zero in on clinically relevant variants. How does a lab report on the outcome of their analysis? We find that most laboratories conduct their variant classification based on the guidelines formulated by the American College of Medical Genetics (ACMG) for inherited diseases. The ACMG guidelines for variant classification… Read more »

NGS-Based Clinical Testing: Part V

Quality Managment

Any validated bioinformatics pipeline must be continuously monitored. Quality management in clinical testing labs ensures that any divergence from predefined quality metrics during the analysis of clinical samples is investigated. For example: There is an insufficient number of sequence reads that passed the predefined base quality score threshold The number of variants identified in a data set may deviate substantially… Read more »

NGS-Based Clinical Testing: Part IV

clinical testing

After the Wet Lab process has been completed, the bioinformatics analysis of the sequencing data work begins. The next three blogs will focus on three aspects of this process. The building blocks of a bioinformatics pipeline, documentation and validation (today’s topic) Quality Management Clinical Reporting The Building Blocks of an NGS PipelineThe bioinformatics process to analyze NGS data occurs in three… Read more »

NGS-Based Clinical Testing: Part III

DNA sequencing

Getting the NGS wet bench process right is not a small undertaking. Targeted NGS assays such as multigene panels or exome sequencing allow for the targeted analysis of genomic regions that are of particular interest. For every sample type, e.g. blood, formalin-fixed paraffin-embedded specimens, saliva etc, there must be a detailed protocol in place outlining how each sample type is going… Read more »

NGS-Based Clinical Testing: Part II

ngs-based clinical testing

We have come a long way since Next-Generation Sequencing (NGS) evolved as a set of technologies in the 1970s. The higher throughput and rapid reduction of costs associated with NGS have lead to the accelerated adoption of clinical testing that we are experiencing today. Currently, it is applied to analyze inherited diseases, tumors, hematologic malignancies and infectious diseases. It is… Read more »

NGS-Based Clinical Testing: Part I

NGS Testing

The adoption of genetic services is key to our ability to provide personalized medicine in the future. The goal is to better diagnose diseases, predict their outcome, and choose the best possible care option for a patient. We still have a long way to go to achieve this goal. While there is agreement about the ultimate goal, there is still… Read more »