Category Archives: How to’s and advanced workflows

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 »

Automating & Standardizing Your NGS Workflow: Part III

         September 3, 2019

In our last part of this series, we showed how to run a pre-built workflow template via VSPipeline to automatically import and filter sample variants to streamline the search for clinically relevant variants. Now, we can deep-dive into our filtered, pathogenic variants to fully understand and capture their final classification and interpretation. Filtered Germline Variants for ACMG Guidelines The VSPipeline… Read more »

Automating & Standardizing Your NGS Workflow: Part II

         August 29, 2019

VSPipeline: Automating your Tertiary Workflows The first part of this “Automating & Standardizing your NGS Workflow” blog series covered the secondary analysis steps of read alignment and variant calling with Sentieon. The next step is to transition into the tertiary analysis via utilization of our workflow automation tool, VSPipeline. VSPipeline operates as a command-line tool meant to simplify the deployment… Read more »

Automating & Standardizing Your NGS Workflow: Part I

         August 5, 2019

Secondary Analysis with Sentieon: Rapid and Accurate Variant Calling This blog post will cover the utilization of secondary analysis tools to produce a list of high-quality variants and associated coverage data. This data will serve as the main, importable content for the tertiary stage of analysis where variants are interpreted and classified for their impact on a patients’ disorder. We… Read more »

Automating & Standardizing Your NGS Workflow

         July 30, 2019

As our regular customers may know, we write our blogs to provide relevant content to any NGS-based analysis with VarSeq. Our goal here at Golden Helix is to provide top quality software and guidance on how to use the software efficiently to perform variant analysis. However, this blog series will take a more general perspective and supply some insight into… Read more »

Shared Data in VarSeq

         July 22, 2019

When using VarSeq; annotations, application settings, and assessment catalogs are all stored locally. Sometimes these resources can grow to large space grabbing directories, causing you to either purchase additional storage devices or getting rid of previously downloaded resources you might need down the road. But there’s hope! You can set where you want all of your data stored to be… Read more »

VarSeq Variant Annotation Normalization

         July 18, 2019

Smoothing Hurdles into Speed Bumps when creating Annotation Sources Although most researchers assume that getting the pile of VCF sequence files is the largest hurdle in moving towards an analysis, there still exists the looming step of normalizing the variant calls in annotation sources to make variant comparison easier. In this ever-refining field of study, VarSeq continually works to increase… Read more »

Clinical Variant Analysis for Cancer: Part V

         July 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. Of course, there is more that can be done. The field is… Read more »

Clinical Variant Analysis for Cancer: Part IV

         June 25, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants Somatic variants can manifest in different ways: Single Nucleotide Variants Indels Fusions and Copy Number Variations 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 contrast… Read more »

Clinical Variant Analysis for Cancer: Part III

         June 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 in the form of a BAM file, to identify loci… Read more »

Clinical Variant Analysis for Cancer: Part II

         June 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. The key paper in this area was published by Li et. al (2017) with the title “Standards and Guidelines for the Interpretation and… Read more »

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

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 for a patient who has an indifference to pain, while… Read more »

Automating Clinical Workflows: Part III

         April 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 report. These posts illustrated the ease with which these complex tasks can be carried out. Today we’ll dig a little bit… Read more »

Automating Clinical Workflows: Part II

         April 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 generated VarSeq project. They can perform the quality control and… Read more »

Automating Clinical Workflows: Part I

         April 3, 2019

Automating a clinical workflow creates a stable and repeatable clinical analysis. 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 through your clinical pipeline, you are going to get the same results today as you will in 6… Read more »

Clinical Variant Analysis: Part I

         February 19, 2019

Clinical Variant Analysis – Applying ACMG Guidelines to Analyze Germline Diseases The clinical interpretation of genetic variants is time-consuming and requires strict attention to detail. Clinicians must thoroughly review any variants that could potentially cause disease using a complex set of guidelines. There are guidelines for the interpretation of variants relating to hereditary risk, germline diagnostics issued by the American… Read more »

How To: VarSeq VCF Import

         February 5, 2019
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The Beginning of Your Tertiary Analysis VarSeq is designed to be your NGS tertiary analysis solution providing users simple but in-depth means of exploring gene panel, exome, and whole genome variants. For those not accustomed to the VarSeq software, the main import file for variant analysis is the VCF. Those who are familiar with the VCF know that there can… Read more »

Top-Quality GWAS Analysis: Part V

         January 28, 2019

As our final part of the ‘Top-Quality GWAS Analysis’ blog series, we will be giving a summary of the values behind GWAS quality control and quality assessment. Performing GWAS can provide insight into the association of genetic variants with traits and complex disorders. Any novel insights into marker-phenotype associations need to be based on performing quality control steps. In this… Read more »

Top-Quality GWAS Analysis: Part IV

         January 24, 2019

Population Stratification This article is going to cover how to factor for population stratification in your association test to continue our blog series on top quality GWAS analysis (additional articles for this series are located at the bottom of this blog). Quality control steps up to this point have included assessing sample and marker statistics, LD pruning on markers, and… Read more »