Golden Helix Blog

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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2019 Abstract Competition Winners

Feb 25, 2019

We would like to thank everyone who entered our 2019 Abstract Competition. This event is an excellent opportunity for our team to hear the unique ways Golden Helix software is being applied around the world. We had a number of remarkable entries this year which made our selection process a…

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Clinical Variant Analysis: Part II

Feb 25, 2019

Clinical Variant Analysis – Classification Criteria of Pathogenic Variants The ACMG Guidelines are utilized for the interpretation of variants. They are primarily applied to diagnose suspected inherited (primarily Mendelian) disorders in a clinical diagnostic laboratory setting. While evaluating variants no matter what the origin, it is important to distinguish between variants…

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Clinical Variant Analysis: Part I

Feb 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…

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New eBook Release: Clinical Variant Analysis

Feb 18, 2019

I am excited to announce the release of my new eBook “Clinical Variant Analysis – Applying ACMG Guidelines to Analyze Germline Diseases“! You can download your complimentary by clicking on the button below. The clinical interpretation of variants in Next-Gen Sequencing is a quickly evolving field, and sound genomic interpretation has never…

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Case Study: Odense University Hospital

Feb 7, 2019

The Department of Clinical Genetics at Odense University Hospital offers a variety of genetic analyses for families of syndromic children and other inherited conditions, averaging 4,000 genetic analyses per year. Their casework spans variant analysis across a broad range of inherited conditions. In 2016, the lab decided to introduce whole…

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How To: VarSeq VCF Import

Feb 5, 2019

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…

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Top-Quality GWAS Analysis: Part V

Jan 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…

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Top-Quality GWAS Analysis: Part IV

Jan 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…

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Top-Quality GWAS Analysis: Part III

Jan 22, 2019

Sample Relatedness Pruning your data based on Linkage Disequilibrium (LD) values and filtering for sample “relatedness” are ideal quality assurance steps following the marker and sample quality filtering described in Part II of this blog series. The value of running an Identity by Decent estimation not only allows you to…

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Top-Quality GWAS Analysis: Part II

Jan 18, 2019

Eliminate Low-Quality Samples and Markers In Part I of this GWAS Analysis series, Dr. Eli Sward provided us with a great overview on the value SVS provides in managing the quality of your SNP or NGS data to maintain the high power and accuracy of your GWAS. He also gave…

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Top-Quality GWAS Analysis: Part I

Jan 16, 2019

Importance of Quality in Association Tests SVS is a research application platform provided by Golden Helix that enables an array of computational analyses including genome-wide association studies (GWAS). GWAS is an observational study that can provide insight into the association of genetic variants with traits and complex disorders. The foundation…

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