Big Picture

Featured in Clinical Lab Manager: Leveraging Next-Generation Sequencing Technology in the Fight Against COVID-19

May 5, 2020

It is an honor to be featured by Clinical Lab Manager where I discuss how Next-Gen Sequencing can be leveraged in the fight against COVID-19.The ongoing COVID-19 pandemic has challenged healthcare systems across the globe. While lockdowns and social distancing measures helped slow the spread, they are not long-term solutions. Most…

Read more →

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

Dec 19, 2019

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…

Read more →

VarSeq Stable 2.1.0 Release Notes

Oct 31, 2018

VarSeq Stable 2.1.0 is Ready for Clinical Validation, See it in Action Next Week This week we are happy to see the general availability of VarSeq 2.1, the culmination of the last five months of work since we launched VSClinical. We have been blown away by the adoption of VSClinical,…

Read more →

Future Direction of Golden Helix

Sep 19, 2018

Celebrating our 20th Anniversary on September 15th, we took some time to reflect on the last two decades in this industry. Two decades of learning, adaption, and growth on the business side as well as the personal side. Employees began their careers with us, made new friends and started their…

Read more →

Bring the Value of VS-CNV to Genomic Research in SVS

Jan 4, 2018

The Golden Helix SNP & Variation Suite (SVS) platform is a powerful and versatile set of tools and algorithms for performing genomic research. That research spans from data originating on genotype micro-arrays to next-generation sequencing. While the majority of SVS users start with genotype data on their samples, any genomic…

Read more →

Secondary Analysis 2.0 – Part V

Aug 22, 2017

An Example of an Integrated Clinical Workflow for CNVs and SNVs In this blog series, I discuss the architecture of a state of the art secondary pipeline that is able to detect single nucleotide variations (SNVs) and copy number variations (CNVs) in one test leveraging next-gen sequencing. In Part I, we…

Read more →

Secondary Analysis 2.0 – Part IV

Aug 15, 2017

Examples of CNV Calling What do CNV calls actually look like? What are some of the key metrics to determine an event? Part IV of the Secondary Analysis 2.0 blog series will answer these questions by walking through some examples of how our CNV caller, VS-CNV, identifies CNVs. Golden Helix…

Read more →

Secondary Analysis 2.0 – Part III

Aug 8, 2017

Detection of CNVs in NGS Data Our Secondary Analysis 2.0 blog series continues with Part III: Detection of CNVs in NGS Data. We will give you an overview of some design principles of a CNV analytics framework for next-gen sequencing data. There are a number of different approaches to CNV…

Read more →

Secondary Analysis 2.0 – Part II

Aug 1, 2017

In this blog series, I will discuss the architecture of a state of the art secondary pipeline that is able to detect single nucleotide variations (SNV) and copy number variations (CNV) in one test leveraging next-gen sequencing. In Part I, we reviewed genetic variation in humans in general and looked…

Read more →

Secondary Analysis 2.0 – Part I

Jul 18, 2017

Human genetic variation makes us unique. On average, humans are to 99.9% similar to each other. Understanding in detail what the nature of the difference in our genetic make-up is all about allows us to assess health risks, and eventually enables Precision Medicine as we determine treatment choices. Furthermore, it…

Read more →

Final thoughts on ESHG 2017

Jun 6, 2017

We are back from another exciting trip to ESHG, hosted in Copenhagen, Denmark last week. We were delighted by the number of researchers and clinicians we were able to connect with. Needless to say,  the weather was outstanding in Copenhagen, which made our stay even more pleasant! Even though this was a European…

Read more →

Final thoughts on ACMG 2017

Mar 28, 2017

Last week was fast and furious for those of us who made it to Phoenix attending ACMG 2017. The event was exceptionally well attended, with great talks and sessions. Here are some of the highlights that are worth mentioning from our perspective. Numerous talks referenced how important the updated Exac/gnomAD…

Read more →

Paying Attention to the Quality Fields in ExAC: A Case Study

Mar 7, 2017

In the past couple of weeks, the topic of the Filter and Quality fields in the popular ExAC population catalog has come up a number of times. It turns out that unlike the 1000 Genomes project, which decided to very heavily filter their variant list to only contain variants they…

Read more →

NGS-Based Clinical Testing eBook

Feb 16, 2017

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…

Read more →

NGS-Based Clinical Testing: Part VI

Jan 26, 2017

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…

Read more →

What to expect from Golden Helix in 2017

Jan 17, 2017

The year 2017 is starting fast and furious for us here at Golden Helix. We just announced a new imputation capability for our SVS product. At the same time, members of our team are on the way to PAG in San Diego to network with our clients in the Plant…

Read more →

NGS-Based Clinical Testing: Part V

Sep 20, 2016

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…

Read more →

Webcast on Big Data in Genomics

Sep 8, 2016

Wednesday, September 21st @ 12:00 pm EDT Every day, the trove of genomic data is growing. Clinics are sequencing targeted genes at high read depths to report out genetic tests. Research groups are adding new exomes and genomes to their disease-specific cohorts. Agricultural breeders are genotyping their herds and flocks…

Read more →

NGS-Based Clinical Testing: Part IV

Sep 6, 2016

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…

Read more →

NGS-Based Clinical Testing: Part II

Aug 25, 2016

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…

Read more →