Author Archives: Gabe Rudy

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About Gabe Rudy

Meet Gabe Rudy, GHI’s Vice President of Product and Engineering and team member since 2002. Gabe thrives in the dynamic and fast-changing field of bioinformatics and genetic analysis. Leading a killer team of Computer Scientists and Statisticians in building powerful products and providing world-class support, Gabe puts his passion into enabling Golden Helix’s customers to accelerate their research. When not reading or blogging, Gabe enjoys the outdoor Montana lifestyle. But most importantly, Gabe truly loves spending time with his sons, daughter, and wife. Follow Gabe on Twitter @gabeinformatics.

  

Customizing Your VSClinical Workflow: Part II

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 »

Customizing Your VSClinical Workflow: Part I

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

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

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 »

Fast Annotations Around the Globe: Our Sydney and Frankfurt Data Mirrors

Server Mirror

If you have watched this blog over time, it would be no surprise that Golden Helix invests a lot in curating genomic annotations for use with our clinical and research analysis products. Often, we spend considerable time on the attention to detail necessary to ensure the best experience for any data source by cleaning, normalizing, documenting and then distributing it through our data annotation server. Many annotations… Read more »

Following the AMP Guidelines with VSClinical: Part II

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 »

Following the AMP Guidelines with VSClinical: Part I

In the world of genomics shaping precision medicine in oncology, the limiting factor is the time-to-sign-out of a fully interpreted molecular profile report. There are many components of the entire testing process that add to the turn-around time of each test. Many of these steps, such as sample prep, sequencing, and automated secondary analysis, are bounded and consistent in their time requirements. The hands-on… Read more »

VSClinical Updates & a Tour of Cancer Annotations – Webcast Q&A

This webcast generated a lot of great questions about the content covered in the video above. I have summarized our Q&A session below and included some questions I didn’t have time to answer during the live event. If you have any further questions, reach out to us at info@goldenhelix.com! Q: Can I upload my existing classifications into a consortium source?… Read more »

Great Time at AMP 2018

      Gabe Rudy    November 6, 2018    No Comments on Great Time at AMP 2018

We just got back from three busy days at the Molecular Pathology (AMP) conference in friendly San Antonio, Texas. Keeping up the Golden Helix conference momentum for the year, we had 3-4 in-booth demonstrations a day covering our CNV calling, variant interpretation, and data warehousing products for NGS-based genetic tests. And in short, NGS based tests for cancer and germline… Read more »

VarSeq Stable 2.1.0 Release Notes

      Gabe Rudy    October 31, 2018    No Comments on VarSeq Stable 2.1.0 Release Notes
VSClinical algorithm

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, outpacing any previous product launch in terms of the pace… Read more »

Using the GRCh38 reference assembly for clinical interpretation in VSClinical: Webcast Q&A

This webcast generated some great questions! If you have any other questions for me that are not answered below, please feel free to ask those by emailing support@goldenhelix.com. Does VSClinical come with support for the new reference genome? Yes! We worked hard to make everything work in VSClinical regardless of your choice of reference genomes. The only caveat is that… Read more »

Clinical Variant Interpretation: Part VII

VSClinical algorithm

Automating the ACMG Guidelines and Providing Scoring Recommendations As we discussed in our recent webcast on VSClinical, the process of scoring the ACMG guidelines requires evaluating evidence for the connection between a variant and the disorder or condition being evaluated by the genetic test for an individual. These lines of evidence cover clinical presentation, gene function, bioinformatic annotations and in-silico… Read more »

Clinical Variant Interpretation: Part IV

VSClinical algorithm

In the last installment of this series, I covered the basics of variant interpretation and how it fits into the genomic testing process. Now we can cover in more detail how VSClinical works, what algorithms and annotation sources power the recommendations and how the ACMG criteria are organized into useful categories. VSClinical is built to make the process of evaluating… Read more »

VSClinical Webcast Q&A

      Gabe Rudy    April 20, 2018    No Comments on VSClinical Webcast Q&A

This week we launched VSClincial with our first webcast to show our powerful new way to perform variant interpretation following the ACMG guidelines. Our audience asked a lot of great questions on the new product and I’d like to highlight a few here. Can VSClinical run on a laptop and/or a locked down environment? Like all of Golden Helix products, you have… Read more »

Clinical Variant Interpretation: Part III

VCF file format

Yesterday we launched VSClincial with our first webcast in what will be a series about this powerful new way to perform variant interpretation following the ACMG guidelines. In this post, I wanted to cover the motivation for VSClinical and how we curated and presented the 33 criteria from the ACMG Guidelines into an intuitive workflow with various bioinformatic evidence and… Read more »

Using GRCh38 for Clinical Interpretation: Now Possible with Our Custom LiftOver Tracks

There are many good reasons why the pursuit of the highest quality genomic interpretation would lead you to the latest human reference. It is more complete and fixes incorrect or partially missing genes that have known implications for human disease. While most major projects cataloging human populations have plans to re-do all their genomic alignments to the new human reference… Read more »

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

Eigenvalue Decomposition

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 information across a cohort can be used in our various… Read more »

The Clinical Utility of the 1000 Genomes Variant Frequencies

We have a lot to thank the 1000 Genomes project for in the genomics community. By the collaborate efforts of many researchers and organizations, the project produced not only the first catalog of rare human variation but in the process standardized many things we take for granted, such as the VCF and BAM file formats. The variant frequencies of the… Read more »

VSWarehouse Updates with the Power of VarSeq 1.4.7

VSWarehouse Updates

With the recent release of VarSeq 1.4.7, we have expanded the concepts of our popular assessment catalog to include CNV and other region-based records and not just variants. To match these capabilities, we have made a major update to VSWarehouse that supports these new record types in the centrally hosted and versioned Catalogs and Reports. Review of the VSWarehouse Genomic… Read more »

VarSeq Updated with CNV Annotations, CNV PhoRank and Region Assessment Catalogs

VarSeq Updated

VarSeq Updated with CNV Annotations, CNV PhoRank, and Region Assessment Catalogs This year we have released multiple advances to support CNV analysis in VarSeq, expanding our target region based VS-CNV caller to handle exomes and low-depth genomes as well as additional supporting algorithms like calling Loss of Heterozygosity regions. To top this off, VarSeq 1.4.7 has been shipped with many… Read more »