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 factor family relatedness in your samples but makes screening for… Read more »
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 a snapshot of what a typical genotype spreadsheet may look… Read more »
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 of GWAS utilizes large cohorts sequenced with single nucleotide polymorphisms… Read more »
Our team is more than ready to escape the cold at Golden Helix HQ for an eventful week at PAG XXVII in San Diego, CA! If you are attending the conference, we hope you will stop by our booth and say hello to the team: Dr. Andreas Scherer, Darby Kammeraad, and myself. We would love the opportunity to connect with… Read more »
Happy New Year. I trust you had a relaxing time over the holidays with family and friends as well as a great start into 2019. Golden Helix certainly had a landmark year. There were many highlights that actually shaped the direction for us in the years to come. Please let me mention a few: Essentially, we had a blast in… Read more »
We are happy to announce that our latest version of SVS includes the ability to call CNVs on low read depth Whole Genome Sequencing (WGS) data. Designed for calling large cytogenetic events, this algorithm can detect chromosomal aneuploidy events and other large events spanning one or more bands of a chromosome from genomes with average coverage as low as 0.05x…. Read more »
We are honored to announce that we have been named one of the Top 10 Biotechnology Solution Providers for the second year in a row by CIO Applications. We are at a point where precision medicine is taking off.The Centers for Medicare & Medicaid Services (CMS) has started to reimburse testing labs for NGS-based tests. This is a game changer… Read more »
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 »
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 »
What is Genomic Prediction? Genomic prediction is an algorithm widely used to improve desirable phenotypic traits in agriculture. For example, the cattle industry uses genomic prediction to improve beef quality and palatability as well as improve dairy production (1,2). By using genomic prediction, researchers can minimize multiple expenses in breeding industries as well as diminish the need for performing cumbersome… Read more »
High product quality is a foundational characteristic of a useful and successful product. Quality testing, therefore, is a necessary, albeit an open-ended task. It can at times seem a limitless undertaking in the present using experience from the past to improve the future. Nonetheless, it is approached as a development stage at Golden Helix that is just as essential as… Read more »
In a recent webcast, our VP of Product and Engineering Gabe Rudy gave us insight into the current capability and benefits to lifting over to the GRCh38 assembly. Golden Helix fully supports this transition into the most recent reference assembly and have developed our tools on both the 38 and 37 fronts. The purpose of this blog is to not… Read more »
The SVS 8.8.3 release was created to incorporate some of the CNV, genome assembly control, and splice site capabilities that are present in VarSeq, as well as clean up and streamline the GWAS workflows (like when using Mixed Linear Model algorithms) for a better user experience. New Product Add-Ons for SVS New Features Designed for calling large cytogenetic events, this… Read more »
This blog will conclude our VSClinical Best Practice Workflow series and focuses on one of our new reports: VSClinical ACMG Gene Panel Template. This template is valuable because it automatically enters your variant interpretation from the ACMG Guidelines into the report and eliminates the need for manual submission. I would like to explain how to properly implement this report into… Read more »
In part one of this series, we discussed how the ACMG Classifier can be implemented in your filter chain to support a best practice workflow. To continue our discussion on best practices of VSClinical, this blog will shed light on other attributes of VSClinical that can add support to your evaluation. Specifically, we will explore how VSClinical can help users… Read more »
VSClinical is our most recent product that allows users to evaluate variants according to the ACMG guidelines. As with any tertiary analysis, there is a need to implement best practices into your workflow and using VSClinical for the ACMG guidelines is no exception. That said, we have put together a Best Practices Blog Series, with the purpose of discussing some… Read more »
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 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 »
We’ve packed our bags and we’re off to The Lone Star State to take part in the Association for Molecular Pathology Annual Meeting and Expo (AMP 2018)! As first-time attendees, we’re looking forward to integrating ourselves in the AMP community and showcasing our clinical stack, including VSClinical released earlier this year. Come on over and introduce yourself, you’ll find us… Read more »
Following a wonderful September with our 20th Anniversary and being awarded an NIH-SBIR Phase 2 Grant, October has been nothing short of exciting for us here at Golden Helix. We know that none of our success could happen without the continuous support all of you show us – so thank you to everyone who is a part of this awesome… Read more »
