Golden Helix Blog

CNV Caller Updates and More with VarSeq 1.4.5

Jun 22, 2017

We have been heads down doing the detailed and careful work to improve our CNV caller algorithm in the past three months since our we launched our Exome capable CNV caller and are very excited about the massive step forward we have made with the VarSeq 1.4.5 release. Additionally, we…

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Calling Cytogenetic CNVs from Shallow Whole Genomes

Jun 21, 2017

Low read depth? Great! We are excited to introduce our new CNV calling algorithm for low and ultra-low read depth Whole Genome Sequencing (WGS) data. This algorithm is designed to call large cytogenetic events with high confidence from low read depth whole genome data, with as few as one million…

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Golden Helix, Inc. – Your Annotation Curation Station

Jun 15, 2017

The current reduced cost and increase availability of genome sequencing has been making academics, clinicians and individuals alike excited with the possibility of increased research depth, diagnosing capability and personal curiosity. And although a freshly sequenced genome is chock-full of tasty letter snippets, the real revelation and education occurs when…

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Cancer Gene Panels Tutorial

Jun 13, 2017

VarSeq enables breakthrough discoveries in cancer diagnostics by supporting gene panel testing and whole exome and genome analysis. We wanted to share our Cancer Gene Panel tutorial which covers a basic gene panel workflow with an emphasis on adding, modifying and manipulating filter chains. This tutorial will start with creating a…

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End-to-End Solution for Clinical Labs Webcast Q&A

Jun 8, 2017

Yesterday’s monthly webcast featured our end-to-end solution for clinical labs. In case you missed it, you can watch the webcast here! There were a number of questions asked in the live event, so in today’s blog post I wanted to recap the Q&A session. Can you go over the requirements…

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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…

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Webcast: Golden Helix’s End-to-End Solution for Clinical Labs

May 25, 2017

We are ending the first half of the year with a webcast featuring our entire clinical software stack: Golden Helix’s End-to-End Solution for Clinical Labs. This webcast is scheduled for Wednesday, June 7th at noon EST, and it’s not one you’ll want to miss! Here are the full details: Wednesday, June 7th…

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Sentieon Genomic Tools Webcast Q&A

May 18, 2017

Yesterday we had an excellent webcast presentation featuring Sentieon’s Dr. Donald Freed. Golden Helix recently partnered with Sentieon to integrate their secondary analysis tools into our software stack, and this presentation is an introduction to their genomic tools. Please check the webcast out here if you missed it! There were a…

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Annotating with gnomAD: Frequencies from 123,136 Exomes and 15,496 Genomes

May 16, 2017

Annotating with gnomAD: Frequencies from 123,136 Exomes and 15,496 Genomes When the Broad Institute team lead by Dan MacArthur announced at ASHG 2016 that the successor to the popular ExAC project (frequencies of 61,486 exomes) was live at http://gnomad.broadinstitute.org/, I thought their servers would have a melt-down as everyone immediately…

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New Tutorial: VSReports

May 11, 2017

The new VSReports tutorial covers a basic VSReports workflow with an emphasis on understanding and exploring report customizations. This tutorial requires an active VarSeq license with the the VSReport feature included. You can go to Discover VarSeq or email [email protected] to request an evaluation license with the VSReports functionality included. VS Reports provides…

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Webcast: The Sentieon Genomic Tools

May 4, 2017

We are excited to announce our next webcast, The Sentieon Genomic Tools – Improved Best Practices Pipelines for Analysis of Germline and Tumor-Normal Samples. This webcast is scheduled for Wednesday, May 17th at noon EST and will focus on our new partnership with Sentieon. Wednesday, May 17th 12:00 pm EST With next-generation sequence…

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Golden Helix announces Partnership with Sentieon

May 1, 2017

Today, we are happy to announce a multi-year partnership with Sentieon, a company that develops bioinformatics secondary analysis tools to process genomic data. This partnership will integrate Sentieon’s secondary analysis tools with Golden Helix software to provide users with a comprehensive solution for genomic data analysis. Sentieon’s suite of secondary analysis…

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New Tutorial: VSWarehouse

Apr 27, 2017

The new VSWarehouse Tutorial covers the basic VSWarehouse workflow.This tutorial focuses on connecting to a VSWarehouse instance from VarSeq, adding an existing VSWarehouse project as an annotation source and using reports and assessment catalogs hosted on VSWarehouse. This workflow requires an active VarSeq license with the VSWarehouse feature included. You can…

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Recent Publications from SVS Users

Apr 25, 2017

We had lots of customers publish their work using our SVS software, and I wanted to share their work with you. Congrats to all! Here are some of the highlights: Francesca Fernandez of the University of Wollongong along with colleagues published Effects of common GRM5 genetic variants on cognition, hippocampal volume…

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CNV User Perspective Webcast Q&A

Apr 20, 2017

Nathan Fortier’s webcast yesterday, CNV Analysis in VarSeq – A User’s Perspective, was an excellent demonstration of our CNV capabilites, so check it out if you missed it. There were a number of questions asked in the live event, so in today’s blog post I wanted to recap the Q&A session. Question:…

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By Popular Request: Our BEAGLE Algorithm Gains Support for Family Structure

Apr 13, 2017

Earlier this year we released our own optimized and integrated BEAGLE implementation for SVS based on the BEAGLE 4.1 and optionally 4.0 algorithms. One of the commonly requested features since that released was to expand the algorithm implementation to be considerate of the parent-offspring relationship between samples to inform and…

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Updated PhoRank with OMIM Phenotype Terms and Improved Rankings

Apr 12, 2017

In our latest VarSeq release, we updated our PhoRank algorithm with the ability to specify OMIM phenotype terms not present in HPO, as well as a general update to the algorithm to improve the results. In this post, we review the fundamentals of how PhoRank determines the ranking of genes…

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Springtime for SVS: Updates to PhoRank, Platform Support and Genotype Imputation

Apr 11, 2017

Recently, we added a natively supported Genotype Phasing and Imputation capability in SNP & Variation Suite 8.7.0. Since then we have had fantastic feedback and adoption as folks take advantage of the BEAGLE 4.0 and 4.1 algorithms from within their existing SNP GWAS and agrigenomic workflows. One piece of feedback…

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CNV Analysis in VarSeq – A User’s Perspective

Apr 6, 2017

We are pleased to announce our next webcast, CNV Analysis in VarSeq – A User’s Perspective. The live event is is scheduled for Wednesday, April 19th at noon EST. Here are the specifics: Wednesday, April 19th 12:00 pm EST Clinical labs must have the ability to go from a collection…

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Updating VarSeq’s Transcript Annotation along with NCBI RefSeq Genes Interim Release

Mar 30, 2017

It may be possible to say that annotating a variant correctly and accurately against gene transcripts is the most important job of a variant annotation and interpretation tool. We take it very seriously at Golden Helix as we support VarSeq and its use by our customers in both research and…

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