Golden Helix Newsletter

 
Whole Genome Sequencing CNV Caller
CNV Caller Updates and More with VarSeq 1.4.5
by Gabe Rudy
VP of Product & Engineering


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 have added the all new Whole Genome large-event caller capable of calling large events on whole genomes (including the cheap ultra-low read depth variety), as well as a command line tool for running all the CNV algorithms and preceding steps using a command line runner.
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Calling Cytogenetic CNVs from Shallow Whole Genomes
Calling Cytogenetic CNVs from Shallow Whole Genomes
by Nathan Fortier
Sr. Software Engineer and FAS


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 aligned reads or 0.02x coverage. The low sequencing cost of these low read genomes, combined with the ease and efficiency of our algorithm, make it an intriguing alternative to existing methods used to identify large chromosomal abnormalities.

The process of calling CNVs from WGS data begins by importing your BAM files into VarSeq and running our new Binned Coverage ...
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Golden Helix, Inc. – Your Annotation Curation Station
Golden Helix, Inc. – Your Annotation Curation Station
by Cody Sarrazin
Product Quality Scientist


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 comparing to an annotation foundation.

In this post, I'll review the annotations Golden Helix provides as part of genomic analysis platforms VarSeq, SNP & Variation Suite and GenomeBrowse. We spend a lot of time digging through public data repositories to bring the best data to your fingertips ...
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Cancer Gene Panels Tutorial
by Darby Kaameraad
Field Application Scientist


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 new project from an empty project template, importing data, creating a filter chain and adding additional annotation sources. The end result will be a new project template that can be used to create new projects in the future ...
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Final thoughts on ESHG 2017
Final thoughts on ESHG 2017
by Andreas Scherer
President & CEO


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! ...
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   CEO Corner
Andreas Scherer
This month we took our CNV analysis capabilities to the next level. Our latest version of VarSeq and VS-CNV now supports calling for whole genomes. We successfully tested this new capability on shallow whole genomes which makes affordable screening tests based on whole genome sequencing a possibility. There are a number of additional improvements that will ship with our latest release. Feel free to read the detailed release notes or contact us directly. Going forward we will focus on creating annotation capabilities for CNVs. This will allow us to reference public CNV-based annotation sources. Also, it will give our customers the ability to build their own CNV assessment catalogues. Stay tuned for more information this Fall!

  Latest Webcast
Webcasts
Golden Helix's End-to-End Solution for Clinical Labs

In this webcast we will provide an overview of our complete end-to end clinical stack. Initially we will walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We will demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call. We then show our powerful tertiary analysis capabilities for gene panels, exome and whole genome data. And finally, we demonstrate how our users can move seamlessly from the variant interpretation stage to a clinical report.
Watch here.

P.S. There are also some Q&A's from the webcast you can read here!

   Customer Success
We love seeing the articles out clients have published citing our software. Here are a few articles we wanting to share that are incredibly diverse and interesting. We hope you enjoy browsing through them!


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About Golden Helix
Golden Helix® is a global bioinformatics firm founded in 1998. Our largest outside investor is GlaxoSmithKline who invested early on into the company. We develop and sell an industry leading clinical solution that supports the analysis of sequencing data and the creation of clinical reports. Clinicians and researchers worldwide trust our solution. Over all these years we have accumulated a significant customer base conducting business with over 350 organizations globally with thousands of users leveraging our various analytics products. Our customers fall into five categories: Large Hospitals, Genetic Testing Labs, Pharmaceutical companies, major research organizations, and government organizations here in the US and internationally. Our work his referenced in over 1,100 publications such as Science, Nature and Nature Genetics.