Golden Helix Blog

Match Gene List algorithm not just for genes

Dec 17, 2015

The most common use of the VarSeq Match Gene List algorithm of course is to determine if the variants in your data set are contained within your genes of interest. As an example of this, say you are working with a whole exome trio and only want to consider those…

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Visualizing Meta-Analysis results with a Forest Plot

Dec 10, 2015

We have just released SVS version 8.4.2, and included in the release is a new script for visualizing Meta-Analysis results with a Forest Plot. You can find full details on all the new and updated features included with the update in our Release Notes. Release Notes from all our software…

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Updates to dbNSFP – The Universal Remote of Annotation Sources

Dec 8, 2015

Probably one our most popular public annotation sources we curate and update is the database of Non-Synonymous Functional Predictions (dbNSFP). In it’s recent update, it has expanded the predictions to include FATHMM-MKL and VarSeq now incorporates this new prediction into its voting algorithm of now 6 different discrete predictions per…

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Handling Singletons & Complex Pedigrees with Gene Count Algorithms

Dec 3, 2015

As VarSeq’s adoption has grown among analysts using whole exome data to diagnose rare diseases, a couple of family designs outside of the common trio of an affected child and both parents have come up frequently. While having both parents provides the maximum power to discover de novo mutations and…

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Tumor-normal demo project comes to VarSeq

Dec 1, 2015

With the release of VarSeq 1.3.1 we have included a new demo project to showcase a single tumor-normal pair analysis workflow. The project can be accessed through VarSeq and VarSeq Viewer by going to File > Open Example Projects > Example Tumor-Normal Pair Analysis. This project contains an exome pair…

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A New and Unexpectedly Powerful VarSeq Feature

Nov 17, 2015

With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of…

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New VarSeq Demo Projects

Nov 12, 2015

As VarSeq gains in popularity, we want to give Viewers and customers alike the opportunity to look at projects that are completed from start to finish. To this end, VarSeq (and VarSeq Viewer!) currently comes with two demonstration projects, Example TruSight Cardio Gene Panel and Example YRI Exome Trio Analysis. To…

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Try out SVS for Free!!

Nov 10, 2015

Give our SVS viewer a try today! Interested in seeing what the SNP & Variation Suite (SVS) software can do? Download the free SVS Viewer! With the SVS Viewer, you can explore and interact with the workflows of a pre-built projects. To get you started, we have included a SNP GWAS…

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Q&A from the Two Clinical Workflows webcast

Nov 5, 2015

Our webcast yesterday featured two clinical workflows and and the ease in moving from an unfiltered variant file to a clinical report containing the variants of interest using VarSeq and VSReports. There were several great questions and I wanted to pass on a few of particular interest. Question: Are annotation sources…

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They’ve isolated the funding gene!

Nov 3, 2015

Bipartisan Budget Act of 2015 Passed! We at Golden Helix, and I are certain that many in our community, are more than pleased to hear that President Obama has signed the “Bipartisan Budget Act of 2015“. Most importantly, the budget agreement raises discretionary spending by $80 billion in fiscal years…

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GxE Mixed-Model Analysis Added by Request in SVS

Oct 29, 2015

After our announcement in August that we would be making GxE Regression available in SVS, we were pleased to receive feedback that this was exactly what our customers had been wanting. Being able to account for environmental effects or gene effects as interacting with the SNPs was essential to those researchers…

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Analyzing a Single Sample Exome in VarSeq

Oct 22, 2015

While VarSeq comes with a number of starter workflows that are stored as templates, customers also have the option of creating filter chains from scratch; analyzing a single exome may require you to do exactly that. In this blog, I’ll go through analyzing a single exome and generating a list…

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Introduction to Sergey Kornilov

Oct 8, 2015

Our final webcast presentation in the series of winners from our Annual Abstract Challenge is first place recipient Dr. Sergey Kornilov. A Postdoctoral Associate in the Child Study Center at Yale University’s School of Medicine, Dr. Kornilov’s submission focused on the genetic basis of developmental language disorders in a geographically…

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Top Five Add-On Scripts for SVS

Oct 6, 2015

While stand-alone SVS is an amazing statistical software package for genomics analysis, adding additional Python scripts to the program can expand SVS’s genomic analysis capabilities. In this post, I’ll take you through the most frequently downloaded Add-On Scripts for SVS and the top five were not what I expected! Coming…

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See you at ASHG 2015!

Oct 1, 2015

The Golden Helix® team is gearing up for ASHG 2015 in Baltimore as I would guess many of you are too. I for one am super excited since I grew up in the Baltimore area and have a fondness for Inner Harbor and crabs! This year, you will find Ashley…

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Clinical Reporting comes to VarSeq

Sep 17, 2015

The next release of VarSeq will ship a new product that is highly relevant to our customers in clinical testing labs. Via VSReports, VarSeq now has the ability to generate clinical-grade reports. These reports are fully customizable, containing focused and actionable data. VS Reports ships with report templates that are…

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Precision Medicine e-Book

Sep 15, 2015

Precision Medicine e-Book “It’s far more important to know what person the disease has than what disease the person has.” – Hippocrates (460 BC – 370 BC) Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century we take the understanding of…

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Introducing VarSeq Viewer!

Sep 10, 2015

With our latest release of VarSeq last Thursday, we are proud to offer the VarSeq ® Viewer to the community, for free! When you download VarSeq ® Viewer, you can explore pre-built projects to interact with the annotations and filters the project provides, visualize selected variants with pile-ups, and export data to…

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Dr. Scherer is a Keynote Speaker at Genomics 2015

Sep 8, 2015

A widely attended conference that is coming up on September 21-23 is the third international conference on Genomics 2015 in San Antonio, Texas. The theme of this year’s conference is “Implications and Impacts of Genomic Advances on Global Health“, which promises to provide some interesting presentations and discussions. Current issues in…

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An Introduction to Hilal Al Shekaili

Sep 3, 2015

The past few months our webcast has featured a winner from our Annual Abstract Challenge, and we are happy to have our second place winner, Hilal Al Shekaili, as our speaker for September. Hilal’s submission surrounded novel genetic variants in a consanguineous family with pyridoxine-dependent epilepsy, and he will speak…

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