Author Archives: Golden Helix

New & Improved ClinVar Annotations

         March 13, 2018
ClinVar

ClinVar is the NCBI variant database that focuses on the categorizing of variant alleles and their interpretation from a clinical standpoint. This has made it a great resource, especially for those seeking variant allele disease correlations and pathogenicity. And this all worked fairly well, but it was changed… Previously, the ClinVar variant track annotation took some time to curate due… Read more »

How we’re curating OMIM: It’s not as easy as you think

         February 13, 2018

Relating human phenotypes to genotypes is the name of the game with OMIM, and as their website says, “is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine.” The Online Mendelian Inheritance in Man (or OMIM) was originally created by Dr. Victor A. McKusick in… Read more »

New and Updated Annotations

         December 7, 2017
Genotype Imputation

Golden Helix is excited to announce a new round of novel and updated annotations; including a frequency track, a region track, and a gene track. All three of these tracks were created with the use of VarSeq and its Convert Wizard functionality. First, the expansive 1000 genomes track (1kG) has been updated to include sub-population allele frequencies and heterozygous and… Read more »

Webcast: An Exploration of Clinical Workflows in VarSeq

         June 29, 2017

Our July webcast presentation will be focused on clinical workflows in VarSeq. We wanted to share the full details with you and hope you are able to attend! Wednesday, July 12th 12:00 PM EST This month’s webcast is a VarSeq exploration, featuring several example workflows and helpful features in VarSeq that can be used in the clinic. We will discuss… Read more »

Golden Helix, Inc. – Your Annotation Curation Station

         June 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 comparing to an annotation foundation. In this post, I’ll review… Read more »

Golden Helix Among 50 Fastest-Growing Tech Companies

         January 3, 2017
Silicon Review

Golden Helix closed out 2016 with a great honor; in December, The Silicon Review Magazine released a special edition naming Golden Helix as one of the fastest-growing technology companies for 2016. You can read the interview with our CEO, Andreas Scherer, Ph.D, here: Delivering industry-leading analytic software and services. We continue to believe that our customers are paramount in this honor, as… Read more »

CADD, OMIM and OncoMD added to SVS

         October 6, 2016
CAD, OMIM and OncoMD

In our SVS 8.6.0 release, we updated our Annotate and Filter Variants feature to utilize our powerful VarSeq annotations. Annotations can be run against gene, interval, variant, and tabular tracks, including RefSeq, ClinVar, CADD, OMIM and OncoMD. The new streamlined dialog allows users to select track specific options and to set up custom filters. While our public annotation repository has… Read more »

Practical VarSeq Example – Cancer Gene Panel

         March 15, 2016

Recently, we were excited to find a new example data set for cancer gene panels. We have included this example data in the latest e-book by Dr. Andreas Scherer, Genetic Testing for Cancer as well as in the latest cancer webcast . This data is from Illumina’s MiniSeq sequencer and the TruSight Cancer panel. The BAM and VCF files for three samples… Read more »

New SVS Meta-Analysis Example Project

         February 9, 2016
SVS 8

New SVS Meta-Analysis Example Project The latest version of the GWAS E-book featured a chapter on Meta-Analysis. We are pleased to make the project used in this chapter available as an example project for SVS (SNP & Variation Suite). This blog post will walk you through the analysis steps used in the example project. This information is also contained in… Read more »

Recent Customer Publications

         January 28, 2016
published

Hope everyone’s new year is off to a great start! Golden Helix has been having wonderful start and have so much to look forward throughout the year. We wanted to share with you the list of our first round of customer publications for 2016, enjoy! Petra Werner of the Children’s Hospital of Philadelphia and colleagues published MESP1 Mutations in Patients with Congenital… Read more »

GWAS Example Project Updated for SVS Viewer

         January 26, 2016
SVS 8

With the release of our updated GWAS E-book, we have recently updated the GWAS example project (SNP Genome-Wide Association Tutorial – Complete). This updated project includes more details about how spreadsheets were generated, how to generate plots and which images were used for the GWAS E-book. This information can be found in the User Notes view in the project navigator and… Read more »

New VarSeq Demo Projects

         November 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 access these projects from the VarSeq start page go to… Read more »

GxE Mixed-Model Analysis Added by Request in SVS

         October 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 working with GWAS. Unfortunately, this did not help our customers who were… Read more »

Analyzing a Single Sample Exome in VarSeq

         October 22, 2015
Exome

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 of variants for further study. After importing the variant data… Read more »

Top Five Add-On Scripts for SVS

         October 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 in at Number Five is the script Convert Dosages to… Read more »

GxE Regression Option to be Available in SVS

         August 26, 2015

We are pleased to announce that another one of the most asked for features is going to be a part of our SNP & Variation Suite™ software, Gene by Environment Interaction Regression (also known as GxE Regression). Earlier this year other highly asked for features were added to SVS including applying a prediction model to a new dataset, cross-validation for… Read more »

Coverage Statistics Come to VarSeq

         August 20, 2015

A prerequisite for clinical NGS interpretation is ensuring that the data being analyzed is of high enough quality to support the test results being returned to the physician. The keystone of this quality control process is coverage analysis. Coverage analysis has two distinct parts. Ensure that there is sufficient coverage to be confident in called variants Make certain that no… Read more »

Quality Assurance: Is it a Boy or Girl?

         August 18, 2015

A common question that comes through support is if there are options in SVS for doing gender inference or checks. There is indeed functionality in SVS for this QC check!  This function is under the Genotype Menu for Sample Statistics; there are a lot of great statistics available to check the quality of your data in SVS, but I’ll walk… Read more »

The 10th Anniversary of GWAS

         July 30, 2015
10th Anniversary of GWAS

GWAS became possible about 10 years ago as the result of several scientific advances. Since then, GWAS has continually developed as a primary method for identification of disease susceptibility genes in humans and other organisms. At Golden Helix we are proud of our history in supporting GWAS analysis from its inception. Our software was used to analyze whole-genome data from… Read more »

Meta-Analysis is now available in SVS!

         July 21, 2015

Earlier this spring we announced that Meta-Analysis was coming to SVS very soon. Now, I am pleased to announce that it is available in the latest release of SVS (version 8.4.0). Meta-Analysis takes the results of two or more GWAS studies for multiple SNPs or markers, and standard meta-analysis statistics are then performed on each SNP and the results compiled into… Read more »