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 »

Our Customers’ Success

         August 13, 2015

August is off to a great start, especially for some of our customers who have recently published. I wanted to take a minute to share their work with you. Gabor Meszaros of BOKU University Vienna and colleagues published Genome-Wide Selection Signatures in Pinzgau Cattle in Potravinarstvo Scientific Journal for Food Industry which used SNP BeadChips to identifygenomic regions near QTL associated… Read more »

Dr. Folefac Aminkeng Publishes in Nature Genetics

         August 11, 2015

Today I wanted to take a moment to recognize a long-time Golden Helix customer, Dr. Folefac Aminkeng of the Canadian Pharmacogenomics Network for Drug Safety and the University of British Columbia on his recent publication A coding variant in RARG confers susceptibility to anthracycline-induced cardiotoxicity in childhood cancer, in Nature Genetics. Aminkeng and his colleagues performed a genome-wide association study in… Read more »

An Introduction to Vivien Sheehan

         August 6, 2015
Dr. Vivien Sheehan

Last month our webcast featured the third place winner of our Annual Abstract Challenge, Dr. Raluca Mateescu, and August’s webcast will feature co-winner, Dr. Vivien Sheehan. Dr. Sheehan’s submission last winter surrounded the pharmacogenomics of hydroxyurea in sickle cell anemia, and we are excited to have her present this research for our Golden Helix community next week (August 12th, register… 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 »

Recent Customer Publications

         July 28, 2015
Customers

Congratulations to all of our customers who have recently published! It’s always a pleasure to see the interesting and useful work conducted in part with the aid of our software, and we hope you enjoy reading about it as well. Bradley Aouzierat of UCSF and colleagues published Association of IFNL3 and IFNL4 polymorphisms with liver-related mortality in a multiracial cohort… Read more »

Analyze Your 23andMe Genotype Files with Golden Helix

         July 22, 2015
23andMe

I was definitely an early adopter when it comes to personal genomics. In a recent email to their customer base announcing their one millionth customer, they revealed that I was customer #44,299. And I have been consistently impressed with the product 23andMe provides through their web interface to make your hundreds of thousands of genotyped SNPs accessible and useful. It… Read more »

Fulgent Diagnostics Implements VSPipeline to Speed Analysis & Interpretation

         July 22, 2015

Today, we are proud to announce our collaboration with Fulgent Diagnostics, a CLIA certified molecular diagnostics lab. Fulgent offers more than 4,000 single gene tests among others and will implement VSPipeline to help speed up their analysis and interpretation process. On our quest to enable precision medicine, we look forward to working with Fulgent and other diagnostics labs in the… 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 »

Tumor/Normal Pair support now available in VarSeq!

         July 16, 2015

VarSeq now supports analysis of paired Tumor/Normal samples! Tumor/Normal support has been one of the most common feature requests for VarSeq since it was launched late last year, and we are excited to make this functionality available to all of our VarSeq users in the latest update (version 1.1.4). VarSeq is a powerful platform for annotation and filtering of DNA… Read more »

Top 5 things you need to know about VSPipeline

         July 14, 2015

Recently, Golden Helix, Inc. announced the addition of VSPipeline to our VarSeq software suite. VSPipeline is a command-line interface that will allow high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command line context, including existing bioinformatics pipeline. So, what is the big deal? Here are the top five… Read more »

Using GWAS to Improve the Economics of the Aquaculture Industry

         July 9, 2015

Recently, customer Xin Geng of Auburn University published a paper using SVS, and we wanted to share his story with you. Please feel free to contact us if you have questions or if you would like to learn more about SVS at info@goldenhelix.com. For PhD graduate student Xin Geng, conducting Genome Wide Association Study (GWAS) to uncover the quantitative trait… Read more »

Comparing Variants using a Venn Diagram

         July 7, 2015
annotate

One of the lesser known functions in SVS allows the user to create Venn diagrams comparing variants found in multiple spreadsheets. These different spreadsheets could come from individuals samples, a case vs. control group or several variant databases. It is a helpful tool for visually comparing different variants. Start by creating spreadsheets for each group/samples you’d like to compare. The… Read more »

An Introduction to Dr. Ralucu Mateescu

         July 2, 2015

A few months ago in Golden Helix’s 2nd Annual Abstract Challenge, Dr. Raluca Mateescu tied for third place with her entry on the palatability of beef. We mentioned in our previous post highlighting all of the challenge winners that Dr. Mateescu would be presenting her work for the Golden Helix community and the time has come! Next week for our… Read more »

The Clinical Genome Conference 2015 Highlights

         June 30, 2015

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of the conference from my perspective: Talking about clinical genomics is no longer a wonder-fest of individual case studies, but a… Read more »

Our Customers’ Success

         June 23, 2015

It is already almost halfway through 2015, and June has been especially busy as far as customer publication goes. We wanted to pass on the articles to you and congratulate our customers on their success!  Elena Gusareva and Kristel Van Steen of the University of Liege and colleagues recently published A cautionary note on the impact of protocol changes for genome-wide… Read more »

Command-line Interface added to Golden Helix’s VarSeq Software

         June 18, 2015

Golden Helix recently announced the addition of VSPipeline to our VarSeq software. VSPipeline is a command-line interface that will allow high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command line context, including existing bioinformatics pipeline. VSPipeline supports the need to efficiently generate VarSeq projects from workflow-encoding project templates…. Read more »