Golden Helix Blog

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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OMIM Coming to VarSeq

Sep 1, 2015

When it comes to down to it, the genomic variants we collect in a research and clinical setting are impossible to interpret without that important link of how genes are related to phenotypes. Indisputably, the Johns Hopkins project to catalog all evidence related to inheritable Mendelian diseases is our best…

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Between Two Bases: Coordinate Representations for Describing Variants

Aug 27, 2015

Have you ever scratched your head when looking up a variant and it seems like the number you have for its position is one off from what it looks like in the file or database? Coordinate systems are a foundational concept in NGS data analysis, and understanding them can save…

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GxE Regression Option to be Available in SVS

Aug 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…

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Coverage Statistics Come to VarSeq

Aug 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…

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Quality Assurance: Is it a Boy or Girl?

Aug 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…

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Dr. Heather Huson uses SVS in the Lab and Classroom to Study Livestock Genetics

Aug 4, 2015

Today we wanted to share a recent client case study that demonstrates how our SVS software is being used both in the classroom and laboratory to do livestock genetic analysis. If you have any questions or would like to learn more about SVS, please contact us at [email protected]. Dr. Heather…

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The 10th Anniversary of GWAS

Jul 30, 2015

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…

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Analyze Your 23andMe Genotype Files with Golden Helix

Jul 22, 2015

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…

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Fulgent Diagnostics Implements VSPipeline to Speed Analysis & Interpretation

Jul 22, 2015

Today, we are proud to announce our collaboration with Fulgent Genetics, 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…

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Meta-Analysis is now available in SVS!

Jul 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…

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Tumor/Normal Pair support now available in VarSeq!

Jul 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…

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Top 5 things you need to know about VSPipeline

Jul 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,…

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Using GWAS to Improve the Economics of the Aquaculture Industry

Jul 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 [email protected]. For PhD graduate student Xin Geng, conducting…

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Comparing Variants using a Venn Diagram

Jul 7, 2015

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…

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An Introduction to Dr. Ralucu Mateescu

Jul 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…

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The Clinical Genome Conference 2015 Highlights

Jun 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…

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