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 info@goldenhelix.com. Dr. Heather Huson is a Professor of Dairy Cattle Genetics at Cornell… Read more »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
Just a few weeks ago we announced our partnership with MedGenome. The news was covered by a number of outlets including: Financial Express Pharmabiz Let me expIain the importance and impact of this announcement. Since Varseq was released, we have received strong interest from testing labs that are leveraging our product to implement cancer diagnostic pipelines. Please feel free to take… Read more »
The support team at Golden Helix is always on-hand to help with your SVS and VarSeq needs. We get some questions more often than others, and this blog will answer some of the most common questions we’ve been seeing lately regarding VarSeq. A common question we receive is if data can be filtered from a locally kept set of variants… Read more »
In recent months we have been updating our public annotation library to include the most recent versions of existing sources as well as include new sources. Each of these annotation sources are compatible with our three major products (SVS, GenomeBrowse and VarSeq) and can be used for visualization, annotation and filtering. NHLBI ESP6500SI-V2-SSA137 Exomes Variant Frequencies 0.0.30, GHI Annotations are… Read more »
Yes, I said it. “Them be fighting words” you may say. Well, it’s worth putting a stake in the ground when you have worked hard to have a claim worth staking. We have explored the landscape, surveyed the ravines and dangerous cliffs, laboriously removed the boulders and even dynamited a few tree stumps. Stake planted. Ok, so now I’m going… Read more »
There are many approaches that one might use to define a variant as potentially deleterious. For example, we often see analysis workflows based on rare, non-synonymous variants, perhaps incorporating additional annotation sources that capture known or predicted consequences of coding variants. Annotations for coding regions of the genome are relatively abundant and familiar to genome scientists. We are comfortable in… Read more »
This year the MAGES symposium has a new name, the Symposium on Advances in Genomics, Epidemiology and Statistics or SAGES! The NIH has also been added to the sponsor list and we’re excited to have the support for this informative symposium! Additionally, we were treated to the addition of a new poster session to accompany the fantastic speakers. The trend… Read more »
