This month we wanted to highlight four publications from a few of our valued customers. Congrats to all! Zuemei Ji and Christopher Amos of Dartmouth University published The Role of Haplotype in 15q25.1 Locus in Lung Cancer Risk: Results of Scanning chromosome 15 in the Oxford Journals which analyzed lung cancer patients and a control study to determine that rs588765-rs16969968 may… Read more »
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 modeled off of the ACMG guidelines, the de-facto gold standard… Read more »
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 the individual characteristics of a person to a new level…. Read more »
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 widely used formats. To get you started, we have included… Read more »
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 the field to be addressed include next-gen sequencing, clinical and… Read more »
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 on his studies next Wednesday, September 9th (register here). To… Read more »
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 repository of this evidence. Online Mendelian Inheritance in Man (OMIM)… Read more »
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? You may be running into the dreaded world of 1-based versus 0-based coordinate representation! If it’s any consolation, I can promise that all the bioinformaticians… Read more »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
