Typically, researchers are looking for rare variants in their next generation sequencing datasets. However, most of the nonsynonymous variants have unknown significance because there is an inherent difficulty in validating large numbers of rare variants or even detecting rare variants with high statistical power. In lieu of this issue, computational tools are needed as they accurately predict the pathogenicity of… Read more »
Did you know you can control your preferred transcript settings for clinical interpretation in VSClinical? Your lab is analyzing the DNA of a tissue sample from a patient with small cell lung cancer. The lab technician has imported the patient data into VSClinical to detect clinically relevant variants and evaluate and score these according to the AMP Guidelines, as well… Read more »
It is common knowledge that variants can be germline or somatic depending on whether the variant was inherited or acquired after birth. A well-known example is cancer-causing mutations in the BRCA genes, wherein the mutation may or may not have been inherited. Understanding the origin of the cancer-causing mutation is important when assessing potential treatment options as well as identifying… Read more »
SVS offers several options to conduct genome wide association tests and mixed linear models. At times, it can be challenging to decide which test, model, or adjustments to use when setting up your analysis. I want to briefly explore the options available in SVS for association tests, and mixed linear models to hopefully facilitate in understanding and choosing which options… Read more »
Thank you to everyone who joined me for yesterday’s webcast, I hope you all enjoyed it. If you missed the live event and are interested in knowing what we talked about, good news, you can watch the recorded version right here! There were so many great questions asked during our Live Q&A that I was unable to answer all of… Read more »
Golden Helix ships a variety of templates that are designed to provide a starting point for users to evaluate variants in VarSeq. Naturally, as users become more familiar with the software, there is a desire and necessity to tailor the template design to accommodate a more thorough variant analysis. To add to these template customizations there are several algorithms and… Read more »
At Golden Helix, we want our new users to hit the ground running with VarSeq and not spend oodles of time getting started building and automating their workflows. To achieve this goal, our team has generated blogs, webcasts, and tutorials that explain and demonstrate workflows that are possible with VarSeq. Each VarSeq tutorial offers step by step instruction in which… Read more »
As many of our users know, VarSeq comes shipped with various project templates that are designed to give users a baseline workflow to get started with their projects. These templates are tailored for various applications including tumor-normal, trios, cancer and hereditary gene panels, and ACMG Guidelines workflows. The templates contain application-specific annotation sources and algorithms that will automatically load into… Read more »
Thank you all for tuning in to yesterday’s webcast, “Simplify Your GWAS & Genomic Prediction with SVS”. I hope you all enjoyed it as much as I did! If you didn’t get a chance to join us for this live webcast, you can watch the recording below. We covered a lot of topics in so little time, but you all… Read more »
SVS is a project-oriented program that manages and analyzes genomic datasets. This webcast statistically and visually explores the relationships among genetic variants within a cattle dataset. Even further, this webcast evaluates genotypes with corresponding phenotypes to assess how well a model can predict a phenotype of interest. Starting with genotypic data from the microarray and the recorded phenotypic data for… Read more »
Huntington’s Disease (HD) Background Huntington’s Disease (HD) is an autosomal dominant neurodegenerative disease that is caused by a mutation in the huntingtin (HTT) gene resulting in 36 or more CAG trinucleotide repeats in exon 1. Individuals affected by HD experience motor disorders including involuntary movements and poor coordination, cognitive impairments showing a decline in thinking and reasoning and psychiatric disorders… Read more »
