Pruning your data based on Linkage Disequilibrium (LD) values is an important quality assurance step for GWAS analysis. In particular, some tests such as Identity by Descent Estimation (IBD), Inbreeding Coefficient Estimation (f) and Principal Component Analysis (PCA) will obtain better results if the markers used are not in linkage disequilibrium with each other. Therefore, Golden Helix’s SVS provides the… Read more »
Variant Normalization: Underappreciated Critical Infrastructure It may surprise you to learn that every variant in the human genome has an infinite number of representations! Of course, although true, I’m being a bit hyperbolic to prove a point. Even seemingly simple mutations like single letter substitutions are legitimately represented differently in the local context of other mutations that can be described… Read more »
ICGC’s database is now available For quite a while, COSMIC has been synonymous with the catalog of “known somatic mutations”. It is the ClinVar of cancer mutations and invests heavily in “expert curation” (having human experts read papers and pull out references to published somatic mutations). But it turns out there is a new kid on the block, and he… Read more »
Our webcast yesterday featured two clinical workflows and and the ease in moving from an unfiltered variant file to a clinical report containing the variants of interest using VarSeq and VSReports. There were several great questions and I wanted to pass on a few of particular interest. Question: Are annotation sources included in VarSeq for free?
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 »