Tag Archives: SVS

Recent Customer Publications

customer

Several of our customers have published recently using our SVS software, and I wanted to share their work with you. Congrats to all! Here are some of the highlights: Francesca Fernandez of the University of Wollongong along with colleagues published Effects of common GRM5 genetic variants on cognition, hippocampal volume and mGluR5 protein levels in schizophrenia in Brain Imaging and Behavior… Read more »

PhoRank in SVS: Gene Ranking for Your Research Genotypes

gene ranking

Since we released our Phenotype Gene Ranking algorithm in VarSeq, it has become a staple of the way people conduct their analysis. It allows for a combination of filtering with ranking to prioritize follow-up interpretations of analysis results. Our PhoRank algorithm will be available in our upcoming SVS release to also aid in the numerous research workflows performed on SNPs… Read more »

Massive Variant Boost to ClinVar & PubMed Citation Fields

ClinVar

It may have been easy to miss in the drum-beat of monthly annotation updates we do here at Golden Helix, but there are a couple of things that are very special about the January update to the ClinVar database: We added new fields including HGVS names of variants and citations in PubMed for variants ClinVar nearly doubled in size by… Read more »

Determining the best LD Pruning options

LD Pruning

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 »

Compute Kinship Matrices & GBLUP on Very Large Sample Sets

Binary Data

Now available in SVS! Increasingly important in the analysis of the genotype to phenotype relationship is accurately accounting for the relatedness of samples. This is especially important to model correctly in plant and animal populations where man-directed breeding shapes the relationship structure. Along with trait association, one of the high-value use cases for genotyping animals and plants is to estimate… Read more »