Category Archives: Bioinformatic support

ExAC CNVs: The First Large Scale Public Exome CNV Variant Set

ExAC CNVs

ExAC CNVs were released publicly with a recent publication, providing the full set of rare CNVs called on ~60K human exomes. While there are many public CNV databases out there, this is the first one that was derived from exome data, and thus includes both extremely rare and very small CNV events. With the recent release of Golden Helix’s CNV calling… Read more »

Annotating Cancer Mutations with CIViC

      Gabe Rudy    November 15, 2016    2 Comments on Annotating Cancer Mutations with CIViC
CIViC database

While clinical assessments of germline mutations have been collected in ClinVar under the stewardship of the NCBI and the collaborate effort of many testing labs, the same type of resource has been missing for mutations that could informal clinical care in Cancer. Or at least, that is what I thought until I started to work with CIViC. With the stewardship of… Read more »

Genotype Imputation and Phasing now in SNP & Variation Suite

Genotype Imputation

One of the tools at the top of the toolbox for researchers working with microarray data is genotype imputation. Genotype imputation is the process of inferring the genotype of one or more markers based on the correlation pattern (aka linkage disequilibrium or LD) of the surrounding markers for which genotypes are known. We have now integrated a natively ported version of BEAGLE into Golden… Read more »

CADD, OMIM and OncoMD added to SVS

CAD, OMIM and OncoMD

In our SVS 8.6.0 release, we updated our Annotate and Filter Variants feature to utilize our powerful VarSeq annotations. Annotations can be run against gene, interval, variant, and tabular tracks, including RefSeq, ClinVar, CADD, OMIM and OncoMD. The new streamlined dialog allows users to select track specific options and to set up custom filters. While our public annotation repository has… 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 »