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 Coming to 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. In tomorrow’s webcast, we will announce the coming integration of a… Read more »

Why Call CNVs: Getting More from your NGS Data

CNV Call

Copy Number Variants have been important to clinical genetics for quite a while now. So, what has made now the right time to be looking at calling CNVs from NGS data? Well, there are a number of good reasons. The dominant one is simply that the NGS data you are already creating for calling variants can be used in many cases… Read more »

Let There Be Genomes: Big Data Genomics Webcast Teaser

Big Data Genomics

Big data is here, but fear not, you don’t need a Hadoop cluster to analyze your genomes or your cohorts of tens of thousands of samples! It turns out, for the kind of algorithms employed in variant annotation and filtering, running optimized local programs is often faster anyway. As we support our diverse customer base, we have definitely seen 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 »