Category Archives: General statistical genetics principles

SVS, Population Genetics, and 1000 Genomes Phase 3

One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes project for some examples.

Genomic Prediction and How it’s Used

Golden Helix is excited to host a webinar on Tuesday August 26th discussing the Genomic Prediction methods which were recently integrated into the SVS software. Genomic prediction uses several pieces of information when calculating its results. Genetic information is used to predict the phenotype or trait for the individuals. The phenotypic trait data can be provided for a subset or for all… Read more »

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in fact, there is more complexity here than you ever really wanted to know about. Andrew Jesaitis covered some of this… Read more »

Population Structure + Genetic Background + Environment = Mixed Model

A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics by authors Bjarni J. Vilhjalmsson and Magnus Nordborg.  Population structure is frequently cited as a major source of confounding in GWAS, but the authors of the article suggest that the problems often blamed on population structure actually result from the environment… Read more »

What is Bioinformatic Filtering?

Recently I gave a presentation on bioinformatic filtering: the process of using quality scores, annotation databases, and functional prediction scores to intelligently and quickly reduce your variant search space. View the recording here» In this webcast, I mention that filtering is something we have been doing for a long time, and that there are some great examples that use exome… Read more »