Bioinformatics recipes

Looking for an alternative to quickly annotate a set of variants identified for example by a GWAS? OpenTargets [https://www.opentargets.org/] has a very useful feature that allows you to solve this problem quickly. Citing the OpenTargets documentation : All variants in the variant index are annotated using our Variant-to-Gene (V2G) pipeline. The pipeline integrates V2G evidence that fall into four main data types: Molecular phenotype quantitative trait loci experiments (QTLs) Chromatin interaction experiments, e.g. Promoter Capture Hi-C (PCHi-C) In silico functional predictions, e.g. Variant Effect Predictor (VEP) from Ensembl Distance between the variant and each gene's canonical transcription start site (TSS) Within each data type there are multiple sources of information produced by different experimental methods. Some of these sources can further be broken down into separate tissues or cell types (features). A full list of data sources used in the V2G pipeline can be seen on...

The very powerful ieugwasr library allows you to query tens of thousands of GWAS summary statistics in R (available in the IEU GWAS collection ) very quickly.   Below I show you a nice example of the potential of this library. Suppose we want to retrieve the strength and direction of association of a group of variants to the 700+ immunophenotypes published by Orrù et al in 2020. First, we need to authenticate with ieugwasr: ieugwasr::get_access_token() Next, we need to extract the identification codes of the summary statistics of the article by Orrù et al " Complex genetic signatures in immune cells underlie autoimmunity and inform therapy ": ieugwasr::get_access_token() gwi At this point, with a few lines of code, we can retrieve the association data for a group of variants (in this case two) and save the results in a file for each variant: i The execution speed is really fast.