How RNA-seq quantification choices reshape eQTL, colocalization and TWAS results
A Nature Genetics analysis of GTEx tissues and seven phenotypes shows that annotation and quantification method choices substantially alter eQTL detection, colocalization and TWAS outcomes. Seemingly minor decisions made early in RNA-sequencing data processing can ripple through entire genetic association pipelines, according to a study published in Nature Genetics Researchers led by S Taylor Head and Arjun Bhattacharya examined how two upstream choicesâthe transcriptomic reference annotation used for quantifying short-read RNA-seq samples and the quantification method itselfâaffect expression quantitative trait locus (eQTL) mapping, colocalization analysis and transcriptome-wide association studies (TWAS) These three approaches are among the most widely used tools for interpreting genome-wide association study (GWAS) loci, helping researchers connect genetic variants to gene…
