Quantification method affects replicability of eQTL analysis, colocalization and TWAS.

Quantification reference annotation and RNA-seq quantification method substantially affect eQTL detection and gene expression prediction, with significant downstream impacts on colocalization and TWAS across GTEx tissues.

• Why it matters: Upstream RNA-seq processing choices are critically unexplored, even though eQTL mapping, colocalization, and TWAS are widely used to interpret GWAS loci.
• What they did: The study analyzed 48 GTEx tissues and 7 phenotypes, comparing how transcriptomic reference annotation and quantification method change eQTL detection, prediction, colocalization, and TWAS outcomes.
• The result: Concordant results across pipelines are enriched for longer genes, genes with more isoforms, and greater expression heritability, supporting standardized practices for reproducible genetic association studies.