Expression Quantitative Trait Loci (eQTLs) have often been used to nominate candidate genes from Genome-wide association studies (GWAS). However, commonly used methods are susceptible to false positives largely due to Linkage Disequilibrium of eQTLs with causal variants acting on the phenotype directly. Our method, causal-TWAS (cTWAS), addressed this challenge by borrowing ideas from statistical fine-mapping. It is a generalization of Transcriptome-wide association studies (TWAS), but when analyzing any gene, it adjusts for other nearby genes and all nearby genetic variants.
We have updated the ctwas package. The new version, multi-group cTWAS (or multi-cTWAS), can analyze GWAS and molecular QTL data from multiple modalities and contexts. You can follow the new tutorials.
Tutorial for the original single-group version used in the cTWAS paper (NG 2024) can be found here.
You can browse source code for the new version and report a bug here. You can also join our Google Group to receive notifications of software updates.