Fine-grained cell-type specific association studies with human bulk brain data using a large single-nucleus RNA sequencing based reference panel

Brain disorders are leading causes of disability worldwide. Gene expression studies provide promising opportunities to better understand their etiology but it is critical that expression is studied on a cell-type level. Cell-type specific association studies can be performed with bulk expression data using statistical methods that capitalize on cell-type proportions estimated with the help of a reference panel. To create a fine-grained reference panel for the human prefrontal cortex, we performed an integrated analysis of the seven largest single nucleus RNA-seq studies. Our panel included 17 cell-types that were robustly detected across all studies, subregions of the prefrontal cortex, and sex and age groups. To estimate the cell-type proportions, we used an empirical Bayes estimator that substantially outperformed three estimators recommended previously after a comprehensive evaluation of methods to estimate cell-type proportions from brain transcriptome data. This is important as being able to precisely estimate the cell-type proportions may avoid unreliable results in downstream analyses particularly for the multiple cell-types that had low abundances. Transcriptome-wide association studies performed with permuted bulk expression data showed that it is possible to perform transcriptome-wide association studies for even the rarest cell-types without an increased risk of false positives.