Cell-type deconvolution of bulk-blood RNA-seq reveals biological insights into neuropsychiatric disorders

Toni Boltz*, Tommer Schwarz, Merel Bot, Kangcheng Hou, Christa Caggiano, Sandra Lapinska, Chenda Duan, Marco P. Boks, Rene S. Kahn, Noah Zaitlen, Bogdan Pasaniuc, Roel Ophoff*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Genome-wide association studies (GWASs) have uncovered susceptibility loci associated with psychiatric disorders such as bipolar disorder (BP) and schizophrenia (SCZ). However, most of these loci are in non-coding regions of the genome, and the causal mechanisms of the link between genetic variation and disease risk is unknown. Expression quantitative trait locus (eQTL) analysis of bulk tissue is a common approach used for deciphering underlying mechanisms, although this can obscure cell-type-specific signals and thus mask trait-relevant mechanisms. Although single-cell sequencing can be prohibitively expensive in large cohorts, computationally inferred cell-type proportions and cell-type gene expression estimates have the potential to overcome these problems and advance mechanistic studies. Using bulk RNA-seq from 1,730 samples derived from whole blood in a cohort ascertained from individuals with BP and SCZ, this study estimated cell-type proportions and their relation with disease status and medication. For each cell type, we found between 2,875 and 4,629 eGenes (genes with an associated eQTL), including 1,211 that are not found on the basis of bulk expression alone. We performed a colocalization test between cell-type eQTLs and various traits and identified hundreds of associations that occur between cell-type eQTLs and GWASs but that are not detected in bulk eQTLs. Finally, we investigated the effects of lithium use on the regulation of cell-type expression loci and found examples of genes that are differentially regulated according to lithium use. Our study suggests that applying computational methods to large bulk RNA-seq datasets of non-brain tissue can identify disease-relevant, cell-type-specific biology of psychiatric disorders and psychiatric medication.

Original languageEnglish
Pages (from-to)323-337
Number of pages15
JournalAmerican Journal of Human Genetics
Issue number2
Publication statusPublished - 1 Feb 2024


  • cell type
  • deconvolution
  • eQTL
  • gene expression
  • neuropsychiatric


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