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Original Research ARTICLE

Front. Genet. | doi: 10.3389/fgene.2020.575928

Cell type-specific annotation and fine mapping of variants associated with brain disorders Provisionally accepted The final, formatted version of the article will be published soon. Notify me

  • 1Children's Hospital of Philadelphia, United States
  • 2Columbia University, United States

Common genetic variants confer susceptibility to a large number of complex brain disorders. Given that such variants predominantly localize in non-coding regions of the human genome, there is a significant challenge to predict and characterize their functional consequences. More importantly, available context-free methods do not take into account tissue/cell specificity of the diseases, limiting the ability to predict the functional consequences of common variants on brain disorders. In this study, we introduce a comparative multi-step pipeline to investigate the relative effectiveness of context-specific and context-free approaches to prioritize disease causal variants. As an experimental case, we focused on schizophrenia (SCZ), a debilitating neuropsychiatric disease for which a large number of susceptibility variants is identified from genome-wide association studies. We tested over two dozen available methods and examined potential associations between the cell/tissue-specific mapping scores and open chromatin accessibility, and provided a prioritized map of SCZ risk loci for in-vitro or in-vivo functional analysis. We found extensive differences between context-free and tissue-specific approaches and showed how they may play complementary roles. As a proof of concept, we found a few sets of genes, through a consensus mapping of both categories, including FURIN to be among the top hits. We showed that the genetic variants in this gene and related genes collectively dysregulate gene expression patterns in stem cell-derived neurons and characterize SCZ phenotypic manifestations, while genes which were not shared among highly prioritized candidates in both approaches did not demonstrate such characteristics. In conclusion, our pipeline enables prioritization of the most likely disease-causal common variants in complex brain disorders.

Keywords: GWAS - genome-wide association study, Schizophreina, fine mapping, variant annotation, brain disorder

Received: 24 Jun 2020; Accepted: 05 Nov 2020.

Copyright: © 2020 Doostparast, Ionita-Laza and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Kai Wang, Children's Hospital of Philadelphia, Philadelphia, United States, wangk@email.chop.edu