An analytical framework for decoding cell type-specific genetic variation of gene regulation

Yanyu Xiao, Jingjing Wang (), Jiaqi Li, Peijing Zhang, Jingyu Li, Yincong Zhou, Qing Zhou, Ming Chen, Xin Sheng, Zhihong Liu, Xiaoping Han () and Guoji Guo ()
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Yanyu Xiao: Zhejiang University School of Medicine
Jingjing Wang: Zhejiang University School of Medicine
Jiaqi Li: Zhejiang University School of Medicine
Peijing Zhang: Zhejiang University School of Medicine
Jingyu Li: Zhejiang University School of Medicine
Yincong Zhou: Zhejiang University
Qing Zhou: Zhejiang University
Ming Chen: Zhejiang University
Xin Sheng: Zhejiang University Medical Center
Zhihong Liu: Zhejiang University Medical Center
Xiaoping Han: Zhejiang University School of Medicine
Guoji Guo: Zhejiang University School of Medicine

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract A deeper understanding of genetic regulation and functional mechanisms underlying genetic associations with complex traits and diseases is impeded by cellular heterogeneity and linkage disequilibrium. To address these limits, we introduce Huatuo, a framework to decode genetic variation of gene regulation at cell type and single-nucleotide resolutions by integrating deep-learning-based variant predictions with population-based association analyses. We apply Huatuo to generate a comprehensive cell type-specific genetic variation landscape across human tissues and further evaluate their potential roles in complex diseases and traits. Finally, we show that Huatuo’s inferences permit prioritizations of driver cell types associated with complex traits and diseases and allow for systematic insights into the mechanisms of phenotype-causal genetic variation.

Date: 2023
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DOI: 10.1038/s41467-023-39538-7

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