Non-coding genomic variants constitute the majority of trait-associated genome variations;however,the identification of functional non-coding variants is still a challenge in human genetics,and a method for systematic...Non-coding genomic variants constitute the majority of trait-associated genome variations;however,the identification of functional non-coding variants is still a challenge in human genetics,and a method for systematically assessing the impact of regulatory variants on gene expression and linking these regulatory variants to potential target genes is still lacking.Here,we introduce a deep neural network(DNN)-based computational framework,RegVar,which can accurately predict the tissue-specific impact of non-coding regulatory variants on target genes.We show that by robustly learning the genomic characteristics of massive variant-gene expression associations in a variety of human tissues,RegVar vastly surpasses all current non-coding variant prioritization methods in predicting regulatory variants under different circumstances.The unique features of RegVar make it an excellent framework for assessing the regulatory impact of any variant on its putative target genes in a variety of tissues.展开更多
基金supported by the General Program of the National Natural Science Foundation of China(Grant No.31771397)the Beijing Nova Program(Grant No.20180059).
文摘Non-coding genomic variants constitute the majority of trait-associated genome variations;however,the identification of functional non-coding variants is still a challenge in human genetics,and a method for systematically assessing the impact of regulatory variants on gene expression and linking these regulatory variants to potential target genes is still lacking.Here,we introduce a deep neural network(DNN)-based computational framework,RegVar,which can accurately predict the tissue-specific impact of non-coding regulatory variants on target genes.We show that by robustly learning the genomic characteristics of massive variant-gene expression associations in a variety of human tissues,RegVar vastly surpasses all current non-coding variant prioritization methods in predicting regulatory variants under different circumstances.The unique features of RegVar make it an excellent framework for assessing the regulatory impact of any variant on its putative target genes in a variety of tissues.
