A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men

BMC Genomics

Lei Yu¹  Haiying Zhang¹  Yonghua Jiang¹  Yong Gao¹  Yanling Hu¹  Xiaobo Yang¹  Jinghan Su¹  Zengnan Mo¹  Aihua Tan¹  Tianyu Li¹  Qingniao Zhou²  Qunying Wu²  Tingxi Lu³  Lianfeng Li³  Chenyang Hou³  Hongli Huang⁴  Chenqi Zhang⁴  Yuanjie Huang⁴  Yuanyuan Zhu⁴  Haofa Kuang⁴  Wei Wei⁴  Weidong Li⁴  Xing Xie⁴ 

[1] Center for Genomic and Personalized Medicine, Guangxi Medical University;Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University;Department of Information and Management, Guangxi Medical University;Life Sciences Institute, Guangxi Medical University;

关键词: Phenomics;    FAMHES cohort;    Biochemical indices;    Shared genetics;    Lipid metabolism;   

DOI  :  10.1186/s12864-019-6363-0

来源: DOAJ

【 摘 要 】

Abstract Background Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically explore shared genetics among 29 biochemical indices based on the Fangchenggang Area Male Health and Examination Survey cohort. Result A total of 1999 subjects with 29 biochemical indices and 709,211 single nucleotide polymorphisms (SNPs) were subjected to phenomics analysis. Three bioinformatics methods, namely, Pearson’s test, Jaccard’s index, and linkage disequilibrium score regression, were used. The results showed that 29 biochemical indices were from a network. IgA, IgG, IgE, IgM, HCY, AFP and B12 were in the central community of 29 biochemical indices. Key genes and loci associated with metabolism traits were further identified, and shared genetics analysis showed that 29 SNPs (P < 10− 4) were associated with three or more traits. After integrating the SNPs related to two or more traits with the GWAS catalogue, 31 SNPs were found to be associated with several diseases (P < 10− 8). Using ALDH2 as an example to preliminarily explore its biological function, we also confirmed that the rs671 (ALDH2) polymorphism affected multiple traits of osteogenesis and adipogenesis differentiation in 3 T3-L1 preadipocytes. Conclusion All these findings indicated a network of shared genetics and 29 biochemical indices, which will help fully understand the genetics participating in biochemical metabolism.

【 授权许可】

Unknown