SimHOEPI:A resampling simulator for generating single nucleotide polymorphism data with a high-order epistasis model

作     者：Yahan Li Xinrui Cai Junliang Shang Yuanyuan Zhang Jin-Xing Liu Yahan Li;Xinrui Cai;Junliang Shang;Yuanyuan Zhang;Jin-Xing Liu

作者机构：School of Computer ScienceQufu Normal UniversityRizhaoChina School of Information and Control EngineeringQingdao University of TechnologyQingdaoChina School of Health and Life SciencesUniversity of Health and Rehabilitation SciencesQingdaoChina 

出 版 物：《Quantitative Biology》 (定量生物学（英文版）)

年 卷 期：2024年第12卷第2期

页      面：197-204页

核心收录：

学科分类：0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 07[理学] 08[工学] 

基　　金：This work was supported by the National Natural Science Foundation of China(Nos.61972226 and 62172254) 

主　　题：high-order epistasis model penetrance table resampling strategy simulation single nucleotide polymorphisms 

摘      要：Epistasis is a ubiquitous phenomenon in genetics,and is considered to be one of main factors in current efforts to unveil missing heritability of complex *** data is crucial for evaluating epistasis detection tools in genome-wide association studies(GWAS).Existing simulators normally suffer from two limitations:absence of support for high-order epistasis models containing multiple single nucleotide polymorphisms(SNPs),and inability to generate simulation SNP data *** this study,we proposed a simulator SimHOEPI,which is capable of calculating penetrance tables of high-order epistasis models depending on either prevalence or heritability,and uses a resampling strategy to generate simulation data *** of SimHOEPI are the preservation of realistic minor allele frequencies in sampling data,the accurate calculation and embedding of high-order epistasis models,and acceptable simulation time.A series of experiments were carried out to verify these properties from different *** results show that SimHOEPI can generate simulation SNP data independently with high-order epistasis models,implying that it might be an alternative simulator for GWAS.