title: SHEsisPlus, a toolset for genetic studies on polyploid species.
abstract: Currently, algorithms and softwares for genetic analysis of diploid organisms with bi-allelic markers are well-established, while those for polyploids are limited. Here, we present SHEsisPlus, the online algorithm toolset for both dichotomous and quantitative trait genetic analysis on polyploid species (compatible with haploids and diploids, too). SHEsisPlus is also optimized for handling multiple-allele datasets. It's free, open source and also designed to perform a range of analyses, including haplotype inference, linkage disequilibrium analysis, epistasis detection, Hardy-Weinberg equilibrium and single locus association tests. Meanwhile, we developed an accurate and efficient haplotype inference algorithm for polyploids and proposed an entropy-based algorithm to detect epistasis in the context of quantitative traits. A study of both simulated and real datasets showed that our haplotype inference algorithm was much faster and more accurate than existing ones. Our epistasis detection algorithm was the first try to apply information theory to characterizing the gene interactions in quantitative trait datasets. Results showed that its statistical power was significantly higher than conventional approaches. SHEsisPlus is freely available on the web at http://shesisplus.bio-x.cn/. Source code is freely available for download at https://github.com/celaoforever/SHEsisPlus.
authors.affiliation: Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.|School of Bio-medical Engineering, Shanghai Jiao Tong University, Shanghai 200230, P.R. China.|Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
authors.forename: Jiawei
authors.initials: J
authors.lastname: Shen
authors.affiliation: Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.|Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Li
authors.affiliation: Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.|Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Chen
authors.affiliation: Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.|Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Song
authors.affiliation: Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.|Shandong Provincial Key Laboratory of Metabolic Disease, the Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.|Institute of Clinical Research, the Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.
authors.forename: Zhaowei
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.|School of Bio-medical Engineering, Shanghai Jiao Tong University, Shanghai 200230, P.R. China.|Shanghai Changning Mental Health Center, Shanghai 200042, P.R. China.|Department of Psychiatry, the First Teaching Hospital of Xinjiang Medical University, Urumqi 830054, P.R. China.
authors.forename: Yongyong
authors.initials: Y
authors.lastname: Shi
mesh_terms: D000465:Algorithms; D015210:Arthritis, Gouty / Q000097:blood / Q000235:genetics*; D002681:China; D003198:Computer Simulation; D004171:Diploidy; D004843:Epistasis, Genetic; D005819:Genetic Markers; D005838:Genotype; D006073:Gout / Q000097:blood / Q000235:genetics*; D006239:Haplotypes; D006801:Humans; D016014:Linear Models; D015810:Linkage Disequilibrium; D008297:Male; D008957:Models, Genetic; D015233:Models, Statistical; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D040641:Quantitative Trait Loci; D012984:Software; D011198:Solanum tuberosum / Q000235:genetics; D014527:Uric Acid / Q000097:blood
chemical_list: D005819:Genetic Markers; D014527:Uric Acid