title: Cross-species identification of insilicomicrosatellite biomarkers for genetic disease.
abstract: Microsatellites appear widely in genomes of diverse species. Variants of repeat number of microsatellites often correlate with risks of genetic disorder or severity of diseases. Using cross-species comparison, the proposed system comprehensively verifies microsatellites of specific genes related to 16 genetic disorders. Genomic information retrieved from 14 frequently used model organisms in biomedical study was thoroughly analyzed, emphasizing conserved and diverse traits. Features of microsatellite sequences among different organisms, including appearing frequency, position, pattern and distribution, could be determined automatically for stating genetically functional conservation and evolutionary correlation. This research found that among mammals and fishes, the microsatellite sequences are conserved in the genes of epidermal growth factor receptor, ataxia telangiectasia mutated and androgen receptor corresponding to cancers, ataxia telangiectasia and hepatocellular carcinoma, respectively. Still, except fruit fly conserved CAG repeats in Huntington and Spinocerebellar ataxia type 2 genes, no microsatellites were conserved in those genes linked to neurological/neurodegenerative disorders among mammal and fish species. In comparison of mammalian species, microsatellite biomarkers identified from 17 genetic disorder-related genes revealed high repeat conservation, especially in human, gorilla and macaque. Obviously, this comparative analysis illustrates microsatellite repeats affecting genetic disorders, highly correlated to evolutionary distance of species. Chief contribution of thisin silicoresearch lies in assisting biologists to identify disease-related microsatellite biomarkers and employ appropriate model organisms for further biomedical studies relying on microsatellite conservation information. Database http://ssrtc.cs.ntou.edu.tw is for academic use.
authors.affiliation: Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan ; Department of Computer Science and Information Engineering, Asia University, Taichung, Taiwan.
authors.forename: Hao-Teng
authors.initials: HT
authors.lastname: Chang
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan.
authors.forename: Yu-Yang
authors.initials: YY
authors.lastname: Lo
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan.
authors.forename: Jhen-Li
authors.initials: JL
authors.lastname: Huang
authors.affiliation: Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.
authors.forename: Wei-Yong
authors.initials: WY
authors.lastname: Lin
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan ; Department of Computer Science and Engineering & Center of Excellence for the Oceans, National Taiwan Ocean University, No. 2, Peining Road, Keelung, 20224 Taichung, Taiwan.
authors.forename: Tun-Wen
authors.initials: TW
authors.lastname: Pai
keywords: Genetic disease; Microsatellite; Simple sequence repeat