Article

BioMedicine

, 4:14

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

Cross-species identification of in silico microsatellite biomarkers for genetic disease

  • Hao-Teng ChangAffiliated withGraduate Institute of Basic Medical Science, China Medical UniversityDepartment of Computer Science and Information Engineering, Asia University
  • , Yu-Yang LoAffiliated withDepartment of Computer Science and Engineering, National Taiwan Ocean University
  • , Jhen-Li HuangAffiliated withDepartment of Computer Science and Engineering, National Taiwan Ocean University
  • , Wei-Yong LinAffiliated withGraduate Institute of Integrated Medicine, China Medical University
  • , Tun-Wen PaiAffiliated withDepartment of Computer Science and Engineering, National Taiwan Ocean UniversityDepartment of Computer Science and Engineering & Center of Excellence for the Oceans, National Taiwan Ocean University Email author 

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 this in silico research 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.

Keywords:

Microsatellite Simple sequence repeat Genetic disease