Identification of putative pathogenic SNPs implied in schizophrenia-associated miRNAs
1 School of Computer Science and Technology, Xidian University, Xi’an 710071, P. R. China
2 College of Mathematics and Information Science, Weinan Normal University, Weinan 714099, P. R. China
BMC Bioinformatics 2014, 15:194 doi:10.1186/1471-2105-15-194Published: 17 June 2014
Schizophrenia is a severe brain disorder, and SNPs (Single nucleotide polymorphism) in schizophrenia-associated miRNAs are believed to be one of the important reasons for dysregulation which might contribute to the altered expression of genes and ultimately result in the disease. Identification of causal SNPs in associated miRNAs may have certain significance in understanding the mechanism of schizophrenia.
For the above purposes, a method based on detection of free energy change is proposed for identification of causal SNPs in schizophrenia-associated miRNAs. A miRNA is firstly segmented, and free energy change is computed after adding an SNP into a segment. The method discovers successfully 6 out of 32 known SNPs and some artificial SNPs could cause significant change in free energy, and among which, 6 known SNPs are supposed to be responsible for most cases of schizophrenia in population.
The proposed method is not only a convenient way to discover causal SNPs in schizophrenia-associated miRNAs without any biochemical assay or sample comparison between cases and controls, but it also has high resolution for causal SNPs even if the SNPs are not reported for their very rare cases in the population. Moreover, the method can be applied to discover the causal SNPs in miRNAs associated with other diseases.