A Comprehensive Approach to Design, Selection and Optimization of Short Tandem Repeat Used in Preimplantation Genetic Diagnosis of Single Gene Disorders

Short tandem repeats (STRs), are DNA sequences that are uniquely scattered throughout the human genome. These markers are ideal candidates for diverse usages including gene mapping, phylogenetic reconstruction, forensic medicine and indirect diagnosis of genetic disorders. Another application of STRs is in PGD (Preimplantation genetic diagnosis) for single gene disorders. Due to wide applications and also huge number of STR markers interspersed in human genome, these markers must be selected among thousands upon thousands markers based on special applications. In this study, SMA (Spinal muscular atrophy) was used as a model of monogenic disorders. Then STR markers flanking to SMA gene region was searched. Among the hundreds of markers, 5 STRs were selected. The size ranges of the STR markers were determined. A sequence alignment was then performed. Primers were designed, PCR reactions were optimized. PCR products were then separated by capillary electrophoresis. In order to accelerate optimization of a set of STR markers for divers applications, in this study a comprehensive strategy for design, selection and optimization of STR marker was presented. For simplicity, all steps were performed on 5 STR loci that are located in SMA region. These can be applied for PGD of SMA. The strategy presented in this study can be used as an example to design a set of STR marker for similar application in a short time and with a low cost.