Computational and experimental hunt for expansion prone tandem CNG repeats in human genomes

Abstract

Introduction: Spinocerebellar ataxias (SCA) are a group of clinically and genetically heterogeneous neurodegenerative disorders. Tandem repeat expansion is the pathogenic mutation in most of SCA cases. The pathophysiology of SCAs is still not completely defined due to the lack of genetic mutation in around 50% of cases worldwide. These uncharacterized cases must be genetically diagnosed for a better understanding and future treatment purposes. In this study, we tried a combination of computational and experimental approaches to find out novel CNG repeat loci that may be associated with SCAs. Methodology: We investigate the human reference genome (hg-37) to find out all the possible CNG repeats present in more than 3 continuous uninterrupted units and annotated their functional locations. For experiment purposes, we targeted 52 loci from exonic and UTR regions and screened them in our 100 control samples through fragment analysis to know their polymorphic status. All the highly polymorphic loci were further investigated in 100 patient samples to know any large repeat expansion. Results: There are 15069 CNG repeat loci present in the human genome. After the examination of 52 loci in the control samples, 19 loci showed a highly polymorphic repeat pattern and were screened in patients. The 1000 genome different population data also suggested the polymorphic status in the available 15 loci data. From the GTEx database, 18 loci proposed the expression in the brain, suggesting any variation in these genes may cause neurological disorders. Conclusion: We tried a different kind of approach to find out tandem repeat expansion mutation in a cost-effective manner. Although we were unable to identify any disease-causing mutation in our patient cohort recently, various studies from different populations of the world have vouched for the genetic changes in these genes like GLS, RAI1, GIPC1, and CNKSR2 resulted in neurological disorders. Moreover, publications on the same identified repeats in GIPC1 for OPMD and GLS for ataxia with developmental delay, confirm the hypothesis to evaluate these repeat loci in different populations and other neurological disorders to identify novel targets.