Analysis of single-nucleotide polymorphisms of PEO1 gene in 55 ethnic groups of India

Abstract

Background: Progressive External Opthalmoplegia (PEO1) or Chromosome 10 open reading frame 2 gene (OMIM ID 606075) encodes Twinkle protein, a phage T7 gene 4-like hexameric helicase, and is associated with mitochondrial DNA (mtDNA) deletions and neuromuscular disease called autosomal dominant PEO (adPEO). Twinkle has also been known to play an important role in the stability and maintenance of the mtDNA. Aims: In this study as an effort of Indian Genome Variation Consortium, we screened the SNPs of PEO1 gene such as rs7184, rs1535349, rs2863095, rs3740484, rs3740488, rs3740489, rs4919511, rs17113613, rs3824783, rs3740485, rs3740486, and rs3740487 in discovery panel (a population set of 40 DNA samples), and four synonymous SNPs, namely rs3824783 (ancestral allele=A), rs3740485 (ancestral allele=T), rs3740486 (ancestral allele=C), and rs3740487 (ancestral allele=A) in a large validation panel composed of 55 Indian subpopulations. Materials and Methods: In present study, a total of 55 Indian subpopulations were identified and collected for validation panel to check the frequencies of SNPs in PEO1 gene. Results and Conclusion: The allelic and genotype frequencies are found to be variable among different ethnic groups of India.