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

Ashutosh Kumar Singh, A. Mitra, S. Rath
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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.
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印度55个民族PEO1基因单核苷酸多态性分析
背景:进行性眼外麻痹症(PEO1)或10号染色体开放阅读框2基因(OMIM ID 606075)编码Twinkle蛋白,这是一种噬菌体T7基因4样六聚解旋酶,与线粒体DNA (mtDNA)缺失和常染色体显性PEO (adPEO)神经肌肉疾病有关。人们还知道,Twinkle在mtDNA的稳定和维持中发挥着重要作用。目的:本研究作为印度基因组变异联盟的一项工作,我们在发现面板(一组40份DNA样本的群体集)中筛选了PEO1基因rs7184、rs1535349、rs2863095、rs3740484、rs3740488、rs3740489、rs4919511、rs17113613、rs3824783、rs3740485、rs3740486和rs3740487四个同源snp,即rs3824783(祖先等位基因= a)、rs3740485(祖先等位基因=T)、rs3740486(祖先等位基因=C)。rs3740487(祖先等位基因=A)在由55个印度亚群组成的大型验证面板中。材料与方法:本研究共收集了55个印度人亚群,用于验证小组,检查PEO1基因snp的频率。结果与结论:印度不同民族间的等位基因和基因型频率存在差异。
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