Trinucleotide repeat length distribution and mitochondrial DNA haplogroup in sub-ethnic group of newar population of Nepal

Abstract

Tandem nucleotide repeats are repetitive DNA in which two or more contiguous, approximate copies of a pattern of nucleotide occur in a DNA sequence. Trinucleotide repeats are a form of tandem repeat which are caused by an expansion of a segment of DNA that contains a repeat of 3 nucleotides (Triplet repeat). Variable number of triplet repeats are constituted in a healthy individual but there is a threshold beyond which a high number of repeats causes disease. This threshold varies in different disorders. Trinucleotide repeat expansions are highly polymorphic and sometimes called dynamic or unstable mutation because the number of repeats increases as the gene passes from parents to offspring. Expansion of disease arises from existence of large normal of normal repetitions (Large Normal alleles). Frequency of large normal alleles’ estimation is the indirect measure of the prevalence of the disease. To investigate the normal allele range of trinucleotide repeat disorder (SCA1, SCA2, SCA3, SCA7, SCA8, SCA12, DM1, DRPLA, FXTAS and HD) blood samples from 55 healthy unrelated individual belonging to Newar sub‐ethnic group, the Maharjan of Nepal were examined. PCR products were subjected to capillary electrophoresis (ABI 3130xl Genetic Analyser) for fragment analysis. In the studied population the normal range of 10 different loci were SCA1, 22 to 36 (CAG)n ; SCA2, 19 to 26 (CAG)n; SCA3, 14 to 36 (CAG)n ; SCA7, 6 to 14 (CAG)n; SCA8, 11 to 32 (CTG)n; SCA12, 9 to 18 (CAG)n; HD, 12 to 28 (CAG)n; FXTAS , 18 to 34 (CGG)n; DRPLA, 7 to 22 (CAG)n; DM1, 1 to 28 (CTG)n . Variability of human mitochondrial DNA has provided valuable data about the genetic history of human. Analysis of the frequency, variation and distribution of mitochondrial DNA haplogroup have been used to evaluate genetic structure of various population residing in different geographical region. Second part of this dissertation concentrates on the mitochondrial DNA haplogroup determination of Newar sub‐ethnic group, the Maharjan of Nepal. Mitochondrial D‐loop is the non‐coding region which has two hypervariable regions that exhibit very high mutation rates, thus, can distinguish recently diverged population. In this study, D‐loop region was sequenced and Individual lineages were constructed on the basis of mtDNA mutations. 5 major haplogroups with different frequencies were observed in mtDNA haplogroup viz. M (58.2%), N (18.2%), H (3.6%), R (12.7%), U (7.3%). Our results indicated presence of South Asian specific haplogroup M, including M3, M5, Z, G etc. in high frequency along with branches R (R9), U (U7, U8). These results indicated Maharjan gene pool was found to harbour almost 57.56% of South Asian, 19.99% of East Asian, 18.85% of Western Eurasian and 3.6% of Central Asia specific gene pool. Key words: Trinucleotide repeat disorder, Haplogroup, Gene pool, D‐Loop