To access, purchase, authenticate, or subscribe to the full-text of this article, please visit this link: http://dx.doi.org/10.1007/s12282-015-0611-1 Byline: Sunaina Thapa (1), Freda Lalrohlui (1), Souvik Ghatak (1), John Zohmingthanga (2), Doris Lallawmzuali (3), Jeremy L. Pautu (3), Nachimuthu Senthil Kumar (1) Keywords: mtDNA; ATP6; ND1; ATP8; OXPHOS; Breast cancer Abstract: Background Mizoram has the highest incidence of cancer in India. Among women, breast cancer is most prevalent and the state occupies fifth position globally. The reason for high rate of cancer in this region is still not known but it may be related to ethnic/racial variations or lifestyle factors. Methods The present study aims to identify the candidate mitochondrial DNA (mtDNA) biomarkers--ND1and ATPase for early breast cancer diagnosis in Mizo population. Genomic DNA was extracted from blood samples of 30 unrelated breast cancer and ten healthy women. The mtNDI and mtATP coding regions were amplified by step-down PCR and were subjected to restriction enzyme digestion and direct sequencing by Sanger method. Subsequently, the results of the DNA sequence analysis were compared with that of the revised Cambridge Reference Sequence (rCRS) using Mutation Surveyor and MITOMAP. Results Most of the mutations were reported and new mutations that are not reported in relationship with breast cancer were also found. The mutations are mostly base substitutions. The effect of non-synonymous substitutions on the amino acid sequence was determined using the PolyPhen-2 software. Statistical analysis was performed for both cases and controls. Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated from logistic regression. High intake of animal fat and age at menarche was found to be associated with a higher risk of breast cancer in Mizo population. Conclusion Our results also showed that ATPase6 as compared to ATPase8 gene is far more predisposed to variations in Mizo population with breast cancer and this finding may play an important role in breast cancer prognosis. Author Affiliation: (1) Department of Biotechnology, Mizoram University, Aizawl, 796004, Mizoram, India (2) Department of Pathology, Civil Hospital, Aizawl, 796001, Mizoram, India (3) Mizoram State Cancer Institute, Zemabawk, Aizawl, 796017, Mizoram, India Article History: Registration Date: 08/04/2015 Received Date: 29/01/2015 Accepted Date: 07/04/2015 Online Date: 21/04/2015 Article note: Electronic supplementary material The online version of this article (doi: 10.1007/s12282-015-0611-1) contains supplementary material, which is available to authorized users.