Indian Journal of Pharmaceutical Sciences 312duplications, inversions and copy number variations are more widely prevalent than initially predicted. Mitochondrial tumor suppressor gene maps on chromosome 8p, in which exon 4-specific deletion is associated with susceptibility towards breast and various other forms of cancer. In this study, 41 head and neck cancer, 15 breast cancer patients and 280 healthy control individuals were analysed for mitochondrial tumor suppressor gene copy number variation. The frequencies of wt/wt (homozygous wild-type), wt/Del (heterozygous variant) and Del/Del (homozygous deletion variant) mitochondrial tumor suppressor gene genotypes were found to be 73.3, 26.7 and 0% in breast cancer patients, 41.5, 58.5 and 0% in head and neck cancer patients and 43, 57 and 0% in healthy individuals, respectively. A significant association of the deletion variant with breast cancer (odds ratio=0.27, 95% confidence interval=0.08-0.87, P=0.0207) was found in our population. In addition, the allele and genotype frequency varied significantly (P<0.0001) among Indian and German populations, reflecting ethnic diversity. This pilot case-control study highlighted the indicative role of mitochondrial tumor suppressor gene deletion in protection from breast cancer in Indian population. However, the findings need to be investigated in larger patient sample size before any conclusive role of mitochondrial tumor suppressor gene copy number variation on cancer risk.Key words: Breast cancer, copy number variation, head and neck cancer, health, pharmacogenetics Copy number variation (CNVs) arise from the genomic rearrangements resulting in the deletion, duplication, insertion and translocations covering about 12% of the human genome [1,2] . Recent studies have highlighted the role of CNVs in complex disorders including susceptibility to cancer [3][4][5] . The association of CNVs in disease susceptibility involving wide range of common human disorders is well compiled and documented by several researchers [6,7] . In order to detect these changes several approaches have been developed and applied till date [8] . Among them, array-based comparative genomics approach by Hinds et al. in 2006 was used to detect common deletions ranging from 70 bps to 7 Kb [9] . Of the 100 CNVs identified, the mitochondrial tumor suppressor gene 1 (MTUS1) encompassing the deletion of complete coding exon 4 (162 bp) was one of them. The breakpoint of the deleted region was redefined and validated in large case-control samples from German population [10] . In 2005, Lupski and Stankiewicz documented the role of CNVs in genetic disorders but the extent to which CNVs contribute to disease development remains poorly understood [11] . However, the exon-specific deletion of MTUS1 gene is an illustration of a CNV associated with the development of cancer [12] .MTUS1 gene, also designated as MTSG1, GK1 or angiotensin II (AT2) receptor-interacting protein (ATIP1) is located at chromosomal position 8p22 spanning over 112 Kb in size. It is found to ...