The discrimination power of the hypervariable regions HV1, HV2 and HV3 of mitochondrial DNA in the Brazilian population

Abstract Analysis of mitochondrial DNA (mtDNA) has been widely applied in the field of human identification, and features a large number of mtDNA molecules per cell, the exclusively maternal inheritance, lack of recombination and high mutation rate found in the control region, and ensure the high level of polymorphism, mainly in hypervariable regions HV1, HV2 and HV3. However, despite highly polymorphic, one of the limitations of using these regions is that many polymorphisms are highly common, resulting in the presence of sequences shared by more than one individual, or maternal lineages, in different populations. The aim of this study was to evaluate the discrimination power of the analysis of hypervariable regions HV1 (16,024–16,365), HV2 (73–340) and HV3 (438–574) of mtDNA in a Brazilian sample containing 290 unrelated individuals. Sequencing was performed using BygDye Terminator v3.1 and capillary electrophoresis was performed on ABI3130. All samples were validated by EMPOP and were classified into 15 haplogroups. Eighty out of 290 individuals presented European haplotypes, 108 showed Amerindian haplotypes and 102 individuals presented African haplotypes. Sixty-nine individuals (23.8%) could not be discriminated by the analysis of hypervariable regions HV1, HV2 and HV3 of mtDNA, and they were distributed in 24 different groups of common sequences. The most common sequence belonged to European haplogroup R0 with 10 individuals showing the same sequence. Trying to increase the discrimination power of common haplotypes and, therefore, individuals, analysis of SNPs in the coding region has been done.