Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM)

Mitochondrial genome analysis is a potent tool in forensic practice and in the understanding of human phylogeny in the maternal lineage. With the development of molecular biology and bioinformatics techniques, high-throughput sequencing has enabled mtDNA analysis during whole genome sequencing, which provides more comprehensive information and raises the power of discrimination. In this study, peripheral blood samples were taken from 194 mother-offspring pairs and sequenced by Ion Torrent Personal Genome Machine and obtained high-coverage mitochondrial sequencing data, demonstrating the mutation levels at each position in the mitochondrial DNA (mtDNA) between maternally related pairs. A total of 14,332 variants were observed at 891 nucleotide positions from 388 individuals, and the result shows that all maternally related pairs shared the same detailed homoplasmic SNPs and haplotypes. With appropriate criteria for avoiding false positives due to sequencing errors and contamination by nuclear mitochondrial pseudogenes, we identified 33 heteroplasmies at a frequency of ≥10% at 32 sites in 30 pairs. The maternally related pairs had the same heteroplasmic sites but with different allele frequencies. The dataset is available through EMPOP under accession number EMP00684 and will serve as an mtDNA reference database in forensic casework in Eastern China.