Mitochondrial DNA (mtDNA) analysis is used by forensic scientists when samples such as teeth, bones, and hairs without a follicle (root) are collected from crime scenes or disaster areas. MtDNA is also used when nuclear DNA is present in very low quantities or is highly degraded and does not provide a full STR profile. Traditionally, mtDNA analysis has been accomplished by amplifying hypervariable regions, a ~600 bp segment of the control region and using Sanger sequencing which is labor-intensive. With the introduction of next-generation sequencing in forensic and anthropology labs, entire mtDNA genomes can now be routinely sequenced and provide additional information on point heteroplasmies, mtDNA genome structure, and the evolution of haplotypes and haplogroups among populations.
A recent study from Lan Yao and colleagues from Chongqing Medical University and Ministry of Public Security, Beijing used the Applied Biosystems Precision ID mtDNA Whole Genome Panel and the Ion PGM System to analyze six bloodstain samples from three forensic cases. These six samples were preserved at room temperature from two months to 12 years on gauze, swabs or FTA paper.1
The samples were extracted and analyzed for quality and quantity using the Applied Biosystems Quantifiler Trio kit, then sequenced by NGS using Ion Torrent technology. The hypervariable regions and some additional regions of interest were sequenced by the Sanger method for concordance analysis. Data was analyzed using UGENE for consensus sequence alignment, HaploGrep and EMPOP for haplotyping, searched for NUMTs, and for private mutations in IGV. Finally concordance between NGS and Sanger methods was found to be 99.86%. To learn more about the complete analyses, especially on low frequency mutations, read the complete paper here.1
In these instances, even amplicon coverage and minimal strand bias which can be generated on the Precision ID Systems for human identification are key factors that may contribute to high quality genetic results for successful identification of human remains.
1. Yao, L., Xu, Z., Zhao, H., Tu, Z., Liu, Z., Li, W., Hu, L., Wan, L., Concordance of mitochondrial DNA sequencing method on bloodstains using Ion PGMTM, Legal Medicine (2018), doi: https://doi.org/10.1016/j.legalmed.2018.02.005
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