Mitogenome Sequencing of 10,000 Population Samples Using a Highly Accurate, Single-Molecule Approach

Sequence analysis of mitochondrial (mt) DNA has been employed by forensic laboratories for more than 30 years; especially in laboratories that work on human identification cases.  The sample types most often targeted are rootless hairs and older skeletal material.  While efforts to obtain nuclear (n) DNA markers from these samples have been relatively fruitful for skeletal material, success with rootless hairs has been limited.  An FBI publication reported that the vast majority of DNA recovered from hair shafts is, in fact, highly degraded nDNA.  More than 95% of the total reads from shotgun sequencing mapped to the nDNA genome, but at an average fragment length of 43-88 base pairs.  Therefore, conventional amplicon approaches, which typically require template lengths of >80 bps, have historically been unsuccessful in producing profile information.  A massively parallel sequencing (MPS) approach that involves the capture of single nucleotide polymorphism (SNP) markers across the human genome has yet to produce consistently reliable results, presumably due to the limited quantities of nDNA in hair shafts when compared to other sample types.  In a recent study, the vast majority of hairs produced random match probabilities lower than unobserved mtDNA haplotypes when using a conventional or MPS approach. Therefore, as stated by numerous members of the forensic community, mtDNA analysis will remain a mainstay for the analysis of rootless hairs and for the analysis of skeletal material with unsuitable amounts of nDNA.  MPS approaches have advanced to the point where full mitochondrial genome (mitogenome) sequences can be generated routinely from as little as 1-5 mm of human hair shaft.  However, large population databases of mitogenome sequences for forensic purposes are not yet available, reducing the value of an mtDNA profile match.  The outcomes of the proposed work will include the generation of highly accurate, single-molecule mitogenome haplotypes from 10,000 population samples; a detailed analysis of the population data, including the rate and location of heteroplasmy through the analysis of deep-coverage data; and evaluation of concordance to previously generated short-read mitogenome MPS data.  These outcomes will address important interests of the criminal justice system and National Institute of Justice, providing the forensic community with better statistical power when considering mitogenome haplotype matches in forensic cases.  Partners for the project include the Institute for Preventative Medicine, Hershey Medical Center; the Institute of Legal Medicine, Medical University of Innsbruck; Mitotyping Technologies, LLC, a division of SoftGenetics; and the Armed Forces DNA Identification Laboratory. CA/NCF