This article describes recently developed approaches to the quality control, alignment, and nomenclature of mitochondria sequences, as well as the establishment of mtDNA reference population databases; and it discusses their application to both mtDNA casework and mtDNA reference population databasing applications.
The authors first note that the DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the question of human identification. Previous recommendations published in 2000 addressed the analysis and interpretation of mitochondrial DNA (mtDNA) in forensic casework, and they still apply; however, in light of the new developments described in this article, the authors introduce guidelines regarding sequence generation and quality control measures based on the known worldwide mtDNA phylogeny, which can be applied to ensure the highest quality population data possible. Although the generation of mtDNA for forensic casework has always been guided by specific standards, it is now well-established that data used to assess the statistical weight of the evidence are required. The proposed guidelines are intended to meet this need. For both casework and reference population databasing applications, the alignment and nomenclature of haplotypes are revised here and the phylogenetic alignment proffered as acceptable standard. In addition, the interpretation of heteroplasmy in the forensic context is updated, and the utility of alignment-free database searches for unbiased probability estimates is highlighted. Finally, the authors discuss statistical issues and define minimal standards for mtDNA database searches. (Publisher abstract modified)