Publication of population data of linearly inherited DNA markers in the International Journal of Legal Medicine.
ABSTRACT This manuscript extends on earlier recommendations of the editor of the International Journal of Legal Medicine on short tandem repeat population data and provides details on specific criteria relevant for the analysis and publication of population studies on haploid DNA markers, i.e. Y-chromosomal polymorphisms and mitochondrial DNA. The proposed concept is based on review experience with the two forensic haploid markers databases YHRD and EMPOP, which are both endorsed by the International Society for Forensic Genetics. The intention is to provide guidance with the preparation of population studies and their results to improve the reviewing process and the quality of published data. We also suggest a minimal set of required information to be presented in the publication to increase understanding and use of the data. The outlined procedure has in part been elaborated with the editors of the journal Forensic Science International Genetics.
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ABSTRACT: Forensic mitochondrial DNA (mtDNA) testing requires appropriate, high quality reference population data for estimating the rarity of questioned haplotypes and, in turn, the strength of the mtDNA evidence. Available reference databases (SWGDAM, EMPOP) currently include information from the mtDNA control region; however, novel methods that quickly and easily recover mtDNA coding region data are becoming increasingly available. Though these assays promise to both facilitate the acquisition of mitochondrial genome (mtGenome) data and maximize the general utility of mtDNA testing in forensics, the appropriate reference data and database tools required for their routine application in forensic casework are lacking. To address this deficiency, we have undertaken an effort to: (1) increase the large-scale availability of high-quality entire mtGenome reference population data, and (2) improve the information technology infrastructure required to access/search mtGenome data and employ them in forensic casework. Here, we describe the application of a data generation and analysis workflow to the development of more than 400 complete, forensic-quality mtGenomes from low DNA quantity blood serum specimens as part of a U.S. National Institute of Justice funded reference population databasing initiative. We discuss the minor modifications made to a published mtGenome Sanger sequencing protocol to maintain a high rate of throughput while minimizing manual reprocessing with these low template samples. The successful use of this semi-automated strategy on forensic-like samples provides practical insight into the feasibility of producing complete mtGenome data in a routine casework environment, and demonstrates that large (>2kb) mtDNA fragments can regularly be recovered from high quality but very low DNA quantity specimens. Further, the detailed empirical data we provide on the amplification success rates across a range of DNA input quantities will be useful moving forward as PCR-based strategies for mtDNA enrichment are considered for targeted next-generation sequencing workflows.Forensic Science International: Genetics 02/2014; 10C:73-79. · 3.86 Impact Factor
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ABSTRACT: Aim. To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors. Method. We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.org) by means of two mtDNA data sets that were submitted for quality control. Results. The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data. Conclusion. Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables.Croatian Medical Journal 04/2014; 55(2):115-20. · 1.25 Impact Factor
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ABSTRACT: Mitochondrial DNA (mtDNA) control region (16024-576) sequences were generated from 281 individuals from South Korea. Robotic liquid handling, a redundant sequencing strategy, and a series of quality control checks were implemented to ensure the high quality of the dataset. This population sample showed a low random match probability (0.25 %) and high genetic diversity (0.9933). The haplogroup breakdown was consistent with previous studies describing Korean mtDNA variation. The 224 unique haplotypes (33 shared) presented will supplement the data already publically available.Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 02/2014; · 2.69 Impact Factor