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.
"has regularly been used for quality control (QC) of published and newly submitted population data (3,4). QMNs form one part of the QC concept performed by EMPOP when mtDNA population data are submitted for publication in Forensic Science International Genetics (5) and International Journal of Legal Medicine (6) and thus contribute to the quality improvement of published mtDNA data sets. Also, all haplotypes presented in the mtDNA database EMPOP (3) undergo rigorous quality control prior to upload. "
[Show abstract][Hide abstract] 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.
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.
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.
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. DOI:10.3325/cmj.2014.55.115 · 1.31 Impact Factor
"As such, submitting population sample data to the database could be an obligatory quality check with which studies have to comply before they are published. This is often demanded for human mtDNA population data (Carracedo et al. 2010, Parson and Roewer 2010, Carracedo et al. 2013). "
[Show abstract][Hide abstract] ABSTRACT: The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype's population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.
"In addition, reporting haplotypes in an unfamiliar format will most likely lead to an increased risk of error at various stages. It has been repeatedly demonstrated that transcription and clerical errors are the main sources of error in proficiency tests (       , GEDNAP blind trial C. Hohoff, personal communication) and occur frequently in population and clinical studies ([12,13,29–31], and as experience from EMPOP QC tests as outlined in  ). It is important to learn from past experience where the simple transition between the incorrect CRS to the corrected rCRS led to a number of errors in the literature    and the fact that both nomenclatures were living together for a large period of time. "
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