EMPOP - an innovative human mtDNA database

In the past few years, the analysis of mitochondrial DNA (mtDNA) has greatly gained in importance. The high copy number, the elevated stability against degradation and the strict maternal inheritance are the main characteristics of the mitochondrial genome, which make it particularly suitable for palaeogenetic inferences and the reconstruction of human evolution. In forensic DNA fingerprinting, mtDNA profiling is established as a technological resource for cases where conventional nuclear DNA markers fail to give satisfactory results (e.g. analyses of hair shafts, remains of bones and teeth). Extant collections of mtDNA sequences are essential for the biostatistical appraisal of mitochondrial profiles, as the frequency of the polymorphisms, i.e. the haplotype, and the phylogeographic assignment of mtDNA lineages can only be determined in adequate mtDNA databases. Existing mtDNA databases have an unacceptable high error-rate which is caused by the complexity of the analytical process and the lack of defined quality criteria for examination of the data. This project aims at 2 main goals: a) the establishment and validation of suitable methods to control the quality of mtDNA data. These methods are developed in collaboration with the Institute of Mathematics, LFU Innsbruck. They are based on the visualisation of genetic variability and the comparison of the data with the world-wide mtDNA phylogeny, which allows for efficient quality assessment. They involve quasi-median networks, compatibility checks, neighbour-joining and logic conditions. b) the generation of etalon datasets for the calibration of the westeurasian, central- and eastasian phylogeny. These data add to the understaning of the asian mtDNA phylogeny and serve as high-quality basis for future investigations. The project is implemented in the international joint project EMPOP (EDNAP Mitochondrial DNA Population Database Project) of the European DNA Profiling Group (EDNAP) with the project management located at the Institute of Legal Medicine in Innsbruck. The institute harbours the Austrian Central DNA Laboratory, which is reputed as international DNA reference laboratory. Blind tests have been conducted under the umbrella of EMPOP. The results clearly indicate that the traditional analytical process is prone to error. First approaches to solve the problem have already been published. EMPOP is conceived as multi-disciplinary scientific ressource, which can be used for different fields such as human evolution, medical genetics and forensic molecular biology.

The FWF Translational Research Project L397 `EMPOP - an innovative human mtDNA database` supported research for the establishment of new standards in forensic mitochondrial DNA (mtDNA) analysis. This project was extremely successful which is not only evident by the numerous high profile publications and lecture invitations to international conferences; within the period of the 3 project years the EMPOP database (http://empop.org) advanced to the prime mover of quality control in mtDNA research and its forensic application. Some of the striking achievements are a recent declaration of the German Federal Court of Justice in favour of EMPOP`s court acceptance, its explicit endorsement by the International Society for Forensic Genetics, its central role for quality control of mtDNA datasets prior to peer-review submission to the two leading forensic journals and its intensive collaborative interaction with academic and governmental organisations around the globe. Numerous continuing collaborations have meanwhile started and a new project application has been granted by the National Institute of Justice to support ongoing research for another 5 years. MtDNA is the most sensitive molecular identifier for forensic identification due to its high copy number in the cell compared to nuclear DNA. Its maternal mode of inheritance renders mtDNA analysis a useful tool in cases where relatedness along the matrilineal lineage is under investigation, but this also limits its statistical evaluation to counting observations in a database. MtDNA databases have been found prone to error in the first years of the past decade and the forensic community faced high profile debates on its credibility with severe consequences for the field - lack of acceptance being the most critical. The current FWF-project funded research to improve this situation. As main achievement a suite of dedicated software tools based on mathematical principles was established to handle, evaluate and store mtDNA data. These tools revealed that 80% of newly generated mtDNA population data still contain individual traceable errors and approximately half of those datasets bear unacceptably high error rates (>10%), that would otherwise have made it into the literature and mtDNA databases. A new search algorithm was developed that is immune to inherent alignment problems of mtDNA sequences and thus provides for the first time mtDNA sequence search results that are based on an objective, non-biased query. As second pillar of the project development of new population datasets was funded that enrich the body of forensically relevant data (a total of 3,380 new haplotypes) and serve as exemplar studies to direct new research strategies. This includes the discussion on appropriate sampling strategies, safe laboratory protocols, adequate a posteriori data evaluation following phylogenetic principles and useful interpretation of the data. Especially in the past years the EMPOP database project advanced to an important internationally renowned resource for mtDNA data generation and interpretation with strong emphasis on the forensic field.