Prediction of biogeographical ancestry in admixed individuals.

Estimation of ancestral affiliation for human genotypes is now possible for major geographic populations and has been employed for forensic casework. Prediction algorithms, such as the Snipper Bayesian classifier, have the ability to classify non-admixed BGA in African (AFR), European (EUR), East Asian (EAS), and most Amerindian (NAM) individuals, but are not always appropriate for admixed individuals. Artificial admixture was simulated for all possible admixture ratios (1:1, 3:1, 2:1:1, and 1:1:1:1) from four grandparents. The simulated genotypes were used to test the accuracy of various prediction algorithms, most successful of which were the population genetics program, STRUCTURE, and a novel genetic distance algorithm (GDA). STRUCTURE was ideal for admixed individuals with 1:1 and 3:1 ratios from AFR, EUR, EAS, and NAM reference populations. Individuals with 1:1:1:1 BGA proportions were more accurately predicted by GDA. The use of hypothetical root genotypes improved the accuracy of GDA predictions for 1:1 and 3:1 admixtures and STRUCTURE classification of 1:1:1:1 admixture. The GDA requires only allele or genotype frequency values from each reference population, which offers a simpler sampling and input formatting procedure than is required by STRUCTURE. It can also be implemented in a spreadsheet without the need for long run times.

Fit for purpose quality management system for military forensic exploitation.

In a previous publication we described a systems approach to forensic science applied in the military domain. The forensic science 'system of systems' describes forensic science as a sub-system in the larger criminal justice, law enforcement, intelligence, and military systems, with quality management being an important supporting system. Quality management systems help to ensure that organisations achieve their objective and continually improve their capability. Components of forensic science quality management systems can include standardisation of processes, accreditation of facilities to national/international standards, and certification of personnel. A fit for purpose quality management system should be balanced to allow organisations to meet objectives, provide continuous improvement; mitigate risk; and impart a positive quality culture. Considerable attention over the last decades has been given to the need for forensic science quality management systems to meet criminal justice and law enforcement objectives. More recently, the need for the forensic quality management systems to meet forensic intelligence objectives has been considered. This paper, for the first time, discusses the need for a fit for purpose quality management system for military forensic exploitation.

Prediction of biogeographical ancestry from genotype: a comparison of classifiers.

DNA can provide forensic intelligence regarding a donor's biogeographical ancestry (BGA) and other externally visible characteristics (EVCs). A number of algorithms have been proposed to assign individual human genotypes to a BGA using ancestry informative marker (AIM) panels. This study compares the BGA assignment accuracy of the population clustering program STRUCTURE and three generic classification approaches including a Bayesian algorithm, genetic distance, and multinomial logistic regression (MLR). A selection of 142 ancestry informative single nucleotide polymorphisms (SNPs) were chosen from existing marker panels (SNPforID 34-plex, Eurasiaplex, Seldin, and Kidd's AIM panels) to assess BGA classification at the continental level for Africans, Europeans, East Asians, and Amerindians. A training set of 1093 individuals with self-declared BGA from the 1000 Genomes phase 1 database was used by each classifier to predict BGA in a test set of 516 individuals from the HGDP-CEPH (Stanford) cell line panel. Tests were repeated with 0, 10, 50, 70, and 90% of the genotypes missing. Comparison of the area under the receiver operating characteristic curves (AUROCs) showed high accuracy in STRUCTURE and the generic Bayesian approach. The latter algorithm offers a computationally simpler alternative to STRUCTURE with little loss in accuracy and is suitable for phenotype prediction while STRUCTURE is not.

Direct-to-PCR tissue preservation for DNA profiling.

Disaster victim identification (DVI) often occurs in remote locations with extremes of temperatures and humidities. Access to mortuary facilities and refrigeration are not always available. An effective and robust DNA sampling and preservation procedure would increase the probability of successful DNA profiling and allow faster repatriation of bodies and body parts. If the act of tissue preservation also released DNA into solution, ready for polymerase chain reaction (PCR), the DVI process could be further streamlined. In this study, we explored the possibility of obtaining DNA profiles without DNA extraction, by adding aliquots of preservative solutions surrounding fresh human muscle and decomposing human muscle and skin tissue samples directly to PCR. The preservatives consisted of two custom preparations and two proprietary solutions. The custom preparations were a salt-saturated solution of dimethyl sulfoxide (DMSO) with ethylenediaminetetraacetic (EDTA) and TENT buffer (Tris, EDTA, NaCl, Tween 20). The proprietary preservatives were DNAgard (Biomatrica(®)) and Tissue Stabilising Kit (DNA Genotek). We obtained full PowerPlex(®) 21 (Promega) and GlobalFiler(®) (Life Technologies) DNA profiles from fresh and decomposed tissue preserved at 35 °C for up to 28 days for all four preservatives. The preservative aliquots removed from the fresh muscle tissue samples had been stored at -80 °C for 4 years, indicating that long-term archival does not diminish the probability of successful DNA typing. Rather, storage at -80 °C seems to reduce PCR inhibition.