Population genetic analysis of 12 X-chromosomal STRs in a Swiss sample.

X-chromosomal STRs are a powerful tool to assess a broad variety of complex kinship scenarios. We introduce herewith the first Swiss X-STR dataset based on 1198 individuals (592 female, 606 male), characterized with the Qiagen Investigator® Argus X-12 QS multiplex kit. Anomalous allele patterns, allele and haplotype frequencies, and forensic and population genetic parameters are presented. We detected linkage disequilibrium within three out of the four designated linkage groups and no apparent intra-national population substructure. We compared the dataset to a global panel of X-STR datasets and it fits well in the European context, as expected.

A Swiss collaborative exercise for Disaster Victim Identification (DVI): Covering situations with different levels of complexity.

The identification of victims of a disaster (DVI) requires the collaboration of different specialists. Within a DVI context, DNA analyses often play an important role. Consequently, forensic genetic laboratories should be prepared to cope with DVI situations, as this can involve large-scale DNA profile comparisons. Six forensic genetic laboratories from Switzerland participated in an exercise where supposedly a plane had crashed. The goal of the exercise was to monitor participants use of dedicated software with ground truth cases and to make them aware of the existence of particular situations that may occur in real cases. For assigning the value of the comparison of the DNA profiles, all participating laboratories used the DVI module of Familias v3.2.1 In addition, one of the 6 laboratories used the Pedigree Searcher from CODIS v7.0. The data (AmpFlSTR® NGM SElect™ profiles) were generated to challenge the participating laboratories: cases with first, second degree biological parents, mutation events, as well as non-paternity cases were included. This study shows that the majority of the participants used the software in an appropriate way. However, a few misleading conclusions were detected for the most challenging situations. These errors belonged to one of the following categories: false pedigree, false association using the higher LR, misleading contextual information (false paternity) and not clustering family members. Specific recommendations are provided in order to reduce misuse of the software and the risk of misinterpretations by using all the relevant information.

Results of a collaborative study on DNA identification of aged bone samples.

AIM: A collaborative exercise with several institutes was organized by the Forensic DNA Service (FDNAS) and the Institute of the Legal Medicine, 2nd Faculty of Medicine, Charles University in Prague, Czech Republic, with the aim to test performance of different laboratories carrying out DNA analysis of relatively old bone samples. METHODS: Eighteen laboratories participating in the collaborative exercise were asked to perform DNA typing of two samples of bone powder. Two bone samples provided by the National Museum and the Institute of Archaelogy in Prague, Czech Republic, came from archeological excavations and were estimated to be approximately 150 and 400 years old. The methods of genetic characterization including autosomal, gonosomal, and mitochondrial markers was selected solely at the discretion of the participating laboratory. RESULTS: Although the participating laboratories used different extraction and amplification strategies, concordant results were obtained from the relatively intact 150 years old bone sample. Typing was more problematic with the analysis of the 400 years old bone sample due to poorer quality. CONCLUSION: The laboratories performing identification DNA analysis of bone and teeth samples should regularly test their ability to correctly perform DNA-based identification on bone samples containing degraded DNA and potential inhibitors and demonstrate that risk of contamination is minimized.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach.

BACKGROUND: Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim's epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim's DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim's fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim's fraction, and then digest the residual victim's DNA with a nuclease. METHODS: The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. RESULTS: For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. CONCLUSIONS: In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.

Differential DNA extraction of challenging simulated sexual-assault samples: a Swiss collaborative study.

In sexual-assault cases, autosomal DNA analysis of gynecological swabs is a challenge, as the presence of a large quantity of female material may prevent detection of the male DNA. A solution to this problem is differential DNA extraction, but there is no established best practice for this. We decided to test the efficacy of a number of different protocols on simulated casework samples. Four difficult samples were sent to the nine Swiss laboratories active in forensic genetics. In each laboratory, staff used their routine protocols to separate the epithelial-cell fraction, enriched with the non-sperm DNA, from the sperm fraction. DNA extracts were then sent to the organizing laboratory for analysis. Estimates of male:female DNA ratio without differential DNA extraction ranged from 1:38 to 1:339, depending on the semen used to prepare the samples. After differential DNA extraction, most of the ratios ranged from 1:12 to 9:1, allowing detection of the male DNA. Compared with direct DNA extraction, cell separation resulted in losses of 94-98% of the male DNA. As expected, more male DNA was generally present in the sperm than in the epithelial-cell fraction. However, for about 30% of the samples, the reverse trend was seen. The recovery of male and female DNA was highly variable, depending on the laboratory involved. An experimental design similar to the one used in this study may be of assistance for local protocol testing and improvement.

DNA preparation from sexual assault cases by selective degradation of contaminating DNA from the victim.

The standard method to purify sperm DNA from vaginal swabs taken from rape victims is to selectively digest the victim's epithelial cells to solubilize the victim's DNA, and then separate the soluble DNA from the intact sperm by centrifugation. A different approach to removing the soluble victim's DNA is to selectively degrade it using a nuclease, DNase I. DNase I reduces the amount of soluble DNA by over 1000-fold, while having virtually no effect on the sperm DNA remaining in the sperm head and inaccessible to the enzyme. Nuclease inactivation and sperm lysis then yield a soluble, pure male DNA fraction. An aliquot of soluble DNA is removed prior to nuclease addition to provide the victim's fraction. Vaginal swabs taken at defined time points following consensual sex and taken from rape victims were processed using the nuclease method or the standard method and the nuclease method gave superior short tandem repeat profiles.