Allelic proportions of 16 STR loci-including the new European Standard Set (ESS) loci-in a Swiss population sample.

Allele frequencies and forensically relevant population statistics of 16 STR loci, including the new European Standard Set (ESS) loci, were estimated from 668 unrelated individuals of Caucasian appearance living in different parts of Switzerland. The samples were amplified with a combination of the following three kits: AmpFlSTR® NGM SElect™, PowerPlex® ESI17 and PowerPlex® ESX 17. All loci were highly polymorphic and no significant departure from Hardy-Weinberg equilibrium and linkage equilibrium was detected after correction for sampling.

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.

Applicability of DNA analysis on adhesive tape in forensic casework.

Adhesive tape is commonly used in crimes and is often the subject of forensic evaluation. DNA analysis of adhesive tape can provide DNA profiles of suspects. The object of this study was to evaluate the applicability of DNA analysis on adhesive tape samples in forensic casework. We retrospectively reviewed all cases involving adhesive tape or similar items received by our institute for DNA analysis during the past 11 years. From 100 forensic cases reviewed, 150 adhesive tape samples were examined. A total of 98 DNA profiles were obtained from these samples. Sixty-two of the profiles provided feasible case-relevant information. In conclusion, DNA profiling of adhesive tape samples can be useful in a variety of forensic cases.

Variants observed for STR locus SE33: a concordance study.

Discordance of STR typing results can be expected between kits that employ different primers for amplification. The complex motif of the SE33 locus and its flanking regions can contribute to the degree of discordant results. Sequence-dependent conformational changes can manifest as length differences under certain electrophoretic conditions and/or use of different primers. The AmpFlSTR® NGM SElect™ PCR Amplification Kit (Life Technologies, Carlsbad, CA), PowerPlex® ESX 17 system (Promega Corporation, Madison, WI), and PowerPlex® ESI 17 system (Promega Corporation) were compared for concordance of allele calls for the SE33 marker in selected samples. A total of 16 samples were identified that were discordant at one of the SE33 alleles by an apparent one nucleotide in size. While the ESX 17 and NGM SElect™ kits yielded concordant results for these 16 samples, the ESI 17 kit generated alleles that differed. The discordant alleles were observed in individuals of African and European descent. Sequence analysis revealed that the one-base difference in size is not due to an indel but is instead the result of a single nucleotide polymorphism (SNP) in the flanking region of the SE33 repeat region. Three different SNPs were observed, one of which is novel. Although these migration anomalies were observed only with the ESI 17 kit, one cannot preclude that a similar phenomenon may occur with the other kits as data sets increase. The type and degree of discordance of STR allele calls among STR kits is an important issue when comparing STR profiles among laboratories and when determining search parameters for identifying candidate associations in national databases.

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.

Bite mark documentation and analysis: the forensic 3D/CAD supported photogrammetry approach.

Bite mark identification is based on the individuality of a dentition, which is used to match a bite mark to a suspected perpetrator. This matching is based on a tooth-by-tooth and arch-to-arch comparison utilising parameters of size, shape and alignment. The most common method used to analyse bite mark are carried out in 2D space. That means that the 3D information is preserved only two dimensionally with distortions. This paper presents a new 3D documentation, analysis and visualisation approach based on forensic 3D/CAD supported photogrammetry (FPHG) and the use of a 3D surface scanner. Our photogrammetric approach and the used visualisation method is, to the best to our knowledge, the first 3D approach for bite mark analysis in an actual case. The documentation has no distortion artifacts as can be found with standard photography. All the data are documented with a metric 3D measurement, orientation and subsequent analysis in 3D space. Beside the metrical analysis between bite mark and cast, it is possible using our method to utilise the topographical 3D feature of each individual tooth. This means that the 3D features of the biting surfaces and edges of each teeth are respected which is--as shown in our case--very important especially in the front teeth which have the first contact to the skin. Based upon the 3D detailed representation of the cast with the 3D topographic characteristics of the teeth, the interaction with the 3D documented skin can be visualised and analysed on the computer screen.

Congenital secondary hypothyroidism due to a mutation C105Vfs114X thyrotropin-beta mutation: genetic study of five unrelated families from Switzerland and Argentina.

We identified five patients with congenital secondary hypothyroidism with isolated thyrotropin (TSH) deficiency originating from three and two unrelated Argentinean and Swiss families, respectively. The affected patients presented with both low TSH as well as low thyroid hormone levels. Further, TSH-releasing hormone (TRH) stimulation failed to increase serum TSH, whereas prolactin increased adequately. These affected children were homozygous for a 1-bp deletion (822delT) in the TSH-beta subunit gene leading to a cysteine 105 to valine conversion (C105V) and to a frameshift with a premature stop codon at position 114 (C105Vfs114X). In a total of 22 families five different mutations located within the coding region of the TSH-beta subunit gene responsible for congenital secondary hypothyroidism have been reported so far (E12X; G29R; Q49X; IVS2 +5, G --> A; C105Vfs114X). Importantly, out of 13 families, including our five families, the C105Vfs114X mutation has been described in 12 unrelated and non-consanguineous families, whereas the remaining four TSH-beta subunit gene mutations have been described in consanguineous families only. Therefore the C105Vfs114X mutation within the TSH-beta subunit gene is the most frequent alteration causing congenital secondary hypothyroidism (13 of 22; 59%) and occurs mainly in unrelated and non-consanguineous families (12 of 13; 92%). As we could exclude a common ancestry by microsatellite marker analysis in our five independent families we concluded that the codon 105 in the TSH-beta subunit gene might be a "hot spot," although a founder effect has been reported in certain cases clustered in a highly specific and restricted geographical area.

Determination of the donor:host blood cell ratio after haematological stem cell transplant by means of semiquantitative detection of short tandem repeat polymorphisms.

An improved method of quantifying the donor:host blood cell ratio after haematological stem cell transplantation (PBSCT) using a variable number of tandem repeat (VNTR) markers is presented. The post-transplant DNA is extracted from the patient's blood and amplified by semiquantitative polymerase chain reaction (PCR) without prior mock transplant and plotting of a standard curve. The amplification products are then analysed by ABI PRISM 310 capillary electrophoresis apparatus. The resultant peak areas are correlated with the corresponding microsatellite allele by GeneScan software and the donor:host cell ratio is calculated. Improvements to PCR amplification conditions are essential for the outcome of the quantification since preferential amplification of alleles in the PCR process can account for the marked deviation found between the results gained by measurement of different microsatellite loci. To assess the accuracy of the method, the post-transplant blood samples of 6 patients who had undergone either myeloablative or non-myeloablative transplantation regimens were analysed retrospectively (median observation time 298 days). By analysing 3 or 4 microsatellite loci we were able to detect full engraftment or mixed chimaerism after transplant with a measurement precision of < or = 4.5 (standard deviation). Sensitivity for different primers ranges from 2% to 5%. The results of the microsatellite analysis correlated well with the corresponding clinical findings. We conclude that post-transplant analysis of microsatellite loci using semiquantitative PCR without standard is suitable for clinical purposes.