The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives

This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group's mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control region or the two hypervariable regions HVI (16024-16365) and HVII (73-340) from DNA extracts, buccal swabs or bloodstains, proceeding in accordance with the protocol and strategies used in each individual laboratory. The results of the collaborative exercises were employed to identify possible sources of errors that could arise during the analysis and interpretation of mtDNA profiles. These findings were taken as a basis to tentatively make suitable arrangements for the construction of a high quality mtDNA database. One hundred fifty mtDNA profiles were submitted to the evaluating laboratory, and disaccording profiles were classified into four groups corresponding to the source of error: clerical errors, sample mix-ups, contaminations and discrepancies with respect to the mtDNA nomenclature. Overall, 14 disaccording haplotypes (16 individual errors) were observed. The errors included 10 clerical errors, 3 interpretation problems, 2 cases of sample mix-up and 1 case of point heteroplasmic mixture, where the 2 sequencing reactions brought inconsistent base calls. This corresponds to an error rate of 10.7% in a virtual mtDNA database consisting of the collaborative exercise results. However, this estimate is still conservative compared to conclusions drawn by authors of meanwhile numerous publications critically reviewing published mtDNA population databases. Our results and earlier published concerns strongly emphasize the need for appropriate safety regulations when mtDNA profiles are compiled for database purposes in order to accomplish the high standard required for mtDNA databases that are used in the forensic context.     

Rapid and simple sex determination method from dental pulp by loop-mediated isothermal amplification

Sex determination from dental pulp DNA was examined by loop-mediated isothermal amplification (LAMP) method. Amelogenin locus was analyzed for sex determination. A set of four specially designed primers was prepared based on database from Gene Bank, and loop primers were designed to shorten the analysis time. Analysis was performed using 32 dental pulp DNA samples removal from permanent teeth stored at room temperature for 1–25 years after extraction. The X allele was detected in approximately 32 min with real-time turbidimeter and the Y allele was detected in approximately 34 min. Analysis time was reduced to half when using loop primers. Visual detection was also possible as the amplified product showed white turbidity. Sex determination by LAMP method was rapid and simple, and it should prove useful in unknown bodies of mass disasters.     

Results of the 2003–2004 GEP-ISFG collaborative study on mitochondrial DNA: Focus on the mtDNA profile of a mixed semen-saliva stain

We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003–2004. Five reference bloodstains from five donors (M1–M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1–M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1–M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.     

Allele frequencies of six miniSTR loci in the population of Northern Portugal

A possible approach to try to recover information from degraded DNA is to reduce the size of the PCR products by designing primers that bind as close as possible to the STR repeat region, known as miniSTRs. Allele frequencies and forensic parameters for the six miniSTRs loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045 were investigated in a sample group consisting of 228 anonymous apparently healthy unrelated individuals living in North of Portugal. The results show that all loci were in Hardy–Weinberg equilibrium. The combined power of discrimination and power of exclusion for the six loci were 0.99999 and 0.9789, respectively. All but one (D4S2364) loci showed a moderate degree of polymorphism (observed heterozygosity >0.6). The allele sizes ranged between 66 and 118 bp in our population, which is beneficial for typing degraded samples than those of a commercial STR kit.     

Psychopathy (PCL-R) Predicts Violent Recidivism Among Criminal Offenders with Personality Disorders in Sweden

Psychopathy as conceptualized with Hare's Psychopathy Checklist Revised, PCL-R, has attracted much research during the 1990s. In the Scandinavian countries, few studies that empirically support the validity of North American risk assessment techniques in our regional context have been published. The purpose of this paper is to explore the predictive power of the PCL-R in a population of personality-disordered violent offenders subjected to forensic psychiatric evaluation in Sweden. Following release from prison (n = 172), discharge from forensic psychiatric treatment (n = 129), or probation (n = 51), a total of 352 individuals were followed for up to 8 years (mean = 3.7 years) with reconviction for violent crime as endpoint variable (base rate 34%). As the estimate of predictive power, the area under the curve of a receiver operating characteristic (AUC of ROC) analysis was calculated. For PCL-R scores to predict 2-year violent recidivism, AUC of ROC was .72 (95% CI: .66–.78). In addition, the personality dimension of psychopathy (Factor 1) and the behavioral component (Factor 2) both predicted 2-year recidivism significantly better than random: AUC of ROC .64 (95% CI: .57–.70) and .71 (95% CI: .65–.77), respectively. We conclude that psychopathy is probably as valid a predictor of violent recidivism in Swedish forensic settings as seen in previous North American studies.     

Allele frequencies and haplotypes of eight Y-short tandem repeats in Bantu population living in Central Africa

Eight Y chromosome short tandem repeats (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II) were used to assess haplotype distribution in non-selected, unrelated Bantu males living in Central Africa [N. Mathias, M. Bayes, C. Tyler-Smith, Highly informative compound haplotypes for the human Y chromosome, Hum. Mol. Genet. 3 (1994) 115-123; L. Roewer, J. Arnemann, N.K. Spurr, K.H. Grzeschik, J.T. Epplen, Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts, Hum. Genet. 89 (1992) 389-394; P. De Knijff, M. Kayser, A. Caglia, D. Corach, N. Fretwel, C. Gehrig, G. Graziosi, F. Heidorn, S. Herrmann, B. Herzog, M. Hidding, K. Honda, M. Jobling, M. Krawczak, K. Leim, S. Meuser, E. Meyer, W. Oesterreich, A. Pandya, W. Parson, G. Penacino, A. Perez-Lezaun, A. Piccini, M. Prinz, C. Schmitt, P. M. Schneider, R. Szibor, J. Teifel-Greding, G. Weishold, L. Rower, Chromosome Y microsatellites: population genetic and evolutionary aspects, Int. J. Legal Med. 110 (1997) 134-149; M. Kayser, A. Caglia, D. Corach, N. Fretwel, C. Gehrig, G. Graziosi, F. Heidorn, S. Herrmann, B. Herzog, M. Hidding, K. Honda, M. Jobling, M. Krawczak, K. Leim, S. Meuser, E. Meyer, W. Oesterreich, A. Pandya, W. Parson, G. Penacino, A. Perez-Lezaun, A. Piccini, M. Prinz, C. Schmitt, P. M. Schneider, R. Szibor, J. Teifel-Greding, G. Weishold, P. de Knijff, L. Rower, Evaluation of Y chromosome STRs: a multicenter study, Int. J. Legal Med. 110 (1997) 125-133, 141-149]. One hundred and sixty-five full haplotypes were obtained from Bantu males. The most common haplotype (DYS19-15, DYS389I-13, DYS389II-30, DYS390-21, DYS391-10, DYS392-11, DYS393-13, DYS385I/II-15,17) was shared by 5.5% of individuals. In the Bantu population in Central Africa, the haplotype diversity and the discrimination capacity of Y-STR may be estimated at 99.14% and 0.5333, respectively.     

Evaluation of the IDS One-Step™ ELISA kits for the detection of illicit drugs in hair

This work presents the validation of a new immunological assay, the One-Step™ enzyme-linked immunosorbent assay (ELISA) tests from International Diagnostic Systems Corp. for the screening of drugs of abuse (cannabis, amphetamines, opiates, and cocaine) in human hair, with subsequent GC–MS confirmation. After decontamination and segmentation into small pieces, 50 mg of hair sample were incubated in 1 ml of methanol during 16 h at 40 °C. A 100 μL aliquot was collected and evaporated to dryness in presence of 100 μL of methanol/hydrochloric acid (99:1, v/v) to avoid amphetamines loss. The dried extract was dissolved in 100 μL of the “sample and standard diluent” solution included in the kit. This solution was submitted to analysis according to the recommended instructions of the manufacturer. During the validation phase, GC–MS confirmations were conducted according to our fully validated and published methods for opiates, cocaine, cannabis, and amphetamines determinations in hair. In a last development step, these procedures were slightly modified to directly confirm ELISA results by GC–MS using the methanolic extract. Ninety-three specimens were simultaneously screened by the ELISA tests (103 for tetrahydrocannabinol (THC)) and confirmed by GC–MS. Twenty were found positive for cannabis (THC: 0.10–6.50 ng/mg), 21 for cocaine (0.50–55.20 ng/mg), 24 for opiates (6-acetylmorphine (6-AM): 0.20–11.60 ng/mg, MOR: 0.20–8.90 ng/mg, codeine (COD): 0.20–5.90 ng/mg), and 13 for amphetamines (AP: 0.20 and 0.27 ng/mg, methamphetamine (MAP): 0.30 and 1.10 ng/mg, methylenedioxymethamphetamine (MDMA): 0.22–17.80 ng/mg). No false negative results were observed according to the Society of Hair Testing's (SoHT) cutoffs (0.5 ng/mg for cocaine, 0.2 ng/mg for opiates and amphetamines, and 0.1 ng/mg for THC). The One-Step™ ELISA kits appear suitable due to their sensitivity and specificity for drug of abuse screening in hair. This technology should find interest in workplace drug testing or driving license regranting, especially when many samples have to be tested with a high rate of negative samples, as ELISA is an easy and high-throughput method.     

Developing STR databases on structured populations: The native South Siberian population versus the Russian population

Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of θ-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus и AmpFlSTR Profiler Plus. The groups differentiate from each other with average θ-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on θ-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on θ-values.     

Haplotype diversity in human mitochondrial DNA hypervariable regions I–III in the city of Caracas (Venezuela)

In order to expand the database of variable DNA for forensic identification purposes in Venezuela, we analyzed the sequence polymorphisms of mitochondrial DNA (mtDNA) hypervariable regions (HVR) I–III from 100 unrelated individuals from the city of Caracas, using PCR amplification and fluorescent-based capillary electrophoresis sequencing method. Dominant haplogroups corresponded to Native Americans followed by African ones. The inclusion of HVR III although useful for sub-haplogroup assignation, added little to the discrimination capacity of our database.     

Genetic variability of RyR2 and CASQ2 genes in an Asian population

We analyzed the coding regions of the cardiac calcium-handling genes, ryanodine receptor 2 (RyR2) and calsequestrin 2 (CASQ2) for genetic variants in a healthy Chinese population (n = 95) and in a cohort of 28 sudden unexplained death victims. Mutations in RyR2 and CASQ2 have been shown to alter calcium homeostasis during excitation–contraction coupling and predispose individuals to fatal cardiac arrhythmias. The genetic screening was accomplished by denaturing high-performance liquid chromatography and DNA sequencing methods. Genetic analysis revealed the following non-synonymous genetic variations: two reported RyR2 polymorphisms; 5654G>A (G1885E) and 5656G>A (G1886S), two reported CASQ2 polymorphisms; 196A>G (T66A) and 226G>A (V76M) and one novel CASQ2 mutation; 529G>C (E177Q). The functional significance of the novel CASQ2 mutation has not been evaluated and characterized. This study shows that multiple genetic variations of the RyR2 and CASQ2 genes exist in the two study populations. The inter-individual genetic variability may underlie the different susceptibility of individuals to developing ventricular tachycardia. The research results will be valuable for which future work involving clinical and forensic samples can be based upon to distinguish potential disease-associated mutations from common polymorphisms.     

Confirmation by LC–MS of drugs in oral fluid obtained from roadside testing

The aim of this study was to assess the effectiveness of two current on-site oral fluid (OF) drug detection devices (OraLab and Dräger), as part of the Spanish participation in the Roadside Testing Assessment Project (ROSITA Project). The study was done in collaboration with the Spanish Traffic Police, in Galicia (NW Spain), during 2004 and 2005. A total of 468 drivers selected at the police controls agreed to participate through informed consent. In addition, saliva samples were collected and sent to the laboratory to confirm the on-site results. For this purpose, two different analytical liquid chromatography–mass spectrometry (LC–MS) methods were used to detect 11 drugs or metabolites in a 300 μL sample. Simultaneous analysis of morphine, 6-acetylmorphine, amphetamine, methamphetamine, MDA, MDMA, MDEA, MBDB, cocaine and benzoylecgonine was carried out using 100 μL of oral fluid, after an automated solid phase extraction. A different LC–MS method was performed to detect Δ⁹-THC in 200 μL of oral fluid using liquid–liquid extraction with hexane at pH 6. Both methods were fully validated, including linearity (1–250 ng/mL, 2–250 ng/mL) recovery (>50%), within-day and between-day precision (CV < 15%), accuracy (mean relative error < 15%), limit of detection (0.5 and 1 ng/mL), quantitation (1 and 2 ng/mL) and matrix effect. All of the positive cases and a random selection of 30% of the negatives were analyzed for confirmation analysis. Good results (sensitivity, specificity, accuracy, positive predictive value and negative predictive value > 90%) were obtained for cocaine and opiates by OraLab, and for cocaine by Dräger. However, the results for the other compounds could be improved for both detection devices. Differences in the ease of use and in the interpretation mode (visual or instrumental) were observed.     

Average Probability that a "Cold Hit" in a DNA Database Search Results in an Erroneous Attribution

Abstract:  We consider a hypothetical series of cases in which the DNA profile of a crime-scene sample is found to match a known profile in a DNA database (i.e., a "cold hit"), resulting in the identification of a suspect based only on genetic evidence. We show that the average probability that there is another person in the population whose profile matches the crime-scene sample but who is not in the database is approximately 2( N  −  d ) p _A , where N is the number of individuals in the population, d is the number of profiles in the database, and p _A is the average match probability (AMP) for the population. The AMP is estimated by computing the average of the probabilities that two individuals in the population have the same profile. We show further that if a priori each individual in the population is equally likely to have left the crime-scene sample, then the average probability that the database search attributes the crime-scene sample to a wrong person is ( N  −  d ) p _A .     

Time-dependent immunohistochemical detection of proinflammatory cytokines (IL-1β, IL-6, TNF-α) in human skin wounds

The proinflammatory cytokines interleukin-1beta (IL-1β), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) hold important functions in the early and late courses of inflammation, trauma and wound healing. In the present study, human skin wounds due to sharp force (n=105) were collected during surgery and autopsy. The wound age mainly varied from several minutes to 5 h, some specimens aged up to 6 weeks. Control specimens from uninjured skin were available in each case. After preparation of cryostat sections, immunohistochemistry was performed according to the APAAP technique, using monoclonal and polyclonal antibodies. The results were evaluated semiquantitatively. All markers were weakly expressed in normal human skin constitutively. However, the staining pattern changed significantly in vital wounds concerning epidermal layers, subepidermal cells, vessels and sweat glands. IL-1β and IL-6 showed enhanced expression after 15 and 20 min at the earliest (increase of epidermal reactivity). After 30–60 and 60–90 min, respectively, marked expression was observed with these markers. Similar alterations were detectable with TNF-α after 15 and 60–90 min. The reactivity of all three markers persisted over several hours, then decreased to basal levels again and sometimes reappeared after days and in granulation tissue. Leukocytes reacting with IL-1β and IL-6 appeared after approximately 2 h. Conclusion: proinflammatory cytokines can serve as a useful tool for the estimation of vitality and wound age, in particular in the early post-traumatic interval prior to leukocyte reaction. Autolysis did not play a role in the samples investigated (postmortem interval up to 8 days). Problems could sometimes rise from constitutive expression. Therefore, it is recommended to examine control samples from the same individual and to compare the reactivity with wound specimens.     

Colonialism and the health transition: Aboriginal Australians and poor whites compared, Victoria, 1850–1985

This paper presents the results of the first two longitudinal historical cradle-to-grave datasets constructed in Australia: the Aboriginal population of the state of Victoria, reconstituted backwards using genealogical research and vital registrations, 1835–1930; and an impoverished European population born at the Melbourne Lying-In Hospital, 1857–1900 and traced until 1985. It investigates the hypothesis that the health transition in indigenous people was different from that of the dominant non-indigenous population. Both of these studied sub-populations were highly stressed, resulting in high infant mortality and persistent tuberculosis mortality. The Aboriginal population suffered the additional burdens of racism and social exclusion, even though after the passage of the 1886 ‘Half-Castes Act’, the majority of Aboriginal Victorians were legally ‘white’. The impact of that legislation and the systematic exclusion of Aboriginal Victorians from federal entitlements in the twentieth century sent the Aboriginal health transition into reverse. The contrasting fates of poor whites and ‘unofficial blacks’ during the health transition demonstrate the health burdens of inequality and racial discrimination, and reveal that ‘the gap’ in life expectancy between Indigenous and non-Indigenous Australians is a historical product of long-term government policy and exclusion from citizenship and its entitlements.     

Influence of rain and malathion on the oviposition and development of blowflies (Diptera: Calliphoridae) infesting rabbit carcasses in Kelantan, Malaysia

The influence of rain and malathion on the initial oviposition as well as development of blowfly species infesting rabbit carcasses decomposing in sunlit and shaded habitats were studied over a period of 1 year in Kelantan, Malaysia. Chrysomya megacephala (Fabricius) was the most dominant species that infested the carcasses, followed by Chrysomya rufifacies (Macquart). In general, rain, depending on its intensity, delayed initial oviposition by 1–2 days and prolonged the pupation period by 1–3 days. The presence of malathion in the carcasses delayed initial oviposition by 1–3 days and prolonged the pupation period by 2–3 days. These findings deserve consideration while estimating postmortem interval since rain is a commonplace occurrence in Malaysia and malathion is one of the common poisons as an agent for choice to commit suicide.     

Sequence polymorphism in the coding region of mitochondrial genome encompassing position 8389–8865

Analysis of the polymorphic sequences in mitochondrial DNA (mtDNA) has been widely applied to forensic tests and anthropology studies. However, these polymorphic data in human have thus far been derived from the displacement-loop and intergenic regions only. Here, we report the identification of clustered polymorphic sites in the mitochondria coding region encompassing position 8389–8865. The DNA sequences of 119 unrelated Chinese were determined by PCR amplification and direct sequencing. The results showed that heteroplasmy was found in five individuals, 39 sites were noted in this 477 bp region, and 41 haplotypes were identified. The probability of identity and allelic diversity were estimated as 0.1265 and 0.8809, respectively. The results suggest that sequence polymorphism from position 8389–8865 in human mtDNA can be used as a marker for identity investigation.     

East meets West in crime in Dutch history

This essay is based on Underworlds — Organized Crime in the Netherlands, 1650–1800 (Cambridge, 1993; translated into Dutch asOp het verkeerde pad — Georganiseerde misdaad in de Noordelijke Nederlanden 1650–1800, Amsterdam, 1994), which presents a more extended discussion of ethnicity, marginality, stigmatization, and the structures and patterns of organized crime in the early modern Netherlands. For all bibliographical references and archival sources, see Underworlds.     

Genetic analysis of 15 STR loci in the population of Zhejiang Province (Southeast China)

Fifteen autosomal STR loci were analyzed from a population sample of 598 unrelated individuals residing in Zhejiang Province. We report allele frequencies distribution and statistical parameters for all 15 STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA. Allele frequencies, the observed heterozygosity (Ho), the polymorphic information content (PIC), and the probability of paternity exclusion (PE) were calculated. All loci were in accordance with Hardy–Weinberg equilibrium (P > 0.05). Our studied population data were compared with the previously published population data of other ethnic groups or areas in China. Our results of present study were valuable for human identification and paternity tests in Zhejiang Province.