LoComatioN: a software tool for the analysis of low copy number DNA profiles

Previously, the interpretation of low copy number (LCN) STR profiles has been carried out using the biological or 'consensus' method-essentially, alleles are not reported, unless duplicated in separate PCR analyses [P. Gill, J. Whitaker, C. Flaxman, N. Brown, J. Buckleton, An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA, Forens. Sci. Int. 112 (2000) 17-40]. The method is now widely used throughout Europe. Although a probabilistic theory was simultaneously introduced, its time-consuming complexity meant that it could not be easily applied in practice. The 'consensus' method is not as efficient as the probabilistic approach, as the former wastes information in DNA profiles. However, the theory was subsequently extended to allow for DNA mixtures and population substructure in a programmed solution by Curran et al. [J.M. Curran, P. Gill, M.R. Bill, Interpretation of repeat measurement DNA evidence allowing for multiple contributors and population substructure, Forens. Sci. Int. 148 (2005) 47-53]. In this paper, we describe an expert interpretation system (LoComatioN) which removes this computational burden, and enables application of the full probabilistic method. This is the first expert system that can be used to rapidly evaluate numerous alternative explanations in a likelihood ratio approach, greatly facilitating court evaluation of the evidence. This would not be possible with manual calculation. Finally, the Gill et al. and Curran et al. papers both rely on the ability of the user to specify two quantities: the probability of allelic drop-out, and the probability of allelic contamination ("drop-in"). In this paper, we offer some guidelines on how these quantities may be specified.     

How reliable is the sub-population model in DNA testimony?

The performance of the sub-population model first proposed by Balding and Nichols [D.J. Balding, R.A. Nichols, DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci. Int. 64 (1994) 125-140] is examined using a simulation approach. This work extends the investigations of Curran et al. [J.M. Curran, J.S. Buckleton, and C.M. Triggs, What is the magnitude of the sub-population effect? Forensic Sci. Int. 135 (2003) 1-8]. In particular the effect of underestimating the coancestry coefficient, theta, and the effect of departures from the modelling assumptions were investigated. The model tends to give strongly conservative estimates if the estimate for the coancestry coefficient is accurate. If this coefficient is underestimated then a larger fraction of cases give non-conservative estimates. Departures from the modelling assumption that the sub-population is in Hardy-Weinberg and linkage equilibria appear to have very little effect.     

The tendency of individuals to transfer DNA to handled items

This research investigates factors influencing the transfer of DNA to handled objects and the process known as 'shedding'. Volunteers were recruited to hold sterile plastic tubes using experiments originally designed by Lowe et al. [A. Lowe, C. Murray, J. Whitaker, G. Tully, P. Gill, The propensity of individuals to deposit DNA and secondary transfer of low level DNA from individuals to inert surfaces, Forensic Sci. Int. 129 (2002) 25-34]. Transferred cellular material was collected from the tubes and STR profiles generated using the AmpFlSTR SGM Plus multiplex with 28 and 34 PCR cycles. Volunteers were asked to hold the tubes with each hand, and to participate in a series of handwashing experiments. The DNA profiling results obtained from the transferred skin cells were compared. An attempt was made to characterize the volunteers as 'good' or 'bad' shedders and to establish which, if any, of the experimental variables were associated with 'good' shedding. Our results suggest that many factors significantly influence shedding, including which hand an individual touches an item with and the time that has elapsed since they last washed their hands. We have found that it may be more complicated than previously reported to categorise a person as being either a 'good' or a 'bad' shedder and that if truly 'good' shedders exist they may be significantly rarer than some have estimated. In the current research no 'good' shedders were observed in a group of 60 volunteers. Given these results, it seems that rather than being applied to individual forensic cases, knowledge of shedding characteristics will be most useful in providing general background data for the interpretation of trace DNA evidence.     

A Japanese computer-assisted facial identification system successfully identifies non-Japanese faces

The method developed by Yoshino et al. in [Forensic Sci. Int. 109 (2000) 225 and Jpn. J. Sci. Tech. Iden. 5 (2000) 9] and already being applied in Japan utilizes a three-dimensional (3D) physiognomic rangefinder combined with a computer-assisted superimposition system. Facial outlines can be compared between two-dimensional (2D) surveillance images and data extracted from 3D images obtained from the rangefinder. Also, the loci of potentially concordant features can be compared and differences measured. The method is largely objective and gives statistics for false positive/false negative findings. This recently developed method by Yoshino et al. is currently being introduced to the Japanese courts. To enable courts outside Japan to assess the admissibility of this new method, studies of non-Japanese faces have been undertaken and shown to produce similar low error rates. The present authors, therefore, consider the Yoshino method to be applicable in a non-Japanese context. As part of this study a comparison of morphological features between two ethnic groups has been undertaken using 3D measurements for the first time and will serve as the foundation for an anthropological database in the future.     

A molecular genetic approach for forensic animal species identification

This study investigated potential markers within chromosomal, mitochondrial DNA (mtDNA) and ribosomal RNA (rRNA) with the aim of developing a DNA based method to allow differentiation between animal species. Such discrimination tests may have important applications in the forensic science, agriculture, quarantine and customs fields. DNA samples from five different animal individuals within the same species for 10 species of animal (including human) were analysed. DNA extraction and quantitation followed by PCR amplification and GeneScan visualisation formed the basis of the experimental analysis. Five gene markers from three different types of genes were investigated. These included genomic markers for the beta-actin and TP53 tumor suppressor gene. Mitochondrial DNA markers, designed by Bataille et al. [Forensic Sci. Int. 99 (1999) 165], examined the Cytochrome b gene and Hypervariable Displacement Loop (D-Loop) region. Finally, a ribosomal RNA marker for the 28S rRNA gene optimised by Naito et al. [J. Forensic Sci. 37 (1992) 396] was used as a possible marker for speciation. Results showed a difference of only several base pairs between all species for the beta-actin and 28S markers, with the exception of Sus scrofa (pig) beta-actin fragment length, which produced a significantly smaller fragment. Multiplexing of Cytochrome b and D-Loop markers gave limited species information, although positive discrimination of human DNA was evident. The most specific and discriminatory results were shown using the TP53 gene since this marker produced greatest fragment size differences between animal species studied. Sample differentiation for all species was possible following TP53 amplification, suggesting that this gene could be used as a potential animal species identifier.     

Ultrasonic assessment of facial soft tissue thicknesses in adult Egyptians

The production of a three-dimensional plastic face on an unknown human skull has been practiced sporadically since the latter part of the last century. In recent years, the technique has been revived and applied to forensic science cases. The morphometric method of forensic facial reconstruction rests heavily on the use of facial soft tissue depth measurements. Moreover, it has been established that measurements made on the living are of more value than those made on the dead. In view of the well-known genetic complexities of the Egyptians, and the lack of knowledge of average facial soft tissue depths of the Egyptians that makes facial reconstruction questionable, it was decided to set up a table of norms for facial tissue thicknesses in 204 adult Egyptians aged 20-35 years. Tissue depths at 17 established landmarks (according to Aulsebrook et al. [Forensic Sci. Int. 79 (1996) 83]) were obtained using ultrasonic probing. The study revealed a unique spectrum of measurements for the Egyptians that might be useful for facial reconstruction purposes with obvious sexual dimorphism in facial soft tissue thickness. Additionally, the study provided evidence for the presence of interpopulation differences in average facial soft tissue thicknesses as evidenced from the comparison of the present data of Egyptians with those previously reported for some other populations.     

Dequenching of infrared luminescence

“Dequenching” has been observed in infrared luminescence as well as ultraviolet fluorescence (Gupta et al., Forensic Sci. Int., 12 (1978) 61 – 64). Thin-layer chromatographic separations of non-luminescing inks can reveal luminescent bands. This dequenched luminescence can also be observed by spot tests with solvents and under transparent adhesive tape.     

Application of automatic image analysis (IBAS system) to age calculation. Efficiency in the analysis of several teeth from a single subject.

In a previous paper (M. López-Nicolás et al., Forensic Sci. Int., 45 (1990) 143-150) we obtained a model of multiple regression to estimate age using computerized image analysis (IBAS) to study teeth. This method should provide more precise measurements of the parameters involved and to test this hypothesis we have carried out a blind study using more than one tooth from the same individual in order to check the diagnostic accuracy of the method. Our results show that individual variability introduced serious errors in tooth age estimation using computerized image analysis. However the study of more than one tooth per individual improves the accuracy of age estimation. Specific cases should therefore be interpreted cautiously, as a degree of variability can be expected using the parameters defined in this method.     

Pronasale Position: An Appraisal of Two Recently Proposed Methods for Predicting Nasal Projection in Facial Reconstruction

This study examines two recently proposed methods for predicting nose projection from the skull, those developed by Stephan et al. (Am J Phys Anthropol 122, 2003, 240) and Rynn et al. (Forensic Sci Med Pathol 6, 2010, 20). A sample of 86 lateral head cephalograms of adult subjects from Central Europe was measured, and the actual and predicted dimensions were compared. Regarding nose projection (the anterior and vertical position of the pronasale), in general, the method of Rynn et al. (Forensic Sci Med Pathol 6, 2010, 20) was found to perform better and with less error variance than the method of Stephan et al. (Am J Phys Anthropol 122, 2003, 240), but the mean difference between the actual and predicted values did not exceed 2.2 mm (6.5% of the actual dimension) in most of the variables tested. The vertical dimensions of the nose were predictable with greater accuracy than the horizontal dimensions. Although the mean error of both methods is not great in practice and thus both methods could be considered to be “accurate,” the real variance of error should not be overlooked.     

Population genetic study in two Transylvanian populations using forensically informative autosomal and Y-chromosomal STR markers

Our study provides population genetic data on two population samples collected in a Hungarian speaking region of Transylvania, Romania. Allele frequency and profile databases were generated on 17 autosomal STR loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, VWA, FGA, TH01, TPOX, CSF1PO, Penta E and Penta D) as well as at the 12 European Y-STR extended haplotype loci (DYS19, DYS389-I/II, DYS390, DYS391, DYS392, DYS393, DYS385 loci, DYS437, DYS438 and DYS439). Data were compared to a Central Hungarian (Budapest region) population sample [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27] that was used as a reference group of the Hungarian population. Calculating the F(ST) indices and with the pairwise comparisons of interpopulation molecular variance (AMOVA) the two populations from Transylvania could be fit into the Hungarian population data showing less substructuring effects as compared to the previous findings in Hungary [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27; B. Egyed, S. Füredi, M. Angyal, I. Balogh, L. Kalmar, Z. Padar, Analysis of the population heterogeneity in Hungary using fifteen forensically informative STR markers, Forensic Sci. Int. 158 (2005) 244-249].     

26-Locus Y-STR typing in a Bhutanese population sample

26 Y chromosome short tandem repeat (STR) loci were amplified in a sample of 856 unrelated males from Bhutan, using two multiplex polymerase chain reaction (PCR) assays. The first multiplex is the Y-STR 20plex described by Butler et al. [J.M. Butler, R. Schoske, P.M. Vallone, M.C. Kline, A.J. Redd, M.F. Hammer, A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers, Forensic Sci. Int. 129 (2002) 10-24], and the second is a novel (but overlapping) 14plex that targets six additional Y-STRs (DYS425, DYS434, DYS435, DYS436, DYS461, DYS462) and also amplifies the amelogenin locus. The 26-loci give a discriminating power of 0.9957, though even at this resolution one haplotype occurs 24 times. We identify novel alleles at five loci and microvariants at a further three, which were characterised by sequencing. Extended (11-locus) haplotypes for these samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).     

Autosomal microsatellite allele frequencies for a nationwide dataset from the Australian Caucasian sub-population

DNA profiling results presented in court must be accompanied by a statistical estimate of its evidential weight. In calculating such statistics, allele frequencies from the tested loci are required. This paper reports allele frequencies and the results of population genetic testing of datasets of autosomal microsatellite profiles from Australian Caucasian donors. In contrast to previous practice in Australia these data have been collated at the national level rather than at the State and Territory level. We consider that this national dataset could be used in forensic DNA casework throughout Australia as previously recommended by Ayres et al. [K.L. Ayres, J. Chaseling, D.J. Balding, Implications for DNA identification arising from an analysis of Australian forensic databases, Forensic Sci. Int. 129 (2002) 90-98].     

Development of a harmonised method for the profiling of amphetamines V: Determination of the variability of the optimised method

This paper is the fifth in a series of six in relation to the development of a harmonised method for the profiling of amphetamine [L. Aalberg, K. Andersson, C. Bertler, H. Borén, M.D. Cole, J. Dahlén, Y. Finnon, H. Huizer, K. Jalava, E. Kaa, E. Lock, A. Lopes, A. Poortman-van der Meer, E. Sippola, Development of a harmonised method for the profiling of amphetamines I. Synthesis of standards and compilation of analytical data, Forensic Sci. Int. 149 (2005) 219-229; L. Aalberg, K. Andersson, C. Bertler, M.D. Cole, Y. Finnon, H. Huizer, K. Jalava, E. Kaa, E. Lock, A. Lopes, A. Poortman-van der Meer, E. Sippola, J. Dahlén, Development of a harmonised method for the profiling of amphetamines II. Stability of impurities in organic solvents, Forensic Sci. Int. 149 (2005) 231-241]. The third paper [K. Andersson, K. Jalava, E. Lock, L. Aalberg, Y. Finnon, H. Huizer, E. Kaa, A. Lopes, A. Poortman-van der Meer, M.D. Cole, J. Dahlén, E. Sippola, Development of a harmonised method for the profiling of amphetamines III. Development of the gas chromatographic method, Forensic Sci. Int., in press] dealt with the optimisation of the gas chromatographic and detection methods whereas the fourth paper [K. Andersson, K. Jalava, E. Lock, Y. Finnon, S. Stevenson, L. Aalberg, H. Huizer, E. Kaa, A. Lopes, A. Poortman-van der Meer, M.D. Cole, J. Dahlén, E. Sippola, Development of a harmonised method for the profiling of amphetamines IV. Optimisation of sample preparation, Forensic Sci. Int., in press] concerned the optimisation of the extraction method prior to GC analysis. This paper is a study of the optimised method in order to determine its stability. Investigations of within and between day variations were carried out in four laboratories. Moreover, variations between laboratories were also determined. Both flame ionisation detector (FID) and MS detection were used. One laboratory studied nitrogen-phosphorous detector (NPD) detection as well. For this task, 12 batches of amphetamine were prepared. Six of them were synthesised via the Leuckart route, three via the nitrostyrene route and three via the reductive amination route [A.M.A. Verweij, Impurities in illicit drug preparations: amphetamine and methamphetamine, Forensic Sci. Rev. 1 (1989) 2-11]. Taking into account all studied target compounds and the average results from four laboratories, the within day variation was around 6% for FID and 5% for MS, the between days variation was around 10% for FID and 8% for MS. For NPD detection, within day variation was 5% and between days variation 9% (only one laboratory). Finally, the inter-laboratory variation was about 12% for FID (four laboratories) and 10% for MS (three laboratories).     

Estimation of the post mortem period by multiple-site temperature measurements and the use of a new algorithm

The estimation of the post mortem period, in cases where death occurred under suspicious circumstances, is usually attempted using temperature measurements taken at a single body site. Early investigations of the validity of such an approach use the abdominal skin surface, the axilla and the rectum as measurement sites (B.H. Knight, Forensic Sci. Int., 36 (1987) 47-55). However, it has recently become more common to use the rectum alone, though the ear and the nasal passages have also been utilized. Whatever site is employed, the estimates are frequently found to be inaccurate. There are several fundamental reasons for these inaccuracies, the most prominent being the unknown variation in the ambient temperature between the time of death and the commencement of measurements, and the unknown body temperature at the time of death. This paper proposes a method of overcoming the above difficulties by taking a series of measurements concurrently at a number of body sites, a technique used by several previous workers (B.H. Knight, Forensic Sci. Int., 36 (1987) 47-55). Initial investigations have shown that an improved estimation of post mortem period is obtainable by the application of a suitable decision-making algorithm.     

Archived or directly swabbed latent fingerprints as a DNA source for STR typing

Former studies [Nature (1997) 387, Electrophoresis 20 (1999) 2870, P. Van Renterghem, D. Leonard, C. De Greef, Progress in Forensic Genetics, Vol. 8, 2000, p. 501, J. Forensic Sci. 45 (3) (2000) 687] have shown that even a single skin contact, documented by a latent fingerprint, can transfer enough DNA for a genetic analysis. It was proven in these studies that it is possible to swab fingerprints from surfaces [Nature (1997) 387, Electrophoresis 20 (1999) 2870, P. Van Renterghem, D. Leonard, C. De Greef, Progress in Forensic Genetics, Vol. 8, 2000, p. 501] and use them as a DNA source. Usually, however, discovered fingerprints are removed with scotch tape and placed on evidence cards for further investigation.In this study, we tried to assess the potential use of latent fingerprints as a DNA source for STR typing. The materials (magnetic powder, soot powder and scotch tape) used for visualization and archiving fingerprints in Germany were tested for their PCR inhibitory characteristics. Then, fingerprints were placed on clean glass surfaces, visualized and tested for their usefulness as a DNA source.Obtained DNA was quantified and tested in an STR system. Partly it proved possible to type fingerprints taken directly from the surface as well as fingerprints removed from the surface with scotch tape.     

Age estimation by a dental method: a comparison of Lamendin's and Prince & Ubelaker's technique

Lamendin et al. (J Forensic Sci 1992;37:1373) developed a general technique to estimate age of adults at death using two dental features: periodontosis and translucency of the tooth root. Prince and Ubelaker (J Forensic Sci 2002;47:107) modified this method, creating a formula for each sex and for different ancestries, and obtained more precise age estimations. In the present study, the validity of each method was tested in 45 males and 34 females of Spanish Caucasian origin, and a novel formula, based on Prince and Ubelaker method, was specifically developed for a population of mixed racial origin (mestizo) from Colombia, and findings obtained were again compared with those yielded by Lamendin adult dental aging technique. The Prince and Ubelaker method proved more accurate than the Lamendin technique in the Spanish Caucasian population, and our Prince and Ubelaker-based formula was also more accurate than the Lamendin et al. In both populations, the Lamendin method showed a higher mean error in estimations of the age of youngest and oldest individuals. These findings confirm the need to create specific formulas for each human group in order to obtain more accurate age estimates.     

Mitochondrial DNA control region population data from Macedonia

Mitochondrial DNA sequences of the entire control region were analyzed in 200 unrelated individuals from Macedonia. A total of 163 different haplotypes were found as determined by 177 polymorphic sites. The probability of a random match was calculated as 1:121 (0.83%). The basic phylogenetic structure of the Macedonian population as derived from its haplogroup distribution is in agreement with other West-Eurasian populations. Upon publication, the population data are going to be available in the EMPOP database (www.empop.org) [W. Parson, A. Dür, EMPOP—a forensic mtDNA database, FSI:Genetics 1 (2) (2007) 88–92; W. Parson, A. Brandstätter, A. Alonso, N. Brandt, B. Brinkmann, A. Carracedo, et al., The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives, Forensic Sci. Int. 139 (2–3) (2004) 215–226.].     

The routine use of C-reactive protein in forensic investigations

In clinical medicine, C-reactive protein (CRP) is extensively used as a general marker for immune system activation, and post-mortem applicability has been established [M.Q. Fujita, B.L. Zhu, K. Ishida, L. Quan, S. Oritani, H. Maeda, Serum C-reactive protein levels in postmortem blood-an analysis with special reference to the cause of death and survival time, Forensic Sci. Int. 130 (2002) 160-166; L. Uhlin-Hansen, C-reactive protein (CRP), a comparison of pre- and post-mortem blood levels, Forensic Sci. Int. 124 (2001) 32-35]. We have analysed the routine use of CRP in non-selected cases. Scarcity of blood available for analysis is a common problem in forensic investigation, and in response to this we have developed a method using liver as a source. In 50 consecutive autopsy cases, we have evaluated method, validated results and discussed their interpretation. In three cases the analysis was not possible. For each of the remaining cases (n=47) we have analysed whole blood, serum and/or liver samples. 57% (n=25) had serum CRP > 10 mg/L. Serum levels were higher than in whole blood or liver. CRP levels in serum and whole blood samples were stable in more than one month after death, making storage for later analysis possible. Liver levels peaked at one week, but after one month putrefaction was obvious. CRP levels were independent of the post-mortem interval. The use of liver as a source has not yet been described in literature. Our results in liver samples correlate well with plasma results, and liver is a good post-mortem alternative when blood is not available. We conclude that CRP measurements are easy, viable and inexpensive in a forensic setting, and that the number of cases with CRP elevation is high in a non-selected forensic material. In cases of doubt, marked elevation of CRP is an indicator of natural mode of death, and in cases of trauma, it indicates vital reaction. It can be used as a pre-autopsy screening, leading to a more extensive search for diseases not easily diagnosed, such as sepsis or ketoacidosis.     

Validation of the X-linked STR DXS6801

This paper presents sequence and population genetic data of the X-linked microsatellite marker DXS6801 (GDB:G00-365-276) which is a tetranucleotide repeat polymorphism representing eight alleles 109-141 bp in length. Data were obtained from a sample of 1146 unrelated German individuals. DXS6801 is located 99.7 cM from Xptel, nearby DXS6809 [Int. J. Legal Med. 117 (2003) 241] and DXS6789 [Forensic Sci. Int. 119 (2001) 42] in Xq21. The new marker could be added to the panel of ChrX STRs, especially usable as a part of the Xq21 linkage group.     

Effect of range wind on the trajectory of shotgun wadding

The mathematical formalism proposed previously in Forensic Sci. Int. (22 (1983) 123–130) to study the undisturbed trajectory of shotgun wadding components has been modified to take into account the effect of wind on the range. The modified equations have been used to gauge the effect of range wind on the ballistic elements of the trajectory of shotgun wadding components.