A collection of idioms for modeling activity level evaluations in forensic science.

This paper presents a collection of idioms that is useful for modeling activity level evaluations in forensic science using Bayesian networks. The idioms are categorized into five groups: cause-consequence idioms, narrative idioms, synthesis idioms, hypothesis-conditioning idioms, and evidence-conditioning idioms. Each category represents a specific modeling objective. Furthermore, we support the use of an idiom-based approach and emphasize the relevance of our collection by combining several of the presented idioms to create a more comprehensive template model. This model can be used in cases involving transfer evidence and disputes over the actor and/or activity. Additionally, we cite literature that employs idioms in template models or case-specific models, providing the reader with examples of their use in forensic casework.

Use of Bayesian networks in forensic soil casework.

Forensic soil comparisons can be of high evidential value in a forensic case, but become complex when multiple methods and factors are considered. Bayesian networks are well suited to support forensic practitioners in complex casework. This study discusses the structure of a Bayesian network, elaborates on the in- and output data and evaluates two examples, one using source level propositions and one using activity level propositions. These examples can be applied as a template to construct a case specific network and can be used to assess sensitivity of the target output to different factors and identify avenues for research.

Calculating LRs for presence of body fluids from mRNA assay data in mixtures.

Messenger RNA (mRNA) profiling can identify body fluids present in a stain, yielding information on what activities could have taken place at a crime scene. To account for uncertainty in such identifications, recent work has focused on devising statistical models to allow for probabilistic statements on the presence of body fluids. A major hurdle for practical adoption is that evidentiary stains are likely to contain more than one body fluid and current models are ill-suited to analyse such mixtures. Here, we construct a likelihood ratio (LR) system that can handle mixtures, considering the hypotheses H1: the sample contains at least one of the body fluids of interest (and possibly other body fluids); H2: the sample contains none of the body fluids of interest (but possibly other body fluids). Thus, the LR-system outputs an LR-value for any combination of mRNA profile and set of body fluids of interest that are given as input. The calculation is based on an augmented dataset obtained by in silico mixing of real single body fluid mRNA profiles. These digital mixtures are used to construct a probabilistic classification method (a 'multi-label classifier'). The probabilities produced are subsequently used to calculate an LR, via calibration. We test a range of different classification methods from the field of machine learning, ways to preprocess the data and multi-label strategies for their performance on in silico mixed test data. Furthermore, we study their robustness to different assumptions on background levels of the body fluids. We find logistic regression works as well as more flexible classifiers, but shows higher robustness and better explainability. We test the system's performance on lab-generated mixture samples, and discuss practical usage in case work.

The use of δ(2)H and δ(18)O isotopic analyses combined with chemometrics as a traceability tool for the geographical origin of bell peppers.

Two approaches were investigated to discriminate between bell peppers of different geographic origins. Firstly, δ(18)O fruit water and corresponding source water were analyzed and correlated to the regional GNIP (Global Network of Isotopes in Precipitation) values. The water and GNIP data showed good correlation with the pepper data, with constant isotope fractionation of about -4. Secondly, compound-specific stable hydrogen isotope data was used for classification. Using n-alkane fingerprinting data, both linear discriminant analysis (LDA) and a likelihood-based classification, using the kernel-density smoothed data, were developed to discriminate between peppers from different origins. Both methods were evaluated using the δ(2)H values and n-alkanes relative composition as variables. Misclassification rates were calculated using a Monte-Carlo 5-fold cross-validation procedure. Comparable overall classification performance was achieved, however, the two methods showed sensitivity to different samples. The combined values of δ(2)H IRMS, and complimentary information regarding the relative abundance of four main alkanes in bell pepper fruit water, has proven effective for geographic origin discrimination. Evaluation of the rarity of observing particular ranges for these characteristics could be used to make quantitative assertions regarding geographic origin of bell peppers and, therefore, have a role in verifying compliance with labeling of geographical origin.

Probabilistic peak detection for first-order chromatographic data.

We present a novel algorithm for probabilistic peak detection in first-order chromatographic data. Unlike conventional methods that deliver a binary answer pertaining to the expected presence or absence of a chromatographic peak, our method calculates the probability of a point being affected by such a peak. The algorithm makes use of chromatographic information (i.e. the expected width of a single peak and the standard deviation of baseline noise). As prior information of the existence of a peak in a chromatographic run, we make use of the statistical overlap theory. We formulate an exhaustive set of mutually exclusive hypotheses concerning presence or absence of different peak configurations. These models are evaluated by fitting a segment of chromatographic data by least-squares. The evaluation of these competing hypotheses can be performed as a Bayesian inferential task. We outline the potential advantages of adopting this approach for peak detection and provide several examples of both improved performance and increased flexibility afforded by our approach.

No evidence of West Nile virus infection in Dutch blood donors.

BACKGROUND AND OBJECTIVES: West Nile virus (WNV) can be transmitted by transfusion through infected blood components. This study aimed to determine the prevalence of WNV infection among Dutch blood donors to assess whether WNV is a possible threat for the Dutch blood supply. MATERIALS AND METHODS: Plasma samples from 61 992 blood donations were pooled in 7,749 test pools of eight donations using a Tecan robot. These samples were collected between April and October 2004. The pools were tested for the presence of WNV RNA by using the Procleix WNV assay. RESULTS: No WNV RNA-positive pools were detected. Based on Poisson distribution statistics, extrapolation of our data to all the Dutch donations in 2004 revealed that between 0 and 55 cases of WNV infection could be expected. CONCLUSIONS: No evidence of the presence of WNV RNA in Dutch blood donor samples from 2004 was found. However, surveillance of this emerging infection is of importance to safeguard the blood supply in the future because the transmission cycle of WNV is complex and hard to predict.

Evaluation of COBAS AmpliPrep nucleic acid extraction in conjunction with COBAS AmpliScreen HBV DNA, HCV RNA and HIV-1 RNA amplification and detection.

BACKGROUND AND OBJECTIVES: This report describes the evaluation of the COBAS AmpliPrep instrument for fully automated generic nucleic acid extraction in conjunction with hepatitis B virus (HBV) DNA, hepatitis C virus (HCV) RNA, and human immunodeficiency virus (HIV)-1 RNA COBAS AmpliScreen amplification and detection using serial dilutions of the WHO international standards (IS) and the PeliCheck reference panels. MATERIALS AND METHODS: Serial diluted samples of the WHO IS and the PeliCheck reference panels were tested 24 times to determine the HBV DNA, HCV RNA and HIV-1 RNA detection limits by Probit analysis. The existence and extent of cross-contamination were assessed by testing alternating high titre HBV DNA-positive and -negative samples. The specificity of the AmpliPrep-AmpliScreen test for HBV was determined by testing 232 minipools consisting of six donations, all negative for HCV/HIV-1 nucleic acid testing (NAT) and HBsAg. In addition, a HBV genotypes A-G panel was tested. RESULTS: The respective 95% detection limits (and 95% CI) on the WHO IS and on the PeliCheck reference panels were 6.7 (4.3-13) IU/ml and 123 (68-301) gEq/ml for HBV DNA, 23 (11-106) IU/ml and 126 (84-233) gEq/ml for HCV RNA, and 187 (108-422) IU/ml and 183 (108-434) gEq/ml for HIV-1 RNA. Based on the WHO IS and the PeliCheck reference panels, no significant differences in sensitivity for HBV and HCV were found between AmpliPrep and the licensed MultiPrep extraction method. The sensitivity of AmpliPrep-AmpliScreen for HIV-1 was probably twofold lower as compared to the MultiPrep-AmpliScreen method. No cross contamination was observed. All 232 minipools were HBV NAT-negative. The AmpliPrep-AmpliScreen test for HBV detected HBV genotypes A-G with equal sensitivity. CONCLUSIONS: The AmpliPrep instrument combined with the AmpliScreen assays for HBV, HCV and HIV-1 is robust and suitable for NAT donor screening. The sensitivity criteria for HIV-1 and HCV as defined by the Paul Ehrlich Institute and the Food and Drug Administration for minipool NAT screening are met by this system. SINGLE SENTENCE SUMMARY: Generic COBAS AmpliPrep nucleic acid extraction in conjunction with COBAS AmpliScreen detection for HBV, HCV and HIV-1.

On the consequences of DNA profile mismatches for close relatives of an excluded suspect.

If the DNA profiles of a crime stain and the reference sample from the suspect do not match, the suspect is excluded as the donor of the crime stain. However, in some situations the DNA evidence can suggest that a close relative of the suspect might match the stain, in particular when the reference sample from the suspect and the crime stain share rare alleles. This finding can be important for the authorities. The forensic scientist has to decide whether or not to notify the authorities in these circumstances. To the best of our knowledge there is not yet an objective rule for making this decision. We propose such a decision rule for brothers of the suspect, investigate its performance and address some ethical, legal, and practical aspects. Our calculations can be simply adjusted for other relatives of the suspect.

Hepatitis G virus RNA and hepatitis G virus-E2 antibodies in Dutch hemophilia patients in relation to transfusion history.

The prevalence of hepatitis G virus (HGV)-RNA and HGV-E2 antibodies was studied in a cohort of Dutch hemophilia patients in relation to clotting products used, age, and coinfection with hepatitis C. Between 1991 and 1995, blood samples were taken from 294 patients with hemophilia A, B, or von Willebrand disease. From each patient one fresh frozen sample was tested for HGV cDNA polymerase chain reaction (PCR) and HCV cDNA PCR. Alanine aminotransferase (ALT) tests were performed on plasma samples of all patients. The presence of HGV-E2 antibodies was tested on plasma samples from a subset of 169 patients representing all age groups. Based on the origin and viral safety of the products used, three subgroups of patients were distinguished. Group A: patients who used viral noninactivated factors derived from small and large donor pools; group B: patients who used factors prepared with inadequate viral inactivation techniques derived from small and large donor pools; and group C: patients treated only with optimally viral inactivated large pool clotting factor or recombinant clotting factor concentrate. The prevalence of HGV-RNA was 18%. In group A patients the prevalence was 71%, in group B 50%, and in group C 6%. When related to age, the highest prevalence of HGV-RNA (35%) was seen in patients born between 1980 and 1989. The prevalence of HGV-E2 antibodies increased with age. Of HGV-RNA-negative patients born before 1950, 96% tested positive. HGV viremia did not affect ALT levels, neither in HCV-RNA positive nor in HCV-RNA negative patients. HGV infection is frequently seen in patients with hemophilia. In older age groups a lower rate of HGV-RNA positivity is seen coinciding with a higher rate of antienvelope antibodies.

Stability of hepatitis C virus RNA during specimen handling and storage prior to NASBA amplification.

The influence of different anticoagulants and pre-amplification storage conditions on the stability of hepatitis C virus (HCV)-RNA, as detected by the quantitative HCV NASBA assay (NASBA-QT), was studied. The HCV-RNA load remained stable for at least 15 months when serum or plasma samples (EDTA and heparin) were directly frozen at -70 degrees C in lysis buffer. At 4 degrees C, the HCV-RNA load in serum or plasma stored with lysis buffer did not decline for at least 14 days. At 30 degrees C, however, the load declined significantly after 7 days. When clotted, whole blood was stored at 4 degrees C, the HCV-RNA load was stable for 72 h. However, when EDTA-anticoagulated whole blood was stored at 4 degrees C, the HCV-RNA load declined significantly after 48 h. In paired plasma and serum samples at baseline the HCV-RNA levels were similar. Heparin did not influence the efficiency of the HCV NASBA-QT assay. Clotted blood as well as EDTA or heparin anticoagulated blood can be used for quantifying HCV-RNA using the NASBA-QT assay. Blood samples should be stored at 4 degrees C after collection and serum or plasma separated within 24 h. Preferably, after separation, samples should be frozen in lysis buffer at -70 degrees C until NASBA-QT analysis.

High prevalence of hepatitis G virus after liver transplantation without apparent influence on long-term graft function.

BACKGROUND/AIMS: Hepatitis G virus is a recently characterized transfusion-transmissible RNA virus. Its pathogenicity remains to be established. We studied its prevalence in liver transplant patients and assessed the long-term influence on the liver graft. METHODS: Thirty-nine adult patients without hepatitis B or C were included; median follow-up was 8 years (range 1-17). Serum samples from before and late after transplantation were investigated for the presence of HGV-RNA. HGV-RNA was detected by cDNA-PCR, using primers from the NS3 region of the viral genome. The latest available yearly liver biopsy was assessed in a coded fashion according to established histological criteria. The outcome in the HGV-positive patients was compared with the outcome in the HGV-negative patients with respect to liver tests and liver histology. RESULTS: The prevalence before and after transplantation was 15.4 and 43.6%, respectively. Liver test results and liver histology did not differ between the HGV and non-HGV groups. In both groups more than 50% of the patients showed normal histology. Mild portal and/or lobular inflammation tended to be more prevalent in the non-HGV group (no statistical difference). CONCLUSIONS: HGV infection is highly prevalent in liver transplant patients. In the absence of co-infection with hepatitis B or C virus, no long-term negative influence on the graft occurs.

A Dutch population study of the STR loci D21S11 and HUMFIBRA.

To introduce a duplex PCR system consisting of the STR loci D21S11 and HUMFIBRA in forensic identity testing we analysed a Dutch Caucasian database of 205 individuals. The combined power of discrimination of the two loci is 0.9978 and there was no evidence for linkage equilibrium between the two loci (p = 0.91). However, we noticed departure from Hardy-Weinberg equilibrium for the D21S11-locus in our database (p = 0.03), but the differences between observed and expected D21S11 allele pair frequencies were of negligible practical significance in forensic calculations.

A Dutch population study of the STR Loci HUMTHO1, HUMFES/FPS, HUMVWA31/1 and HUMF13A1, conducted for forensic purposes.

We report on a Dutch population study of the STR loci HUMTHO1, HUMFES/FPS, HUMVWA31/1, and HUMF13A1, in which we used multiplex amplification and automated fragment detection. Genotype and allele frequencies showed no deviation from Hardy-Weinberg and linkage equilibrium. The improved Bonferroni procedure was used to combine the results of several tests. The power of discrimination of a complete profile exceeded 0.9998. We compared the allele frequencies in the Dutch sample to the frequencies in other populations using a bipilot to visualize alleles and populations simultaneously. The Dutch sample was similar to most other Caucasian samples. The data demonstrate that the genetic systems in this report are a valuable tool for forensic identity testing in The Netherlands.

Dutch Caucasian population data on the loci LDLR, GYPA, HBGG, D7S8, and GC.

To introduce the loci LDLR, GYPA, HBGG, D7S8, and GC (PM loci) in Dutch forensic identity testing, allele and genotype frequencies were determined in a Dutch Caucasian population sample, which had previously been typed for the HLADQA1 locus [12]. All 6 loci met Hardy-Weinberg equilibrium expectations, and there is little evidence for association between pairs of loci. The combined power of discrimination for all 6 loci is 0.9997. The allele frequencies of the PM loci were similar to 2 other Caucasian populations [3, 10], and differed from 3 non-Caucasian populations [3].