Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

[STR and RFLP polymorphism in paternity determination based on family investigation]

This paper shows a paternity examination of a deceased putative father carried out on the basis of his family investigation. Statistical evaluation proved the defendant's paternity using STR and RFLP analyses with the probability of more than 99,999% (PI > 100 000). The restriction analysis has proven considerably more informative than the amplification analysis, which means seven RFLP markers correspond with the similar paternity indices of the fifteen STR markers.

Usefulness of ligation-mediated PCR genotyping in tracking outbreak-associated Mycobacterium tuberculosis strains

With the emergence of a multidrug resistant tuberculosis (MDR-TB) outbreak, the availability of a rapid typing method to carry out a nationwide prospective survey for the tracking of newly emerging MDR-TB foci became a priority. For this purpose, we have applied the IS6110 PCR-based genotyping assay, namely, LM-PCR (ligation-mediated PCR). The latter relies on ligation of a synthetic oligonucleotide priming site to a restriction site flanking IS6110. Sequences between the IS element and the restriction site are then amplified using an IS6110 specific outward primer and an oligonucleotide specific to the ligated priming site. Although it was found slightly less discriminative than the standard IS6110 restriction fragment length polymorphism analysis (IS6110 RFLP), LM-PCR allowed for the rapid and prospective identification of new outbreak-related cases within a large pool of circulating M. tuberculosis isolates. In comparison to IS6110 RFLP LM-PCR was found simple enough to justify its implementation in laboratories involved in MDR-TB surveillance at a nationwide scale.

California's Proposition 69: a dangerous precedent for criminal DNA databases

On November 2, 2004, California voters approved Proposition 69, “The DNA Fingerprint, Unsolved Crime, and Innocence Protection Act” by a margin of approximately 60 to 40 percent. Given the limited amount of information provided to voters during the initiative process, it is unclear how many of the yea-sayers were apprised of the full implications of this measure. Indeed, by voting “yes” on Proposition 69, California has elected to house the most radical and costly state criminal DNA database in the country. This dangerous expansion of California's database poses tremendous threats to civil liberties and social justice while offering little, if anything, by way of increasing the safety of its citizens.

Prior to November 2, California law required the permanent retention of DNA samples from felons convicted of serious, violent crimes. The new law expands the database to include DNA samples from all felons and individuals with past felony convictions - including juveniles - and, beginning in five years, all adults arrested for any felony offense.

Selection of international molecular standards for DNA fingerprinting of Theobroma cacao

A collaborative international program was initiated to identify and describe the genetic diversity of living germplasm collections of Theobroma cacao genotypes that are maintained in several international collections scattered throughout tropical cacao growing countries of the world. Simple sequence repeat (SSR) DNA analysis was identified as the most appropriate molecular tool for DNA fingerprinting these collections during an international forum representing academic, government and industry scientists in the cacao community. Twenty-five SSR primers, which had been previously described, were evaluated as potential candidates to define an efficient, standardized, molecular fingerprinting protocol for T. cacao accessions. These primers have been evaluated for reliability, widespread distribution across the cacao genome, number of alleles produced by the SSR primers in cacao and their ability to discriminate between cacao accessions. Approximately 690 cacao accessions were used to evaluate the utility of these SSR primers as international molecular standards, and a small number of test samples of T. cacao were sent to two other independent laboratories for verification. DNA fragments were selectively amplified by PCR, using the SSR primers labeled with fluorescent dyes, and separated by capillary electrophoresis. Based on this study, the 15 SSR primers that had the highest reproducibility and consistency within a common genotype, while allowing the differentiation of separate divergent genotypes, were selected as international molecular standards for DNA fingerprinting of T. cacao.

Role of tuberculosis laboratories in Saudi Arabia. A call to implement standardized procedures

There is no doubt that the laboratory is the backbone for the diagnosis of tuberculosis (TB). Only through testing in the laboratory can the physician confirm suspicion of TB despite any previous clinical and x-ray findings. Recent visits to several laboratories in the Kingdom of Saudi Arabia showed that some need considerable improvement. Unless there are standardized procedures to diagnose TB, and safety measures are implemented in all laboratories, it will be impossible to diagnose accurately and control TB. The laboratories should be redesigned to conform to international TB Diagnostic Centers, with well trained staff and proper safety procedures.

Validation study of the TrueAllele automated data review system

The New York State Convicted Offender DNA Databank is the first U.S. lab to complete an internal validation of the TrueAllele expert data review system. TrueAllele is designed to assess short tandem repeat (STR) DNA data based on several key features such as peak height, shape, area, and position relative to a standard ladder and use this information to make accurate allele calls. The software then prioritizes the allele calls based on several user-defined rules. As a result, the user need only review low-quality data. The validation of this system consisted of an extensive optimization phase and a large concordance phase. During optimization, the rule settings were tailored to minimize the amount of high-quality data viewed by the user. In the concordance phase, a large dataset was typed in parallel with the ABI software Gene Scan and Genotyper (manual review) and TrueAllele (automated review) for comparison of allele calls and sample state assignment. Only one significant difference was discovered out of 2048 samples in the concordance study. In this case, TrueAllele revealed a spike in the profile that was interpreted as a DNA peak by the analyst in Genotyper. TrueAllele was designed to focus the review on poor data and to eliminate the need for complete reanalysis technical review. This validation project proved TrueAllele to be dependable for use at the NYS Convicted Offender DNA Databank.

SWGDAM developmental validation of a 19-locus Y-STR system for forensic casework

A Scientific Working Group on DNA Analysis Methods (SWGDAM) developmental validation study was carried out on two Y-STR multiplex systems (MPI and MPII) that collectively permit the co-amplification of 19 Y-STR markers, including DYS393, DYS392, DYS391, DYS389I, DYS389II, Y-GATA-A7.2 (DYS461), DYS438, DYS385a and DYS385b (MPI); DYS425, DYS388, DYS390, DYS439, DYS434, DYS437, Y-GATA-C.4, Y-GATA-A7.1 (DYS460), Y-GATA-H.4, and DYS 19 (MPII). Performance checks subsequent to PCR parameter optimization indicated that MPI and MPII were suitably reproducible, precise and accurate for forensic use. The sensitivity of the systems was such that a full 19-locus Y-STR profile was obtainable with 150-200 pg of male DNA, and some loci were detectable even with as little as 20-30 pg of input DNA. Primate specificity was demonstrated by the lack of cross-reactivity with a variety of commonly encountered bacterial and animal species, with the single exception of a monomorphic canine product that was outside of the size range of human alleles from any of the 19 loci. Not surprisingly, cross-reactivity was observed with a number of male and female nonhuman primates. Environmentally compromised samples produced full or partial Y-STR profiles. For example, a semen stain exposed to the outdoor elements for six months still gave a 13-locus Y-STR profile. Although a limited number of female DNA artifacts were observed in mixed stains in which the male DNA comprised 1/300 of the total, the full 19-locus male profile was easily discernible. Even at a 1500-to-2000-fold dilution of male DNA with female DNA partial Y-STR profiles were obtained. Furthermore, the potential utility of MPI and MPII for forensic casework is exemplified by their ability to dissect out the male haplotype in a variety of case-type samples, including, inter alia, post-coital vaginal swabs, admixed male and female bloodstains, the nonsperm fraction from a differentially extracted semen stain, and determination of the number of male donors in mixed semen stains.

Preparation of degraded human DNA under controlled conditions

DNA typing through analysis of short tandem repeats (STRs) and mitochondrial DNA (mtDNA) by means of the polymerase chain reaction (PCR) and sequencing are the common methods for the forensic identification of persons and reconstruction of kinship, especially when skeletal human remains have to be analyzed. Furthermore, samples typically found at crime scenes may be both quantitatively and qualitatively inadequate since they may contain very scarce and often degraded DNA due to exposure to heat, light, humidity, and microorganisms. In order to improve the performance of STR typing technology in those cases where DNA availability is limited, it would be desirable to have a source of degraded DNA with known properties. For this purpose, we have developed a method to prepare artificially degraded DNA under controlled conditions. By treatment of genomic DNA with sonication and DNAse I we have produced DNA fragments within a defined range of lengths. STR typing of this degraded DNA with a commercially available multiplex kit could only produce partial profiles as indicated by the absence of STR alleles with sizes >200 bp. This artificially degraded DNA can be used for the improvement and standardization of STR typing protocols when only highly degraded DNA is available for analysis.

A call for mtDNA data quality control in forensic science

There is increasing evidence that many of the mitochondrial DNA (mtDNA) databases published in the fields of forensic science and molecular anthropology are flawed. An a posteriori phylogenetic analysis of the sequences could help to eliminate most of the errors and thus greatly improve data quality. However, previously published caveats and recommendations along these lines were not yet picked up by all researchers. Here we call for stringent quality control of mtDNA data by haplogroup-directed database comparisons. We take some problematic databases of East Asian mtDNAs, published in the Journal of Forensic Sciences and Forensic Science International, as examples to demonstrate the process of pinpointing obvious errors. Our results show that data sets are not only notoriously plagued by base shifts and artificial recombination but also by lab-specific phantom mutations, especially in the second hypervariable region (HVR-II).

The application of an automated allele concordance analysis system (CompareCalls) to ensure the accuracy of single-source STR DNA profiles

A powerful method for validating a scientific result is to confirm specific results utilizing independent methodologies and processing pathways. Thus, we have designed, developed and validated an automated allele concordance analysis system (CompareCalls, patent pending) that performs comparisons between two independent DNA analysis platforms to ensure the highest accuracy for allele calls. Application of this system in a quality assurance role has shown the potential to eliminate greater than 90% of the STR analysis required of a DNA data analyst. While this system is broadly applicable for use with any two independent STR analysis programs, either prior to or following human data review, we are presenting its application to data generated with the ABI Prism Genotyper software system versus data generated with the SurelockID system. With the automated allele concordance analysis system, the GeneScan DNA fragment data generated from an ABI 377 gel image are analyzed in two independent pathways. In one analysis pathway, the GeneScan data are imported into Genotyper software where STR labels are assigned to the fragment data based upon the criteria of the Kazam 20% macro. The "Kazam" macro provided with the Genotyper program works by labeling all peaks in a category (or locus) and then filtering (or removing) the labels from peaks, such as those in stutter positions, that meet predefined criteria. In the second pathway, the GeneScan data are imported into the SurelockID analysis platform where STR labels and error messages are assigned to the fragment data based upon hard-coded allele calling criteria and quality parameters. The resulting STR allele calls for each analysis platform are then compared, utilizing the automated allele concordance analysis system. Any differences in the STR allele calls between the two systems are flagged in a discordance report for further review by a qualified DNA data analyst. The automated allele concordance analysis system guides the DNA data analyst to the discordant data generated by either analysis platform. Additionally, the analyst is also directed to data that are of less than pristine quality which may have an increased potential for errors in interpretation by either analysis platform or by a human DNA data analyst. Implementation of an automated allele concordance analysis system will yield high-quality data for CODIS and free the human DNA data analyst to perform other critical duties within the laboratory.

Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome

As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

Cell line DNA typing in forensic genetics--the necessity of reliable standards

The incorporation of reference DNA is crucial to the validation of any DNA typing protocol. This paper aims to provide a panel of reference DNAs for actual forensic profiling strategies, i.e. autosomal and gonosomal STR typing as well as mtDNA sequencing. We have characterised three human lymphoid cell lines, GM9947, GM9948 and GM3657, and considered 58 autosomal and gonosomal microsatellites as well as the mitochondrial control region sequence. Well-established markers and STRs recently developed for forensic use were involved. K562 DNA samples which we purchased from two different suppliers were also analysed. They revealed conflicting results with regard to the ChrX STR marker genotype. Hence, we suggest that K562 is no longer used for the calibration of profiling techniques. Our investigation establishes a panel of one female and two male DNA samples as an STR allelic ladder calibration tool and offers information on six alleles of each autosome (AS) marker, three alleles of each X chromosome (ChrX) marker and two alleles of each ChrY marker. In addition, sequences of the mitochondrial control region of the three DNAs are communicated in order to provide sequencing quality control.

The GEDNAP blind trial concept part II. Trends and developments

This article presents a review of the developments in the GEDNAP blind trials over the period covering the past 10 years (1993-2003), demonstrating the changing approach to DNA investigations in the European community as a whole. The results of the trials also identify the most common types of error encountered which can also occur during routine DNA typing and ways of recognising such errors are suggested.

STR analysis of artificially degraded DNA—results of a collaborative European exercise

Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. Experiences with degraded DNA from casework samples show that every sample may exhibit different properties in this respect, and that it is difficult to systematically assess the performance of routinely used typing systems for the analysis of degraded DNA samples. Using a batch of artificially degraded DNA with an average fragment size of approx. 200 bp a collaborative exercise was carried out among 38 forensic laboratories from 17 European countries. The results were assessed according to correct allele detection, peak height and balance as well as the occurrence of artefacts. A number of common problems were identified based on these results such as strong peak imbalance in heterozygous genotypes for the larger short tandem repeat (STR) fragments after increased PCR cycle numbers, artefact signals and allelic drop-out. Based on the observations, strategies are discussed to overcome these problems. The strategies include careful balancing of the amount of template DNA and the PCR cycle numbers, the reaction volume and the amount of Taq polymerase. Furthermore, a careful evaluation of the results of the fragment analysis and of automated allele calling is necessary to identify the correct alleles and avoid artefacts.

Comparative study of three different DNA fingerprint techniques for molecular typing of Shigella flexneri strains isolated in Romania

In this study, 97 epidemiologically unrelated Shigella flexneri strains isolated during 1994 (69 isolates) and 1997 (28 isolates) were characterised by ribotyping, enterobacterial repetitive intergenic consensus sequence-based PCR typing, and pulsed-field gel electrophoresis. Number of strains belonging to each of the six serotypes is selected equal to their distribution in Romania. The isolates comprise 24 ribotypes based on combination of two restriction patterns obtained with HindlII and PstI, respectively, 7 enterobacterial repetitive intergenic consensus (ERIC)-PCR types, and 92 XbaI pulsed-field gel electrophoresis (PFGE) patterns grouped in 31 pulsotypes at Dice coefficients of 85% similarity. We find no significant difference in the distribution of isolates collected during the two periods. Macrorestriction analysis by PFGE offers maximal discrimination. There seems to be little genetic variability among circulating S. flexneri strains of serotype 2a, suggesting that even a combination of several molecular techniques, including PFGE, could not easily differentiate an outbreak strain from temporally associated independent isolates.

Normalizing the background and removing the trend in one-dimensional DNA fingerprint images

Maximizing an individual's genetic information from its DNA fingerprint image depends on the number of bands distinguished from the background. To approach this goal, the background should be normalized while the information is preserved. Morphological operators have been used by some authors to normalize the background for two-dimensional gel images. Methods such as mean, median and "maxpolygon" are presented in this work to normalize the background in DNA fingerprint images. Mean and median methods will lead to some deformations. Visual evaluation of the results show that the original shape of the column signals are better preserved by the maxpolygon.

God's signature: DNA profiling, the new gold standard in forensic science

In the mid-1980s, when the first DNA profiling techniques were developed, the name DNA 'fingerprinting' was widely used. At the time, fingerprinting was a well-established forensic method, and it was rarely questioned in the courts. Fingerprint examiners were permitted to describe matching prints as evidence of individual identity, and they were not required to give probability estimates. Despite its nominal association with the older technique, DNA 'fingerprinting' went through a period of controversy, especially in the US courts. The association with fingerprinting was questioned, and experts were required to qualify their testimony with probability figures. Heated debate occurred in scientific publications and law courts about the statistical and population genetic assumptions that went into the probability calculations presented in court cases. However, by the late 1990s DNA profiling was so widely accepted that it became a basis for invidious comparison with all other forms of forensic evidence, including fingerprinting. In the past three years, the admissibility of fingerprint evidence has been challenged in several US federal and state courts. This article discusses the socio-legal and socio-technical issues that led to the inversion of credibility that characterized the intertwined history of the two techniques.

Expert witness in paternity testing in Germany

In Germany, paternity testing can be ordered by a judge as well as by private persons. In the case of private counselling, the expert has the duty to inform the parties on all medical, legal and ethical aspects. Informed consent must be given by each individual included in an exploration of family relationships. Due to the rapid progress of DNA typing in even minute amounts after polymerase chain reaction amplification, genotypes of short tandem repeat systems can be elicited by extraction from single cells. Therefore, the number of unlawful investigations of paternal relationships is steadily increasing. Here the requirements for paternity testing laboratories and sanctions for unlawful exploration of a person's genotypes are discussed. A new Federal law should be drafted.