Report of the European DNA profiling group (EDNAP)--towards standardisation of short tandem repeat (STR) loci

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports.

Genotyping of STR and DIP-STR Markers in Plasma Cell-Free DNA for Simple and Rapid Noninvasive Prenatal Diagnosis of Zygosity of Twin Pregnancies

Due to the high rate of complications, special medical care must be provided especially for monozygotic twin pregnancies, which are characterized as having 2.5 times higher mortality of fetuses. In recent years, examination of cell-free DNA (cfDNA) circulating in maternal plasma has become a useful noninvasive method of prenatal diagnosis. However, fetal DNA constitutes only 3-20% of plasma cfDNA during pregnancy. Short tandem repeats (STRs) are routinely used in forensic examination of DNA mixtures and are able to identify 5% minority components. Haplotypes of deletion/insertion polymorphisms and STRs (DIP-STRs) are able to detect even 0.1% minority components of DNA mixtures. Thus, STRs and DIP-STRs seem to be a perfect tool for detection of fetal alleles in DNA isolated from maternal plasma. Here, we present a novel noninvasive prenatal diagnosis technique of determination of pregnancy zygosity based on examination of feto-maternal microchimerism of plasma cfDNA with the use of STRs and DIP-STRs. Our preliminary results based on 22 STR loci showed 67% sensitivity, 100% specificity and 82% accuracy for prenatal detection of twin dizygosity. The corresponding values for seven DIP-STRs were 13%, 100% and 54%, respectively. Owing to assay performance, low DNA input requirements, low costs (below 10 USD per patient) and simplicity of analysis, genotyping of STR/DIP-STR markers in maternal plasma cfDNA may become a useful supplementary test for noninvasive prenatal diagnosis of twin zygosity in cases when chorionicity and zygosity cannot be reliably determined by ultrasound examination and prognostic value may be provided by a DNA test determining pregnancy zygosity.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

SkydancerPlex: A novel STR multiplex validated for forensic use in the hen harrier (Circus cyaneus)

The hen harrier (Circus cyaneus) is a bird of prey which is heavily persecuted in the UK because it preys on the game bird red grouse (Lagopus lagopus scoticus). To help investigations into illegal killings of hen harrier, a STR multiplex kit containing eight short tandem repeat (STR) markers and a chromohelicase DNA binding protein 1 (CHD 1) sexing marker was developed. The multiplex kit was tested for species specificity, sensitivity, robustness, precision, accuracy and stability. Full profiles were obtained with as little as 0.25 ng of template DNA. Concurrent development of an allelic ladder to ensure reliable and accurate allele designation across laboratories makes the SkydancerPlex the first forensic DNA profiling system in a species of wildlife to be fully validated according to SWGDAM and ISFG recommendations. An average profile frequency of 3.67 × 10(-8), a PID estimate of 5.3 × 10(-9) and a PID-SIB estimate of 9.7 × 10(-4) make the SkydancerPlex an extremely powerful kit for individualisation.

Evaluation of blood, buccal swabs, and hair follicles for DNA profiling technique using STR markers

AIM

To study the short tandem repeat (STR) pattern of DNA from the blood, buccal swabs, and hair follicles of the recipients of allogenic hematopoietic stem cell transplantation to examine whether these tissues contain donor derived cells.

METHODS

The study enrolled 25 patients who sustained engraftment. Peripheral blood, buccal swabs, and hair follicles were collected on days 21-30, 90, and 180 after transplantation and the chimeric status of the recipients was evaluated.

RESULTS

Donor derived cells existed in the blood and buccal swabs, but not in hair follicles, which can be used to obtain the pre-transplant sample of the recipient after transplant.

CONCLUSION

Peripheral blood and buccal swab do not serve as a reliable source of recipient's origin for DNA analysis of individuals who underwent allogenic hematopoietic stem cell transplantation at least within 6 months after transplant.

Multi-template polymerase chain reaction

PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

Constructing STR multiplexes for individual identification of Hungarian red deer

Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations.

DIP-STR: highly sensitive markers for the analysis of unbalanced genomic mixtures

Samples containing highly unbalanced DNA mixtures from two individuals commonly occur both in forensic mixed stains and in peripheral blood DNA microchimerism induced by pregnancy or following organ transplant. Because of PCR amplification bias, the genetic identification of a DNA that contributes trace amounts to a mixed sample represents a tremendous challenge. This means that standard genetic markers, namely microsatellites, also referred as short tandem repeats (STR), and single-nucleotide polymorphism (SNP) have limited power in addressing common questions of forensic and medical genetics. To address this issue, we developed a molecular marker, named DIP–STR that relies on pairing deletion–insertion polymorphisms (DIP) with STR. This novel analytical approach allows for the unambiguous genotyping of a minor component in the presence of a major component, where DIP–STR genotypes of the minor were successfully procured at ratios up to 1:1,000. The compound nature of this marker generates a high level of polymorphism that is suitable for identity testing. Here, we demonstrate the power of the DIP–STR approach on an initial set of nine markers surveyed in a Swiss population. Finally, we discuss the limitations and potential applications of our new system including preliminary tests on clinical samples and estimates of their performance on simulated DNA mixtures.

Performing the Union: the Prüm Decision and the European dream

In 2005, seven European countries signed the so-called Prüm Treaty to increase transnational collaboration in combating international crime, terrorism and illegal immigration. Three years later, the Treaty was adopted into EU law. EU member countries were now obliged to have systems in place to allow authorities of other member states access to nationally held data on DNA, fingerprints, and vehicles by August 2011. In this paper, we discuss the conditions of possibility for the Prüm network to emerge, and argue that rather than a linear ascent towards technological and political convergence and harmonisation, the (hi)story of Prüm is heterogeneous and halting. This is reflected also in the early stages of implementing the Prüm Decision which has proven to be more challenging than it was hoped by the drivers of the Prüm process. In this sense, the Prüm network sits uncomfortably with success stories of forensic science (many of which served the goal of justifying the expansion of technological and surveillance systems). Instead of telling a story of heroic science, the story of Prüm articulates the European dream: one in which goods, services, and people live and travel freely and securely.

Evaluation of genetic diversity and population structure in a commercially important freshwater fish Prochilodus costatus (Characiformes, Prochilodontidae) using complex hypervariable repeats

We used complex hypervariable repeats to evaluate the genetic diversity and structure of Prochilodus costatus (Characiformes), an ecologically and economically important species endemic to the São Francisco River basin. Hydroelectric dams along the river have led to population fragmentation, which can limit gene flow. Restocking from hatcheries has been used to repopulate declining populations. To determine how fragmentation and hatchery supplementation affect P. costatus population structure, we studied populations from three sites up and downstream of the Gafanhoto Dam (Pará River, State of Minas Gerais). High levels of genetic diversity were found within populations (0.926 to 0.873); the three populations showed significant differentiation (F(ST) = 0.16), suggesting that populations from the three sites were affected by fragmentation of the river and by hatchery contributions. These results will be useful for developing a management and conservation plan for fish species in this area.

Forensic trace DNA: a review

DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements.

A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat loci

In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci (BM1824, BM2113, ETH10, ETH225, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH3, TGLA53, BM1818, CSRM60, CSSM66, HAUT27 and ILSTS006) for bovine genotyping (Bos taurus). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis.

A cautionary tale: Lack of consistency in allele sizes between two laboratories for a published multilocus microsatellite typing system

For species with low genetic diversity, typing using the differences in PCR fragment length resulting from variations in numbers of short tandem repeats has been shown to provide a high level of discrimination. This technique has been called multilocus microsatellite typing (MLMT) or multiple-locus variable-number tandem repeat analysis, and studies usually employ genetic or sequence analyzers to size PCR fragments to a high degree of precision. We set out to validate one such system that has been developed for Aspergillus fumigatus (H. A. de Valk, J. F. G. M. Meis, I. M. Curfs, K. Muehlethaler, J. W. Mouton, and C. H. W. Klaassen, J. Clin. Microbiol. 43:4112-4120, 2005). The sizes of the alleles were compared both by sequencing and from two genotyping laboratories, where they used capillary electrophoresis (CE) for sizing. Size differences of up to 6 bases were found between the actual sizes reported by sequencing and the sizes reported by CE. In addition, because the two genotyping laboratories used different machines and running conditions, differences of up to 3 bases were identified between them. As the microsatellite markers used differ by repeat units of 3 or 4 bases, it was not possible to assign PCR fragments to the correct alleles without confirming the sizes of a range of alleles by direct sequencing. Lines of best fit were plotted for each CE machine against actual sizes and will therefore enable unsequenced PCR fragments to be assigned to the correct alleles. This study highlights the care required to ensure that an MLMT system undergoes a suitable correction procedure before data can be merged between different laboratories involved in the typing of individual species.

Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample

We investigated 15 polymorphic short tandem repeat (STR) loci (D1S1656, D7S1517, D8S306, D8S639, D9S304, D10S2325, D11S488, D12S391, D14S608, D16S3253, D17S976, D18S1270, D19S253, D20S161, and D21S1437) which are not included in the standard sets of forensic loci. The markers were selected according to the complexity of the polymorphic region: Of the 15 investigated loci, 7 loci showed a simple repeat structure (D9S304, D10S2325, D14S608, D16S3253, D18S1270, D19S253, and D21S1437), 3 loci (D7S1517, D12S391, and D20S161) consisted of compound repeat units, and 5 loci (D1S1656, D8S306, D8S639, D11S488, and D17S976) showed a more complex polymorphic region partly including different repeat blocks and incomplete repeat units, which resulted in a relatively high proportion of intermediate alleles. A population study on a sample of 270 unrelated persons from Austria was carried out. We did not observe significant deviations from Hardy-Weinberg expectations. The combined probability of exclusion for the 15 loci was 0.99999998. In combination with the conventional set of STR markers included in commercially available kits (no linkage was observed between these 15 loci and the Powerplex 16 System loci), these markers are approved as highly discriminating forensic tools, also suitable for the analysis of difficult paternity and kinship constellations.

A proposed nomenclature for 15 canine-specific polymorphic STR loci for forensic purposes

We performed a population study on 15 polymorphic STR loci (FH2010, FH2079, PEZ2, VWF.X, FH2054, FH2087Ub, FH2611, WILMS-TF, PEZ12, PEZ15, PEZ6, FH2087Ua, ZUBECA4, ZUBECA6, FH2132) on 131 randomly selected dogs. Alleles were identified and grouped according to their estimated fragment length using fixed allelic bins encompassing one base-pair. The allele assignment was confirmed by sequence analysis of homozygote and cloned heterozygote alleles. In order to develop a uniform repeat-based nomenclature, extensive sequence analysis was performed on a selection of alleles from each STR locus. The proposed nomenclature refers to the internationally recognised recommendations for human-specific STR loci in forensic applications. The 15 canine-specific STR loci were grouped into 3 classes (simple STRs, compound STRs and complex/hypervariable STRs) according to their complexity and variability within the repeat structure. Finally, we evaluated the precision of fragment size estimation on a capillary electrophoresis platform and demonstrated reproducibility of fragment length estimation for single base-pair intermediate alleles.

Characterisation of variant alleles at the HumD21S11 locus implies unique Australasian genotypes and re-classification of nomenclature guidelines

Several variant alleles of the HumD21S11 locus have only been reported in Australasian population samples. Fifteen such alleles were observed in Caucasian and Australian Aborigine sub-population databases compiled from residents of the state of Western Australia. Each variant was sequenced to authenticate the allelic designation and determine the structural conformation. Nine novel structural variants are described. The structure of the repeat region of these rare alleles combined with the STR designation brings aspects of the HumD21S11 nomenclature guidelines into question, in particular the designation of common incomplete repeats (or "0.2's"). The conformation of the sequences provides evidence in support of a genetic relationship between the Australian Aborigine and the Papuan people.

Sequence analysis of STR polymorphisms at locus ACTBP2 in the Taiwanese population

A highly polymorphic sequence structure is reported in the human beta-actin related pseudogene 2 (ACTBP2) (SE33) locus in members of the Taiwanese Han population. A total of 100 unrelated members of the Taiwanese Han population were used in the study. Alleles that shared the same size but differ in their sequence are described to allow for inter laboratory sharing of data. PCR products amplified from this locus were separated by single-strand conformation polymorphism electrophoresis, the single-stranded DNA bands were excised from the gels, a second amplification performed, and then the PCR products were sequenced. All the alleles differed by either 2 or 4 bp. Sequence variations were observed as deletions or insertions in the repeat units AG (or AA) and AAAG. Additionally, transitions in the flanking regions were recorded. A total of 27 alleles with 71 associated genotypes were recorded if the alleles were defined by size, but 68 alleles with 88 associated genotypes were noted with the alleles were scored on the basis of sequence variation. The power of discrimination (Pd) of this single locus was 0.9874 making the human ACTBP2 a good alternative marker for individual identification and paternity testing.

Molecular stability of DNA typing short tandem repeats in the mammary tree of patients with breast cancer

Archival pathologic specimens are a rich source for the studies of hereditary diseases, cancer genetics, and identification cases in forensic science. In this study, the intraindividual consistency of eight identifying microsatellite polymorphisms (i.e., HMTH01, vWFA31, F13A, MITMH26, FES-FPS, CD4, TPOX, CSF1PO)in a cohort of 40 patients with invasive breast carcinoma were analyzed. Nests of cancer and adjacent morphologically normal ductal-lobular structures (TDLUs) were microdissected as discrete regions from hematoxylin-eosin-stained slides. As controls for each case, DNA templates were prepared from TDLUs located in nontumor quadrants and from unaffected breast skin. Over 1,400 carefully controlled PCR reactions were reviewed, and no evidence was found for microsatellite mismatches among intraindividual cancer and control DNAs. The negative results, supported by validation experiments, strongly argue that alterations of simple repeats are rare somatic events during the onset and progression of breast cancer. This study suggests that PCR artifacts may be a relevant cause of misdiagnosis of microsatellite instability in human sporadic cancer.

Sizing short tandem repeat alleles in capillary array gel electrophoresis instruments

A 96-capillary array gel electrophoresis Applied Biosystems 3700 instrument has been used to analyse AMPF/STR SGM Plus short tandem repeat (STR) loci for forensic applications. This multiplex consists of ten STR loci plus the Amelogenin locus and currently forms the basis of the UK National DNA database that currently holds more than 1 million profiles. Of particular interest is the accuracy of allele designation that is determined by comparison with standard control allelic ladder markers. Some loci have higher standard deviations than others. In particular the high-molecular-weight HUMFIBRA alleles have high standard deviations of the order of 0.15 and it is these alleles that are most likely to be misdesignated. However, this risk is minimised by the analysis of at least five different allelic ladders across the array to estimate the mean size of each allele. In conjunction with this, a series of guidelines that can be programmed into expert systems are used to minimise risks of misdesignation. The efficacy of the procedures utilised are tested by computer simulation and demonstrated to be robust.

Allelic structure and distribution of two STR loci, D8S580 and D22S442, in the Japanese population

The allelic frequency and structural characteristics of two STR loci D8S580 and D22S442 were investigated using blood samples from 143 unrelated healthy Japanese individuals. Thirty-eight alleles in D8S580 locus and 13 alleles in D22S442 locus were identified. The discrimination power, heterozygosity, and the polymorphic information content of those loci displayed high values (0.98, 0.88, and 0.87 in D8S580 and 0.97, 0.86 and 0.85 in D22S442), and their frequency distributions met Hardy-Weinberg equilibrium expectations. The allelic pattern of D8S580 was complex and differentiated into three groups (group I: alleles 184-194bp; group II: alleles 203-223, 235, 239, 243, 252 and 255bp; group III: alleles 227-286bp). Most of their alleles contained five categories of repeat units (A: aaaag; B: aaag; C: aagg; D: caag; E: agaa). On the other hand, D22S442 contained only two types of repeat units (A: agga; B: aggg). The present study, hence, proves that both D8S580 and D22S442 are highly polymorphic and represent stable genetic markers applicable to forensic investigations.

Criminal DNA databases: the European situation

In the last 5 years, a number of European countries have successfully introduced national databases holding the DNA profiles from suspected and convicted criminal offenders as well as from biological stain materials from unsolved crime cases. At present, DNA databases are fully or partially in operation in the UK, The Netherlands, Austria, Germany, Finland, Norway, Denmark, Switzerland and Sweden. Furthermore, in the other European countries, specific legislation will be enacted soon, or the introduction of such databases is being discussed to initiate a legislative process. Numerous differences exist regarding the criteria for a criminal offender to be included in the database, the storage periods and the possibility to remove database records, the possibility to keep reference samples from the offenders as long as their respective records are being held, and the role of judges in the process of entering a database record or to perform a database search. Nevertheless, harmonization has been achieved regarding the DNA information stored in national databases, and a European standard set of genetic systems has been recommended which is included either in part or completely in the DNA profiles of offenders and crime stains for all European databases. This facilitates the exchange of information from database records to allow the investigation of crime cases across national borders.

A brief history of the formation of DNA databases in forensic science within Europe

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which a nucleus of forensic scientists agreed on an uniform system. This collaboration spread to incorporate most of the established forensic science laboratories in Europe and continued through two major changes in the technology. At each step agreement was reached on which systems to use. From the beginning it was realised that DNA databases would provide the criminal justice systems with an efficient way of crime solving and consequently some local databases were created. It was not until the introduction of the amplification technology linked to the analysis of short tandem repeats that a sufficiently sensitive and robust system was available for the formation of efficient and effective DNA databases. Comprehensive legislation enacted in the UK in 1995 enabled forensic scientists to set up the first national DNA database which would hold both personal DNA profiles together with results obtained from crime scenes. Other countries quickly followed but in some the legislation has severely restricted the amount and type of data which can be retained and, therefore, effectiveness of the databases is limited. The widespread use of commercially produced multiplex kits has produced a situation in which nearly all European laboratories are using compatible systems and there is, therefore, the potential for the introduction of a pan-European DNA database. However, the exchange of results between countries is hampered by the various legislations which currently exist.

Reliability of SE33 typing by capillary electrophoresis

A ladder of 24 ACTBP2 (SE33) alleles was separated 175 times by denaturing capillary electrophoresis on an ABI Prism 310 Genetic Analyzer using polymer POP-4. The mean standard deviation of fragment size determination was 0.083 bp. Fragments in the whole allelic range of ACTBP2 could be typed with high precision and reproducibility if adjacent fragments differed by at least two nucleotides. The capacity of resolving 1 bp differences was tested by repeatedly running a ACTBP2*14.2/14.3/31.2/31.3 allelic mixture. The 14.2/14.3 fragment pair could be separated in 98%, the 31.2/31.3 fragment pair only in 65% of all runs. Reliable separation of this difficult fragment mixture could exclusively achieved by using POP-6.

DNA evidence, probabilistic evaluation and collaborative tests

Forensic scientists working in 12 state or private laboratories participated in collaborative tests to improve the reliability of the presentation of DNA data at trial. These tests were motivated in response to the growing criticism of the power of DNA evidence. The experts' conclusions in the tests are presented and discussed in the context of the Bayesian approach to interpretation. The use of a Bayesian approach and subjective probabilities in trace evaluation permits, in an easy and intuitive manner, the integration into the decision procedure of any revision of the measure of uncertainty in the light of new information. Such an integration is especially useful with forensic evidence. Furthermore, we believe that this probabilistic model is a useful tool (a) to assist scientists in the assessment of the value of scientific evidence, (b) to help jurists in the interpretation of judicial facts and (c) to clarify the respective roles of scientists and of members of the court. Respondents to the survey were reluctant to apply this methodology in the assessment of DNA evidence.

Report of the European Network of Forensic Science Institutes (ENSFI): formulation and testing of principles to evaluate STR multiplexes

This paper describes a collaborative exercise organised under the auspices of the European Network of Forensic Science Institutes (ENFSI). The purpose of this EU (European Union) funded group is to carry out research to enable STR loci to be compared between European laboratories, ultimately leading to the formation of a pan-European database. Accordingly, an exercise was designed to evaluate a prototype STR multiplex system manufactured by Applied Biosystems (ABD). Each laboratory was sent 12 samples to analyse along with a multiplex kit. Of specific interest was the definition of parameters to define the efficiency of the system. Stutter, split allelic peaks (differing by one base), pull-up, heterozygous balance and between locus balance were all objectively measured. Once the important parameters are defined it is possible to directly compare performances of different multiplexes and the different laboratories carrying out the tests. Since the multiplex used was a prototype system, this exercise cannot be regarded as a proficiency test.

Results of collaborative study regarding the standardization of the Y-linked STR system DYS385 by the European DNA Profiling (EDNAP) group

Y-chromosome linked short tandem repeat (STR) loci are inherited as a closely linked haplotype, which appears to remain stable in a given paternal lineage over many generations. In forensic cases, Y-linked STRs are particularly useful for the identification of human remains as well as in rape cases with mixed male/female stain samples. DYS385 is derived from tandemly duplicated segments of the Y chromosome thus giving rise to two fragments of variable length which do not behave like alleles but genotypes. The European DNA Profiling (EDNAP) group has carried out a collaborative exercise among 14 participating laboratories using DYS385 for typing of five unknown bloodstains and a control sample. Furthermore, population data from eight different European countries with samples sizes between 91 and 150 male individuals were collected. The results confirm previous observations that DYS385 is one of the most informative Y-linked STR loci. It could also be demonstrated that reproducible results can be obtained independently from the electrophoretic separation and detection methods used. Thus DYS385 may serve as a useful complementation to the routinely used autosomal STR systems in special cases.

Segregation analysis of tetra- and pentanucleotide short tandem repeat polymorphisms: deviation from Mendelian expectations

Short tandem repeat (STR) polymorphisms are powerful tools for linkage studies, chromosome mapping and population analysis. The instability of these microsatellite regions is a prevailing event in several tumors and human genetic diseases and, despite various reports associating instability-related genes and meiosis control, the dynamics of these STR regions in normal cells/individuals has frequently been disregarded. Having previously assayed somatic instability in gastric cancer for some tetra- and pentanucleotide STRs and given the increased application of this type of marker for routine forensic expertise, we report the results of an extensive analysis of segregation in nuclear families of a normal population for the same loci. No mutations were detected in 2374 parent/offspring allelic transfers at TH01, TPO, VWA31/A, MBPB, and CD4 STR loci. Nonsignificant differences were found between gene frequencies of parental and offspring generations. However, the segregation analysis revealed significant deviation from Mendelian expectations for: VWA31/A locus - alleles 19, 17 and 14 and TH01 locus - allele 6. In particular, parental meiosis strongly favored specific allele transmission, depending upon the sex of the offspring. Specific mating types are apparently responsible for most of these abnormal segregations. These results suggest selective factors working either at the gametic or zygotic levels.

Report of the European DNA Profiling Group (EDNAP)--an investigation of the hypervariable STR loci ACTBP2, APOAI1 and D11S554 and the compound loci D12S391 and D1S1656

This paper describes the results of three collaborative exercises which continues the EDNAP theme to explore whether uniformity of DNA profiling results could be achieved between European laboratories using STRs. In an earlier exercise, complex hypervariable AAAG-repeat STR loci were investigated, but reproducibility was found to be poor because of the variation of techniques used by participating laboratories. In the exercise reported here, an internal allelic ladder composed of ACTBP2 and D11S554 fragments was distributed. This ladder was used to size ACTBP2 analysed by a "singleplex" PCR amplification and D11S554 combined with APOAI1 in a separate "duplex" reaction. Laboratories were asked to test 7 blood stains, one of which was a known control, and to report the results to the co-ordinating laboratory. The exercise demonstrated that ACTBP2 showed good reproducibility between laboratories, whereas further testing would be needed to validate APOAI1 and D11S554 for interlaboratory comparisons. In separate exercises, the simple loci D12S391 and D1S1656 were tested; both of these showed excellent reproducibility between laboratories.

HLA-B35 frequency variations correlate with malaria infection in Sardinia

The hypothesis of a possible selective role of malaria in HLA allele frequency variations was investigated in Sardinia by typing completely 1,039 individuals for HLA: 536 from six lowland villages exposed to malaria until 1948, and 503 from six highland villages with no history of malaria. Another 1,928 individuals from 136 villages scattered all over the island were studied to establish if the HLA allele frequencies among villages correlated with the malaria incidence and/or altitude above sea level. Only the HLA-B35 allele yielded significantly higher frequencies in the lowland versus the highland villages (P<1 x 10(-5)). The observed B35 variance was 9.5 times higher than expected in the absence of selection, showing an adaptive origin. The highly significant positive correlation found between HLA-B35 frequency and malaria in 136 villages suggests that malaria has been the selective factor for HLA-B35 in Sardinia.

Normal and anomalous electrophoretic behavior of polymerase chain reaction-based DNA polymorphisms in polyacrylamide gels

The electrophoretic mobility of five single tandem repeats (STRs) and four amplified fragment length polymorphisms (AFLPs) in polyacrylamide gels was tested under denaturing and nondenaturing conditions. Relative anomalous mobility in nondenaturing conditions was found in one AT-rich AFLP (3'ApoB) and in two AT-rich STRs (HUMACTBP2 and HUMF13A1). In these cases, highly anomalous electrophoretic behavior was found even when changes were made in the %T value alone. In such cases typing results were affected by the gel composition. The mobility of these systems was nevertheless normal under denaturing conditions. As a consequence of this study, we recommended that the typing of these systems should only be performed under denaturing conditions and we also recommend the further study of the electrophoretic behavior of repetitive DNA polymorphisms, especially AT-rich systems, before they are used in forensic or genetic applications.

Genetic analysis of the short tandem repeat system D12S391 in the German and three Asian populations

Genomic DNA samples from 222 individuals from Southern China, 154 individuals from Thailand, 100 individuals from Japan as well as from 124 German individuals were analysed for the short tandem repeat (STR) locus D12S391. Typing was carried out by polymerase chain reaction (PCR) amplification and subsequent polyacryramide gel electrophoresis and silver staining. In total, 12 alleles could be distinguished in two of the populations. Among Chinese, allele 19 is the most common with a frequency of 0.225, and among Germans, allele 18 with a frequency of 0.186. In the Thai population only 11 alleles could be distinguished and allele 19 is the most common with a frequency of 0.198. In Japanese, two previously unknown alleles 27 and 28 were detected, 14 alleles could be distinguished, and allele 18 is the most common with a frequency of 0.295. The expected exclusion chance for Chinese, Thai, Japanese and Germans in paternity cases is 0.67, 0.71, 0.67 and 0.75, respectively, and the discrimination power in identification cases is 0.95, 0.96, 0.95 and 0.97, respectively. Testing of the observed genotype distributions for Hardy-Weinberg equilibrium did not reveal any significant deviations. Segregation studies of 124 meioses among German families did not reveal any mutations at the D12S391 locus. In casework studies two variant alleles were detected with a trimeric repeat each (17.3 and 18.3), which have been confirmed by sequencing.

Screening of a highly polymorphic microsatellite for microheterogeneity in human identification

Single-strand conformation polymorphism (SSCP) analysis combined with automated laser fluorescence detection is proposed as a comprehensive, rapid and sensitive method for screening sequence variation of the human beta-actin-related pseudogene (HUMACTBP2). Eleven sequenced alleles representing each type of known sequence variant of HUMACTBP2 locus were studied. Allelic variants of the same size but different sequence structures are easily resolved on the basis of their secondary conformation. Fifty ACTBP2 amplification products previously typed on a denaturing gel were repeatedly examined to determine the utility of SSCP analysis in terms of ease of interpretation and reproduction capabilities of the conformational patterns. Eleven sequenced ACTBP2 allelic variants were used as external conformation standards in polymerase chain reaction (PCR)-SSCP subtyping. This enabled identification of polymorphism in a particular length variant and therefore consistent discrimination between heterozygous samples appeared identical on denaturing gels. Of five "homozygous" samples, one was shown to be heterozygous for two distinct alleles of the same size but different sequences. Thus, the method provides a unique possibility for detecting false homozygotes. The technique complements both denaturing gel electrophoresis and DNA sequencing in studies on the overall variability of the ACTBP2 locus.