Does zero really mean nothing?-first experiences with the new PowerQuant(TM) system in comparison to established real-time quantification kits.

DNA quantification is an important step in the molecular genetic analysis of a forensic sample, hopefully providing reliable data on DNA content for a subsequent generation of reproducible STR profiles for identification. For several years, this quantification has usually been done by real-time PCR protocols and meanwhile a variety of assays are commercially available from different companies. The newest one is the PowerQuant(TM) assay by Promega Inc. which is advertised with the promise that a determined DNA concentration of 0 ng/µl in a forensic sample guarantees the impossibility to achieve true STR results, thus allowing to exclude such samples from STR analysis to save time and money. Thus, the goal of this study was to thoroughly verify the quantification step with regard to its suitability as a screening method. We have evaluated the precision and reliability of four different real-time PCR quantification assays by systematically testing DNA dilutions and forensic samples with various DNA contents. Subsequently, each sample was subjected to the Powerplex® ESX 17 fast kit to determine a reliable cutoff level for exclusion of definitely negative samples from STR analysis. An accurate quantification of different cell line DNA dilutions was not possible with any kit. However, at least the PowerQuant(TM) assay provided suitable data analyzing forensic samples, whereas in other systems up to 46 % of negative samples still displayed reliable STR analysis results. All in all, the PowerQuant(TM) assay represents a big step forward, but the evaluation of real-time PCR quantification results has still to be done with great care.

Alteration of STR profiles in ovarian carcinoma cells during primary culture.

PURPOSE: Cell authentication is a necessary procedure to avoid scientific data from cell culture experiments with cross-contamination or false classification. A genetic fingerprint pattern of a specimen by short tandem repeats (STR) is self-evident. Due to high amount of chromosomal rearrangements, known in epithelia ovary cancer cells and the instable STR pattern described in other tumour entities like leukaemia, this study explores the suitability of STR profiling for primary cultured epithelial ovary cancer cells. METHODS: STR profiles of epithelial ovary cancers of 16 patients were compared with corresponding blood and corresponding primary cell cultures. The primary cell cultures of epithelial ovary tumours were passaged up to 28 times. In between, cultures were cryo conserved and recultured again, two to five times per patient. RESULTS: In two cases, the STR pattern of tumour lost alleles (1/16 and 3/16) in comparison of corresponding STR-pattern from blood. In comparison to blood, cell culture of a third case, lost four alleles (4/16) accompanied with morphologic changes after 14th passage. It is equal after cryo conservation of the seventh passage from the same patient. The only changes in STR profiles we recognized are losses of alleles. Remaining STR markers allow authentication. CONCLUSIONS: Very likely, the allelic drop-outs beyond passage 14 assume complex genetic losses of heterozygosis resulting in changed growth behaviour of cells. All other STR-profiles of remaining 15 patients analysed in this study are stable over all passages and freeze-thaw processes. Thus, ovary cancer cell cultures in research should be authenticated by STR-profile in general.

About the power of biostatistics in sibling analysis-comparison of empirical and simulated data.

The determination of potential sibship is a common task in routine kinship analysis, but often the putative parents are not available for analysis anymore. Then, a sibling analysis has to be conducted investigating only the potential siblings, thus reducing the power of the conclusion. In an attempt to determine meaningfulness of biostatistical calculations, 346 dizygotic twin pairs, 30 confirmed half siblings, and 112 unrelated people (to generate 6216 pair comparisons) were studied, all genetically typed using at least the Powerplex® 16 STRs. From every pair, the probabilities for a full sibship (identical parents) and half sibship (different fathers) were calculated using a commercially available computer program. Additionally, we simulated marker data for one million pairs of full sibs, half sibs, and unrelated persons each. Ninety-five percent of full sibling pairs demonstrated a likelihood ratio (LR) > 9 (W-value > 90 %) and less than 4% of these showed a LR < 3 (W-value < 75%) for full sibship after analysis of 15 STRs. The results for half siblings are less unambiguous. Here, only 57% achieved a LR > 9 and 23% a LR < 3. Regarding the unrelated pairs, more than 90% had a LR < 1/9 and only 2% reached a LR > 9. All in all, our results show that 15 to 20 STRs have sufficient power for analyses in kinship. Moreover, our data provide a statistical basis for the determination of the information content of a LR/W-value in a sibship case. Investigating an identical number of full siblings and unrelated pairs, it could be shown that 92% of pairs with a LR > 9 for full sibship probability really are full siblings. So, setting a cutoff level for full sibship at LR > 9, less than 10% of pairs will be wrongly assumed as full siblings even though they are unrelated.

The auditory ossicles as a DNA source for genetic identification of highly putrefied cadavers.

Genetic identification of putrefied bodies is a common task in forensic medicine. With advancing putrefaction, however, DNA integrity is rapidly decreasing and genetic typing of tissue might be impaired or impossible. Since DNA stability is generally higher in hard tissues, bones or teeth are frequently used as DNA source in such cases. However, isolation of DNA from hard tissues is usually very time-consuming and labor-intensive. This can be especially important in (forensic) cases where time is short and identification has to be carried out as fast as possible. Here, we present the identification of dead bodies by analyzing DNA from the auditory ossicles. These minuscule bones provided DNA of sufficient quality and quantity for identification purposes in all 40 investigated cases. Additionally, processing of the bones proved to be amazingly easy and fast, and a successful extraction is possible using a variety of different methods. We present a detailed protocol, results, and cases in which this new method has been successfully applied.

Usefulness of SNPs as Supplementary Markers in a Paternity Case with 3 Genetic Incompatibilities at Autosomal and Y Chromosomal Loci.

BACKGROUND: In kinship testing, investigation of 15 short tandem repeats (STRs) usually provides decisive genetic information for resolving relationship cases. However, in complex deficiency cases, in cases with more than 2 mutations at different STR loci or when close (untested) relatives of the alleged father are suggested to be the biological father of the child, STR typing alone may not be sufficient. In these cases, the application of supplementary markers such as single nucleotide polymorphisms (SNPs) is recommended. METHODS: We describe a paternity case with 3 genetic incompatibilities (Penta D, VWA, and DYS385) between the alleged father and the child after analyzing 23 autosomal and 16 Y chromosomal STR loci. The question arose as to whether the alleged father could be excluded and a related person could be the biological father of the child, or whether the observed genetic incompatibilities were mutations. Interestingly, the 2 excluded full brothers of the alleged father possessed identical genetic incompatibilities at locus VWA and DYS385 as the alleged father. RESULTS AND CONCLUSIONS: Additional performance of a 50-plex SNP assay demonstrated that the observed mismatches were indeed mutations and the alleged father was the biological father of the child. The results show the usefulness of SNPs as supplementary markers in relationship testing when STR analyses show ambiguous results.

Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10(-4) (95% credible interval [CI], 1.38 × 10(-5) - 2.02 × 10(-3)) to 7.44 × 10(-2) (95% CI, 6.51 × 10(-2) - 9.09 × 10(-2)) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.

Allele frequencies for the 16 short tandem repeats of the Powerplex ESX17 kit in a population from Turkey.

Allele frequencies for those short tandem repeats (STRs) used in forensic routine analysis are necessary for any biostatistical calculation. In this study, allele frequencies for the STRs of the Powerplex ESX kit including the five STRs D1S1656, D2S441, D10S1248, D12S391 and D22S1045 only recently added to the German database standard in an admixed population from Turkey are presented.

Allele frequencies for 11 X chromosomal short tandem repeats in a population from Turkey.

X chromosomal STRs are nowadays an important part of forensic genetic analysis, especially in complex kinship cases. In this study, allele frequencies and forensic efficiency parameters of the 11 X chromosomal STRs DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377 and DXS7423 in an admixed population from Turkey are presented.

The new guidelines for paternity analysis in Germany-how many STR loci are necessary when investigating duo cases?

The requirements in the new German guidelines for paternity analysis have not only changed according to the so-called Gendiagnostikgesetz, the new German law regulating human genetic as well as paternity analyses, but also regarding the minimal number of short tandem repeats (STRs) which should be investigated (15 STRs) and the minimal required average exclusion chance (99.999 %). Even in paternity analyses involving only two people (e.g., father and child or mother and child), this exclusion chance is mandatory. A retrospective analysis of 330 father-child cases from our routine investigations showed in 142 cases (43 %) an individual exclusion chance below 99.999 % when using 15 STRs as required, in our routine work provided by the Powerplex® 16 kit which is reported to have an average exclusion chance of 99.988 %. Therefore, these same 330 father-child pairs were additionally analysed using the Powerplex® 21 kit and 120 of these duos were additionally analysed using the Powerplex® ESX17 kit enabling the analysis of 20 or 16 loci respectively. Now, an individual exclusion chance of more than 99.999 % could be achieved in 95.5 % (Powerplex® 21; calculation without the results of D6S1043), 98.8 % (Powerplex® 21; calculation with the results of D6S1043, using allele frequencies established in this study for a German and a West African population) and 98.3 % (Powerplex® ESX17). These data clearly demonstrate that in duo cases, more than the required 15 STR loci have to be investigated to obtain sufficient results.

Prediction of people's origin from degraded DNA--presentation of SNP assays and calculation of probability.

The characterization of externally visible traits by DNA analysis is already an important tool when investigating ancient skeletal remains and may gain similar importance in future forensic DNA analysis. This, however, depends on the different legal regulations in the different countries. Besides eye or hair color, the population origin can provide crucial information in criminal prosecution. In this study, we present the analysis of 16 single-nucleotide polymorphisms (SNPs) combined to two robust SNaPshot assays with a detection threshold of 25-pg DNA. This assay was applied to 891 people from seven different populations (West Africa, North Africa, Turkey, Near East, Balkan states, North Europe, and Japan) with a thorough statistical evaluation. The prediction model was validated by an additional 125 individuals predominantly with an ancestry from those same regions. The specificity of these SNPs for the prediction of all population origins is very high (>90 %), but the sensitivity varied greatly (more than 90 % for West Africa, but only 25 % for the Near East). We could identify West Africans with a certainty of 100 %, and people from North Africa, the Balkan states, or North Europe nearly with the same reliability while determination of Turks or people from the Near East was rather difficult. In conclusion, the two SNaPshot assays are a powerful and reliable tool for the identification of people with an ancestry in one of the above listed populations, even from degraded DNA.

Good shedder or bad shedder--the influence of skin diseases on forensic DNA analysis from epithelial abrasions.

The successful analysis of weak biological stains by means of highly sensitive short tandem repeat (STR) amplification has been increased significantly over the recent years. Nevertheless, the percentage of reliably analysable samples varies considerably between different crime scene investigations even if the nature of the stains appears to be the same. It has been proposed that the amount and quality of DNA left at a crime scene may be due to individual skin conditions (among other factors). Therefore, we investigated DNA from handprints from 30 patients acutely suffering from skin diseases like atopic dermatitis, psoriasis or skin ulcer before and after therapy by STR amplification using the new and highly sensitive Powerplex® ESX17 kit in comparison to 22 healthy controls. Handprints from atopic dermatitis patients showed a correct and reliable DNA profile in 90% and 40% of patients before and after therapy, respectively. Regarding psoriasis patients, we detected full DNA profiles in only 64% and 55% of handprints before and after therapy. In contrast, in ulcus patients and controls, full DNA profiles were obtained in much lower numbers. We conclude that active skin diseases like atopic dermatitis or psoriasis have a considerable impact on the amplificable DNA left by skin contact with surfaces. Since up to 7% of adults in European countries suffer from one of these diseases, this could explain at least partially the varying quality of DNA from weak stains.

Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany.

The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800-2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool.

Causes of delivery and outcomes of very preterm twins stratified to zygosity.

The increasing rates of preterm birth among twins implicate that solid data on associated risks and outcomes are required. Assessment of zygosity is often based on clinical criteria (evaluation of placenta; same gender, birth weight discordance as surrogate criteria for monochorionic/monozygotic twins). The aim of this study was to compare clinical versus genetic assessment of zygosity and to compare causes of preterm delivery as well as outcome data of very-low-birth-weight (VLBW; birth weight <1,500 g) twins stratified to zygosity. In a multicenter study, we selected n=176 sets of same gender twins and determined zygosity genetically. In a subgroup of 123 sets of twins, the attending physicians at the study centers were asked to document the parameter 'zygosity' (monozygotic/dizygotic) on the basis of their clinical judgment. Concordance between genetic and clinical assessment was 62.7% for monozygotic twins and 88.9% for dizygotic twins, respectively. Outcome parameters (death, BPD, ROP, NEC, IVH) were comparable in both groups. Genetically dizygotic twins were significantly more often born due to intrauterine infection (33% vs. 20% in monozygotic twins, p<.01) and antenatal antibiotics were more frequently given to mothers of dizygotic twins (62% vs. 47% in monozygotic twins, p<.01). Obstetric complications such as twin-twin-transfusion-syndrome were only seen in monozygotic twins as expected. The unexpected increase of antenatal antibiotic treatment and birth due to intrauterine infection in dizygotic twins should be confirmed in additional VLBW twin-cohorts.

The SNPforID Assay as a Supplementary Method in Kinship and Trace Analysis.

OBJECTIVE: Short tandem repeat (STR) analysis using commercial multiplex PCR kits is the method of choice for kinship testing and trace analysis. However, under certain circumstances (deficiency testing, mutations, minute DNA amounts), STRs alone may not suffice. METHODS: We present a 50-plex single nucleotide polymorphism (SNP) assay based on the SNPs chosen by the SNPforID consortium as an additional method for paternity and for trace analysis. The new assay was applied to selected routine paternity and trace cases from our laboratory. RESULTS AND CONCLUSIONS: Our investigation shows that the new SNP multiplex assay is a valuable method to supplement STR analysis, and is a powerful means to solve complicated genetic analyses.

STR-typing of ancient skeletal remains: which multiplex-PCR kit is the best?

AIM: To comparatively test nine co mmercially available short tandem repeat (STR)-multiplex kits (PowerPlex 16, 16HS, ES, ESI17, ESX17, S5 [all Promega]; AmpFiSTR Identifiler, NGM and SEfiler [all Applied Biosystems]) for their efficiency and applicability to analyze ancient and thus highly degraded DNA samples. METHODS: Fifteen human skeletal remains from the late medieval age were obtained and analyzed using the nine polymerase chain reaction assays with slightly modified protocols. Data were systematically compared to find the most meaningful and sensitive assay. RESULTS: The ESI, ESX, and NGM kits showed the best overall results regarding amplification success, detection rate, identification of heterozygous alleles, sex determination, and reproducibility of the obtained data. CONCLUSION: Since application of these three kits enables the employment of different primer sequences for all the investigated amplicons, a combined application is recommended for best possible and--most importantly--reliable genetic analysis of ancient skeletal material or otherwise highly degraded samples, e.g., from forensic cases.

Genetic identification of highly putrefied bodies using DNA from soft tissues.

The identification of putrefied bodies is a common task in forensic routine work. The deceased are usually identified by dental records, fingerprinting, or--in cases where no such data are available--DNA analysis. However, with progressive putrefaction, DNA integrity is rapidly decreasing. Genetic analysis may then be greatly impaired, if not impossible. The aim of our study was to establish an efficient procedure to successfully extract and amplify DNA from soft tissues of bodies in different stages of putrefaction. Soft tissues-unlike teeth or bones-usually allow the application of fast and easy-to-use extraction protocols. DNA was extracted from different tissues (aorta, kidney, liver, and skeletal muscle) taken at autopsy using a commercially available DNA extraction kit, and DNA quality and quantity were controlled by agarose gel electrophoresis and real-time polymerase chain reaction (PCR). Presence of mitochondrial DNA was tested using a highly sensitive duplex PCR. Short tandem repeat analysis was done using the AmpFlSTR Identifiler kit. Additionally, mitochondrial DNA sequencing was performed. After DNA extraction from at least two different tissues-preferably the kidney and the aorta-with the extraction kit based on the Nucleobond method, a successful amplification of at least eight loci was possible in 17 out of 18 cases, and 12 or more loci could be amplified in 15 cases.

Allele frequencies of 11 X-chromosomal loci of two population samples from Africa.

Eleven X-chromosomal STRs from two multiplex PCR approaches (DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377, and DXS7423), located in four different X-chromosomal linkage groups, were typed in two population samples from Africa, Morocco, and Madagascar. Forensic efficiency parameters such as polymorphism information content and mean exclusion chance were calculated. A deviation from the Hardy­Weinberg equilibrium could not be found. The investigation of four father­daughter and five mother­son meioses (from Morocco) revealed no mutations in any STR analyzed. Our data were compared with European, African-American, and Asian populations from the literature.

First experiences using the new Powerplex® ESX17 and ESI17 kits in casework analysis and allele frequencies for two different regions in Germany.

DNA databases are the most efficient tools in criminal investigations with unknown perpetrators. Due to a significant number of random matches in cross-border DNA profile exchanges, the European Network of Forensic Science Institutes (ENFSI) proposed the addition of further short tandem repeats (STRs) to European DNA databases. Therefore, the new Powerplex® ESX17 and Powerplex® ESI17 kits from Promega comprised the 11 established DNA database STRs and additionally the well-known loci D1S1656 and D12S391, as well as D2S441, D10S1248, and D22S1045. The latter three STRs are thereby established as so-called mini-STRs to fulfill the increasing requirements regarding sensitivity and reproducibility for analysis of minute amounts of DNA. Here, we provide allele frequencies for the five additional STRs from two populations from Germany. A test regarding suitability and robustness of the new kits for routine trace analysis showed that it is more likely to obtain a meaningful profile using Powerplex® ESX17 and Powerplex® ESI17 kits compared to the Powerplex® ES kit. However, for both new kits the range of template DNA amount is rather small, e.g., slightly more DNA than recommended resulted in DNA profiles which could not be reliably evaluated due to allelic drop-in or imbalances and overshoots. In our opinion, the new kits are very promising new tools in forensic trace analysis even though handling and evaluation should yet be carried out with great caution.

The new Powerplex® ESX17 and ESI17 kits in paternity and maternity analyses involving people from Africa--including allele frequencies for three African populations.

Paternity and maternity investigations in immigration procedures are frequently done in Germany. Since mostly only one parent and one or more children are investigated, the occurrence of possible mutational events has to be interpreted with great care and the analysis of as many STRs as possible is recommended. The new Powerplex® ESX17 and Powerplex® ESI17 kits from Promega comprising both eleven established STRs and additionally the loci D1S1656, D2S441, D10S1248, D12S391, and D22S1045 (in different order) are potential tools in such paternity or maternity analyses, but only few allele frequency data for the five new loci exist. Here, we provide allele frequencies for the five additional STRs from three different populations from Africa. In addition, we present two maternity cases and one paternity case in which a clear inclusion or exclusion of the alleged parent could only be achieved by the additional application of the new Powerplex® ESX17 kit.

Genetic control of global gene expression levels in the intestinal mucosa: a human twin study.

Phenotypic variation between individuals, such as different mRNA expression levels, is influenced by genetic and nongenetic factors. Although several studies have addressed the interplay between genotypes and expression profiles in various model organisms in the recent years, the detailed and relative contributions of genetic and nongenetic factors in regulating plasticity of gene expression in barrier organs (e.g., skin, gut), which are exposed to continuous environmental challenge, are still poorly understood. Here we systematically monitored the level of genetic control over genomewide mRNA expression profiles in the healthy intestinal mucosa of 10 monozygotic and 10 dizygotic human twin pairs with microarray analyses. Our results, which are supported by real-time PCR and analysis of molecular phylogenetic conservation, indicate that genes associated with energy metabolism and cell and tissue regeneration pathways are under strong genetic control. Conversely, genes associated with immune response seem to be mainly controlled by exogenous factors. Further insights into the relative extent of genetic and nongenetic determinants of transcriptomal profiles and their influence on physiological and pathophysiological mechanisms are crucial to understanding the key role played by gene-environment interactions in health and disease.