Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination

Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (KD) of a protein-antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled ("conformational") antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA-aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.

Antibody Epitope and Affinity Determination of the Myocardial Infarction Marker Myoglobin by SPR-Biosensor Mass Spectrometry

Myoglobin (MG) is a biomarker for heart muscle injury, making it a potential target protein for early detection of myocardial infarction. Elevated myoglobin levels alone have low specificity for acute myocardial infarction (AMI) but in combination with cardiac troponin T have been considered highly efficient diagnostic biomarkers. Myoglobin is a monomeric heme protein with a molecular weight of 17 kDa that is found in skeletal and cardiac tissue as an intracellular storage unit of oxygen. MG consists of eight α-helices connected by loops and a heme group responsible for oxygen-binding. Monoclonal antibodies are widely used analytical tools in biomedical research and have been employed for immunoanalytical detection of MG. However, the epitope(s) recognized by MG antibodies have been hitherto unknown. Precise molecular identification of the epitope(s) recognized by antibodies is of key importance for the development of MG as a diagnostic biomarker. The epitope of a monoclonal MG antibody was identified by proteolytic epitope extraction mass spectrometry in combination with surface plasmon resonance (SPR) biosensor analysis. The MG antibody was immobilized both on an affinity microcolumn and a gold SPR chip. The SPR kinetic analysis provided an affinity-binding constant K_D of 270 nM for MG. Binding of a tryptic peptide mixture followed by elution of the epitope from the SPR-MS affinity interface by mild acidification provided a single-epitope peptide located at the C-terminus [146-153] [YKELGFQG] of MG. The specificity and affinity of the epitope were ascertained by synthesis and affinity-mass spectrometric characterization of the epitope peptide.

Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C-Met by Proteolytic Affinity-Mass Spectrometry

C-Met protein is a glycosylated receptor tyrosine kinase of the hepatocyte growth factor (HGF), composed of an α and a β chain. Upon ligand binding, C-Met transmits intracellular signals by a unique multi-substrate docking site. C-Met can be aberrantly activated leading to tumorigenesis and other diseases, and has been recognized as a biomarker in cancer diagnosis. C-Met aptamers have been recently considered a useful tool for detection of cancer biomarkers. Herein we report a molecular interaction study of human C-Met expressed in kidney cells with two DNA aptamers of 60 and 64 bases (CLN0003 and CLN0004), obtained using the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Epitope peptides of aptamer-C-Met complexes were identified by proteolytic affinity-mass spectrometry in combination with SPR biosensor analysis (PROTEX-SPR-MS), using high-pressure proteolysis for efficient digestion. High affinities (K_D , 80-510 nM) were determined for aptamer-C-Met complexes, with two-step binding suggested by kinetic analysis. A linear epitope, C-Met (381-393) was identified for CLN0004, while the CLN0003 aptamer revealed an assembled epitope comprised of two peptide sequences, C-Met (524-543) and C-Met (557-568). Structure modeling of C-Met-aptamers were consistent with the identified epitopes. Specificities and affinities were ascertained by SPR analysis of the synthetic epitope peptides. The high affinities of aptamers to C-Met, and the specific epitopes revealed render them of high interest for cellular diagnostic studies.

Epitope Identification and Affinity Determination of an Inhibiting Human Antibody to Interleukin IL8 (CXCL8) by SPR- Biosensor-Mass Spectrometry Combination

The polypeptide chemokine Interleukin-8 (IL8) plays a crucial role in inflammatory processes in humans. IL8 is involved in chronic inflammatory lung diseases, rheumatoid arthritis, and cancer. Previous studies have shown that the interaction of IL8 with its natural receptors CXCR1 and CXCR2 is critical in these diseases. Antibodies have been used to study the receptor interaction of IL8; however, the binding epitopes were hitherto unknown. Identification of the antibody epitope(s) could lead to a molecular understanding of the inhibiting mechanism and development of improved inhibitors. Here, we report the epitope identification and the affinity characterization of IL8 to a monoclonal anti-human IL8 antibody inhibiting the receptor binding by a combination of surface plasmon resonance (SPR) biosensor analysis and MALDI-mass spectrometry. SPR determination of IL8 with the immobilized antibody revealed high affinity (K_D, 82.2 nM). Epitope identification of IL-8 was obtained by proteolytic epitope-extraction mass spectrometry of the peptide fragments upon high pressure trypsin digestion, using an affinity microcolumn with immobilized anti-IL-8 antibody. MALDI-MS of the affinity-bound peptide elution fraction revealed an assembled (discontinuous) epitope comprising two specific peptides, IL8 [12-20] and IL8 [55-60]. Identical epitope peptides were identified by direct MALDI-MS of the eluted epitope fraction from the immobilized anti-IL8 antibody on the SPR chip. SPR determination of the synthetic epitope peptides provided high affinities confirming their binding specificity. The previously reported finding that the anti-Il8 antibody is inhibiting the IL8-CXCR1 interaction is well consistent with the overlapping region of epitope interactions identified in the present study.

Short amplicon STR multiplex for stain typing

We developed a short tandem repeat (STR) typing kit based on DNA database systems that are included in, for example, the Interpol Standard Set of Loci recommendations (i.e., TH01, VWA, D3S1358, FGA) and the gender typing system Amelogenin. Two different multiplex sets were tested using the fluorescent dyes FAM, JOE, and VIC. The PCR results were compared to the commercially available AmpFISTR Blue kit, which contains the STRs D3S1358, VWA, and FGA. The advantage of our multiplex compared with the Blue kit was the generation of shorter amplicons (<200 bp) and the higher combined power of discrimination.

A very long ACTBP2 (SE33) allele

Analysing a buccal swab we found a long allele in the STR system ACTBP2. For confirmation we sequenced the isolated PCR product and found a sequence structure common in alleles of type III. Based on the repeat array the new allele is assigned as allele "49".

Population genetic comparisons of three X-chromosomal STRs

The X-chromosomal short tandem repeats (STRs) DXS6800, DXS101 and DXS8377 were analysed in male and female population samples from Germany and Austria using a PCR multiplex approach. We investigated 135 family trios from Innsbruck (Austria) and surrounding areas and 50 families and further male and female samples from Ulm (Germany) and surrounding areas. The comparisons of the allele frequencies gave similar distributions for Innsbruck and Ulm although minor variations were found for some alleles. Additionally, some differences were found when comparing the allele frequencies of the male and female samples independently. The forensic efficiency values demonstrate that especially DXS101 and DXS8377 are highly informative markers for kinship analysis and deficiency cases. Based on the investigated meiotic events no new mutations were detected.

Unusual presentation of central nervous system relapse with oculomotor nerve palsy in a case of CD56-positive acute myeloid leukemia following allogeneic stem cell transplantation

Allogeneic stem cell transplantation (allo-SCT) plays an important role in the treatment of infants and children with acute myelogenous leukemia (AML). Leukemic relapse after allo-SCT is responsible for a high rate of treatment failure. Extra-medullary relapse (EMR), without involvement of bone marrow, is rare compared to medullary relapse. CD56, the neural cell adhesion molecule, may contribute to the higher frequency of CNS relapse in CD56-positive AML. We observed an isolated EMR on the oculomotor nerve of a 17-month-old girl 12 weeks after cord blood transplantation (CBT), who was transplanted because of CD56-positive AML. Diagnosis of relapse was suspected clinically and confirmed by magnetic resonance imaging (MRI), and fluorescence-activated cell sorter (FACS) and chimerism analysis of cerebrospinal fluid (CSF). Therapy consisted of intra-thecal chemotherapy, CNS irradiation, and systemic immunomodulation by cyclosporin A (CsA) and basiliximab withdrawal. Twenty-one months after relapse, the patient shows full remission of symptoms and previously described oculomotor nerve infiltration.

Somatic mutations at STR loci--a reason for three-allele pattern and mosaicism

Two families are analysed in which one of the parents exhibited a three-allele pattern at the ACTBP2 locus. Since the alleles were obviously segregated independently to the children, a generalised mosaicism must be assumed involving at least two tissues in one of them and at least four tissues in the other one. The intensity of the PCR amplified alleles in both three-allele individuals indicate an occurrence in a very early embryonic stage. Occurrence was most probably due to a single step mutation in both cases. Forensic implications would include paternity testing as well as stain analysis.

Less is more--length reduction of STR amplicons using redesigned primers

PCR primers closely flanking the repeat region were redesigned to reduce the amplicon length of the selected STRs down to approximately 100 bp for the shorter alleles (loci HumTH01, D10S2325, DYS19 and DYS391). Highly degraded DNA (e.g. formalin-fixed tissue) and very low amounts of DNA could be more successfully typed using the new redesigned primers compared to the established sequences generating longer amplicons.

Assessment of shooting distance on the basis of bloodstain analysis and histological examinations

A 28-year-old man was shot using a pump-gun. The main question to be resolved was whether the biological stain pattern on the suspect's trousers, and in particular the bloodstains, can provide evidence to assess the shooting distance between the suspect and the position of the victim's body. The biological stain pattern (i.e. bloodstains and brain tissue) showed backspatters from the shot entrance wound on the back of the head, while the victim was lying face down and the suspect was standing close behind his head.

Population genetic diversity in relation to microsatellite heterogeneity

Nine populations (Germans, Turks, Moroccans, Ovambos, Ugandans, Chinese, Japanese, Papuans, and Australian Aborigines) were investigated using six microsatellite systems (HumCD4, Hum F13B, HumFES/FPS, HumTH01, HumVWA, and D21S11), so-called STRs (short tandem repeats). Allele frequency data and sequencing results were used to compare the population genetic diversity among these populations. The genetic differences varied depending on the STR applied. According to the systems investigated, we defined three categories of STR microvariation: LOMs (low microvariation systems), INMs (intermediate microvariation systems), and HIMs (high microvariation systems). LOMs (STRs: CD4, FES, F13B, TH01) are characterised by a number of repeats between 5-15 and a stable repeat sequence. INMs and HIMs each showed an increasing number of repeats and additional sequence variation in the repeat motifs. The rate of new mutations was associated with the extent of microvariation. The reconstruction of phylogenetic trees led to a clustering in an early split of the African populations followed by further branching of the Asian/Melanesian and the Caucasian groups.

Microsatellite structures in the context of human evolution

Six microsatellite - or short tandem repeat (STR) - systems with uniform repetitive sequences (HumTH01, HumCD4, HumFES/FPS, HumF13B, HumTPO, HumLPL) and three compound repeat systems (HumVWA, HumFIBRA, D21S11) were used, including data from the literature, to determine genetic distances among eight populations worldwide. The TH01- and VWA homologous loci in nonhuman primates (chimpanzees, gorillas, orangutans, rhesus monkeys, ring-tailed lemurs) were compared and found to be shorter than in humans. Microsatellites of lower complexity were most efficient for the separation of major ethnic groups. The loci of higher complexity showed a leveling of the diversity differences among populations, which could be attributed to higher mutation rates.

D18S535, D1S1656 and D10S2325: three efficient short tandem repeats for forensic genetics

Three short tandem repeat (STR) polymorphisms characterized by PCR product length < 175 bp were investigated. D18S535 and D1S1656 contained a 4 bp unit as basic repeat motif, D10S2325 a 5 bp unit. The heterozygosity rates were 0.76 (D18S535), 0.88 (D10S2325) and 0. 90 (D1S1656), leading to a combined discrimination power of 0.9999. In contrast to D10S2325 and D18S535, which showed a homogeneous repeat array without any variation in the repeat motifs, repeat length and sequence variation was found for D1S1656. Robust typing results could be observed for all three STRs using highly degraded DNA.

German shepherd dog is suspected of sexually abusing a child

A rare case of provoked anal penetration of an 11-year-old boy by a male German shepherd dog was confirmed by the results of morphological, serological and molecular genetic investigations. These results were of great importance to refute the suspicion on two adults. Some serious doubts remained in the version of the course of the event as presented by the boy. Some weeks later when confronted by a psychologist, the boy admitted having deliberately stimulated the dog manually and caused the animal to penetrate him.

Tetranucleotide STR system D8S1132: sequencing data and population genetic comparisons

In the present investigation of the D8S1132 locus 31 selected alleles were sequenced. In total there were 9 distinguishable alleles found to increase in size by regular 4 bp increments from 134 to 170 bp with a repeat array following the pattern (TCTA)n TCA (TCTA)n. One-third of the sequenced alleles exhibited an altered repeat sequence TCTG TCTA at the 3' flanking region of the repeat array. A nomenclature for the designation of D8S1132 alleles is proposed on the basis of this sequence data and in accordance with the ISFH recommendations. The allele distribution of the D8S1132 locus has been investigated in three German populations (Halle-, Münster-, and Wiesbaden area) with frequencies ranging from 0.004 to 0.24. No deviation from Hardy-Weinberg equilibrium could be observed. The heterozygosity was 0.83 and the discrimination power 0.96 for the Halle population.

Genetic variation at five STR loci in subpopulations living in Turkey

Five short tandem repeat (STR) systems HumVWA, HumTH01, HumCD4, HumF13B and HumFES were investigated in 2 subpopulations living in Turkey (Laz Turks and Kurds). The population genetic data were compared to a Turkish population sample from the Adana area. A closer genetic relationship was found to the Laz Turks than to the Kurdish sample which was also confirmed by phylogenetic tree reconstruction with seven populations from three major ethnic groups (Caucasian, Asian and African). In contrast to the Laz and Adana populations the Kurdish sample showed relatively low heterozygosity values and deviations from Hardy-Weinberg equilibrium in four of the five systems.

DNA typing of epithelial cells after strangulation

DNA typing was carried out on epithelial cells which were transferred from the hands of the suspect onto the neck of the victim. In an experimental study 16 suspect-victim combinations were investigated for estimating the typing success. Alternatively to an attack against the neck, the upper arm was used for "strangulation". PCR typing was carried out using the short tandem repeat systems (STRs) HumCD4, HumVWF31A (VWA) and Hum-FIBRA (FGA) and the success rate was > 70% for all 3 systems. In most of the cases mixed patterns containing the phenotype of the suspect and the victim were obtained. In a case where strangulation was the cause of death, epithelial cells could be removed from the neck of the victim. The DNA pattern of the suspect could be successfully amplified using four STRs, demonstrating the applicability of this approach for practical casework.

[DNA degradation in formalin fixed tissues]

The intensity of DNA degradation in fixed tissues is dependent on the fixation solution and the fixation time. The aim of this study was the investigation of DNA degradation over fixation times of up to 70 days in different tissues (muscle, brain, liver, bone) and with different formalin concentration (2%, 4%, 8%; unbuffered). An additional test was performed to see whether the fixed tissues could be individualized using PCR analysis. The smallest amounts of DNA were extracted from liver and brain and the largest from muscle and bone. The amount of DNA that could be extracted decreased with increasing formalin concentration, while at the same time DNA degradation increased. With the PCR-VNTR system HUMTH01, all fixed samples could be typed regardless of the fixation time and the formalin concentration.

HumFES/FPS and HumF13B: population genetic data from north Italy

DNA extracted from 119 unrelated individuals was analysed by the polymerase chain reaction at the polymorphic microsatellite loci HumFES/FPS (n = 115 individuals) and HumF13B (n = 119 individuals). The samples were collected from Caucasians living in the area of Milano (northern Italy). After horizontal polyacrylamide electrophoresis, 8 alleles were observed for HumFES/FPS, and 5 for HumF13B. Testing for Hardy-Weinberg equilibrium showed no significant deviation. The allele frequency data were compared with a German and a Turkish population sample.

Detection and significance of adenoviruses in cases of sudden infant death

Respiratory tract infections have been thought to act as a trigger mechanism in sudden infant death. In 118 autopsy cases of infant death, paraffin-embedded or frozen lung tissues were investigated by means of a nested polymerase chain reaction (PCR) to detect adenovirus (AV) DNA. The primers used are general primers and allow the detection of most pathogenic adenoviruses with high specificity and sensitivity and independently of devitalization of viruses or degradation of viral DNA. For the investigation three groups were established: there were 13 cases of unnatural death, 78 cases of natural death without histological signs of interstitial pneumonia, and 27 cases with interstitial pneumonia. The first group was AV negative. In the group without interstitial pneumonia AV was detected in 10.2% of the cases. In the group with interstitial pneumonia the frequency of AV detection was almost 26%. The results obtained demonstrate an association between interstitial pneumonia and detection of AV DNA, indicating that AV may play an important part in pulmonary infection in infants. Histological evidence of interstitial pneumonia was not observed in all AV-positive cases, perhaps because nonspecific virus-related changes occurred only in early stages of viral infection. Comparison of the AV frequency in SIDS (25%) and non-SIDS cases (4%) indicates an association between pulmonary AV infections and sudden death. These results support the working hypothesis of respiratory infections acting as a trigger mechanism in sudden infant death.

Population genetic comparisons among eight populations using allele frequency and sequence data from three microsatellite loci

Eight different population samples (Moroccans, Ovambos, Papuans, Australian aborigines, Germans, Turks, Japanese and Chinese) were studied using the tetranucleotide short tandem repeat systems HumTHO1 (THO1), Hum VWFA31 (VWA) and HumACTBP2 (ACTBP2). Ten alleles were differentiated in THO1, 11 alleles in VWA and 28 alleles in ACTBP2. THO1 showed 1 bp deletions in the repeat region, VWA sequence and structure variations of the 4-bp repeat motif and ACTBP2 sequence, structure and length variations in the repeat array and deletions/insertions (1-6 bp) in the flanking regions. A phylogenetic tree was constructed (UPGMA method) leading to branches which grouped Germans and Turks, Japanese and Chinese, and Papuans and Australian aborigines.

PCR analysis of the short tandem repeat (STR) system HUMVWA31. Allele and genotype frequencies in an Italian population sample

A population study in a sample of 211 unrelated individuals from 2 cities in North and Central Italy was carried out to investigate the short tandem repeat (STR) system HUMVWA31. Separation of PCR- amplified DNA fragments was performed by high-resolution horizontal denaturing polyacrylamide gel electrophoresis (PAGE) followed by silver staining. The 7 common alleles were found, together with a new smaller allele. Distribution of the observed genotypes did not deviate from Hardy-Weinberg (H-W) equilibrium. The power of discrimination for this locus was 0.93 and the chance of exclusion was 0.61. Good agreement was found between the allele frequencies in 2 Italian population samples and previous studies on Caucasians. The results of this study suggest that this STR system may be a useful tool in forensic investigations.

Population genetic study from the Zagreb area using 3 STR systems

Population genetic studies were carried out on Caucasians from north-west Croatia (Zagreb-area) using the short tandem repeat (STR) systems HumTHO1, HumVWA and HumACTBP2. After electrophoresis in PAG, 6 alleles could be identified for HumTHO1 in a sample size of 100 unrelated individuals and 7 alleles were found for VWA. For ACTBP2, 25 alleles have been identified. No significant deviations from Hardy-Weinberg equilibrium could be observed.

Structure of new mutations in 2 STR systems

Isolated father/child mismatches in cases with a high probability of paternity (W > 99.9%) have been investigated using short tandem repeat (STR) systems. According to the high probability of paternity new mutations could be assumed in these cases. A new mutation could be observed in 3 cases using the STR system HumACTBP2. Two of these cases showed a deletion and 1 case an insertion of 1 repeat (AAAG-motif) which could be verified by sequencing. In another paternity case a new mutation--1-repeat insertion (TCTA-motif)--in the HumVWA system was detected and verified by sequencing. These findings led to a new mutation rate of 0.7% (n = 453 meioses) for HumACTBP2 and 0.2% for HumVWA (n = 484 meioses).

Microsatellite polymorphisms reveal phylogenetic relationships in primates

We amplified, via PCR, DNA segments from intron 1 of the tyrosine hydroxylase gene (TH01) and intron 40 of the von Willebrand factor gene (VWA) in ten nonhuman primate genera. In humans both introns contain polymorphic microsatellites with tetrameric repeats. Compared to the allelic ranges in human populations relatively short repeat arrays could be detected for the nonhuman primates typed, presumably reflecting an ancient precursor state at both microsatellite loci. Furthermore, our results provide evidence for an association of the average number of repeats present in different primate genera and their divergence time from man. DNA sequencing of VWA orthologues revealed a relatively high variability in the arrangement of repeats in the 5'-repeat arrays, the generation of which could probably be explained by polar mutational events.

CMV-DNA detection in parenchymatous organs in cases of SIDS

A nested PCR approach has been developed especially for the detection of small amounts of cytomegalovirus (CMV) DNA in autopsy samples. Lung tissue and submandibular glands in 118 cases of infant death (92 SIDS cases, 13 natural deaths due to other defined causes and 13 unnatural deaths) were investigated by this technique and compared to the results obtained by other CMV detection methods (histology, immunohistochemistry, in situ hybridization and PCR). CMV-DNA could be detected in the lung tissue in 7 cases of SIDS using nested PCR. Compared to conventional PCR (3 positive cases in lung tissue) the nested approach always gave glear results and showed less additional bands. In all cases where CMV could be detected in the lungs, positive results were also obtained in the submandibular glands. The nested PCR method proved to be a more sensitive technique than the other detection methods including PCR and hot start, and even minimal amounts of target DNA could be detected in the presence of human and bacterial background DNA.

Phenotype differences of STRs in 7 human populations

A maximum of 6 STR systems (TH01, VWA, ACTBP2, FES, F13B, D21S11) was investigated in 7 human populations (Germans, Turks, Moroccans, Japanese, Chinese, Papuans, Ovambos). In each population no deviations from Hardy-Weinberg equilibrium were observed. Out of each population the phenotypes of 50 individuals (comprising 3 to 6 STRs) were randomly selected. Based on the phenotype frequencies interpopulation comparisons were carried out using the frequencies of each other population. Within major ethnic groups only minor differences in phenotype frequencies were found. Between major ethnic groups differences of up to several orders of magnitude could be observed. The most discriminative STRs for interpopulation comparisons were TH01, FES and F13B.

Observation of null alleles apparently due to deletions

After examining 2 paternity cases in 17 classical, 4 RFLP and 5 PCR-VNTR systems, isolated pseudo-exclusions were observed in the polymorphism D2S44 (YNH24). In both cases the "exclusions" were due to apparent opposite homozygosity. The application of different restriction enzymes, PCR amplification and varying electrophoretic conditions each led to an equivalent result of a 1-band-pattern with a mismatch between both father/child pairs. From these results the authors conclude that a complete or almost complete loss of the alleles is the most probable explanation.

GEDNAP IV and V. The 4th and 5th Stain Blind Trials using DNA technology

In the collaborative exercise GEDNAP IV one EDTA blood sample (2 ml) and 5 bloodstains (0.5 ml on cotton) were investigated and in GEDNAP V, a total of 8 bloodstains (0.5 ml on cotton), including 2 mixed bloodstains. DNA typing was carried out using the RFLP systems YNH24/Hinf I and MS43a/Hinf I and the PCR systems HLA DQ alpha, D1S80, ApoB and YNZ22. In both exercises approximately 20 laboratories obtained results using the RFLP systems. Of the PCR systems, D1S80 was the most commonly used (14 labs in GEDNAP IV; 18 labs in GEDNAP V). The interlaboratory standard deviation for YNH24 in both exercises was approx. 0.6%, for MS43a 0.7-2.2% (GEDNAP IV) and 0.4-1.4% (GEDNAP V), depending on the fragment size. The fragment size calculation performed in each laboratory yielded a standard deviation twice that obtained when the fragment size calculation was performed centrally (IfR, Münster). In GEDNAP III, a system-specific corridor was developed to define the limits of deviation; this was modified for the present study by combining the fragment size ranges of YNH24 and MS43a. In both studies a subgroup of laboratories was involved in preliminary exercises using three PCR VNTRs and the system HLA DQ alpha. Owing to the substantial variation in experience of the participating laboratories with PCR typing the results obtained in these two studies do not fulfil the basic quality criteria of the GEDNAP studies.

Frequency profiles of 3 STRs in a Turkish population

Population genetic studies were carried out on Caucasians from southern Turkey (n = 204 individuals) using the short tandem repeat (STR) systems HumTHO1, HumVWA and HumACTBP2. After electrophoresis in polyacrylamide gels, 6 alleles could be identified for HumTHOI, 7 alleles for VWA and 26 alleles for ACTBP2. No significant deviations from Hardy-Weinberg equilibrium could be observed.

D1S80 (pMCT118): analysis of 3 ethnic subpopulations living in Brussels

Population genetic studies were carried out on 3 ethnic subpopulations living in Brussels (119 Belgians, 120 Turks and 137 Moroccans). DNA extraction was performed using the Chelex method. After DNA amplification the DNA fragments were separated electrophoretically in horizontal polyacrylamide gels. A total of 32 alleles (between 21 and 25 alleles in each subpopulation) including 8 "interalleles" could be differentiated. The allele frequencies were compared with population data from a German study and no significant differences could be observed.

Comparison of different methods for CMV detection

The submandibular glands were investigated in 77 cases of SIDS using histology, immunohistochemistry (IHC), in situ hybridization (ISH) and PCR to detect cytomegalovirus (CMV) inclusion disease. The aim of the investigation was to establish the detection of CMV by PCR as a model for the detection of other types of virus by PCR, especially for the detection of viruses which affect the respiratory system of babies. In 14 cases the CMV detection was possible. Typical changes of duct cells associated with CMV infection were observed in 9 by histology and in 4 further cases by IHC. In comparison to these methods, ISH showed a higher sensitivity but only one more positive case was found. Theoretically the PCR method is more sensitive than ISH and more convenient from the practical aspect. Detection of CMV by PCR was possible in 10 out of 14 positive cases. All PCR positive cases were cases showing an active disease but not latent infection.

Population data and forensic efficiency values for the STR systems HumVWA, HumMBP and HumFABP

Population studies were carried out on Caucasians from north-west Germany using the short tandem repeat (STR) systems HumVWA (locus: 12p12-12pter), HumMBP (locus: 18q23-pter) and HumFABP (locus: 4q28-q31). After electrophoresis 9 alleles could be identified for HumVWA in a sample size of 321 unrelated individuals and 4 alleles were found for HumFABP in 106 individuals. For HumMBP-A 10 alleles and for HumMBP-B 7 alleles and 1 intermediate allele were determined in a sample size of 143 individuals. No deviations from Hardy-Weinberg equilibrium could be observed. In a small family study (HumVWA-n = 129; HumMBP-n = 59; HumFABP-n = 48) no new mutations could be found for HumMBP-A and HumFABP whereas 2 mutations were found in HumMBP-B and one mutation in HumVWA. Positive results could be obtained from 1 ng-20 pg (HumVWA, HumFABP) and 1 ng-100 pg (HumMBP) template DNA.

[Individualized DNA analysis in insurance medicine clarifications]

DNA investigations for the clarification of problems in insurance medicine can be subdivided into 3 groups (1) Traffic accidents (2) identification (3) questionable fraud cases. The development in individualisation by DNA analysis has progressed from the initial restriction fragment length polymorphisms (RFLPs) to the PCR-based polymorphisms. PCR systems are characterised by a very high sensitivity of detection and a high degree of success with highly degraded biological material. The current possibilities for DNA analysis are described and exemplified with special reference to PCR-based polymorphisms.

Forensic validation of the STR systems SE 33 and TC 11

Population studies on Caucasians from northwest Germany were carried out using the short tandem repeat (STR) systems SE 33 (Locus: ACTBP2) and TC 11 (Locus: 11p15.5). After electrophoresis in PAG 26 alleles could be identified for SE 33 in a sample size of 180 unrelated individuals and 6 alleles were found for TC 11 in 110 individuals. The combined mean exclusion chance for both systems was 0.96 and the discrimination index 0.999. No significant deviations from Hardy-Weinberg equilibrium could be demonstrated. In a small sample of families (SE 33 - n = 21; TC 11 - n = 30) no new mutations could be found. Positive and reproducible results for both STRs could be obtained from 50 pg template DNA.

DNA typing of debris from fingernails

In 3 series paired volunteers were asked to gently scratch each other with the fingernails to produce superficial abrasions only of the stratum corneum. In a 4th series scratch marks were produced in the skin of cadavers but additionally including the deeper epidermal layers. Debris was removed using a thorough technique in series 1 and 2 and a careful technique in series 3. After DNA extraction, the debris was typed using the STR systems HUMACTBP2 (SE33), HUMTH01 (TC11) and HUMVWFA31 (VWA). In the material obtained from series 1 (i.e. scratching with no prior cleaning of the nails) and series 2 (i.e. cleaning of the nails prior to the experiment) the debris was removed with a sharp instrument and only the DNA pattern of the person who carried out the scratching could be detected. In the 3rd series extraneous material was removed very carefully from under the fingernails to avoid contamination with DNA from the nails. In 71% of these cases DNA patterns of the person who had been scratched or mixed DNA patterns of both persons could be detected. In the experiments with postmortem skin the DNA pattern of the cadaver could be detected in all cases. These results show that in crime cases where the perpetrator has been scratched by the victim, sufficient material can be obtained from under the fingernails for DNA typing if removal of the particles is carried out with sufficient care.

DNA extraction from mixtures of body fluid using mild preferential lysis

A modification to the DNA extraction method "preferential lysis" (Gill et al. 1985) is proposed which can be applied to DNA mixtures of vaginal cells and spermatozoa. In mixtures with a low sperm content the further loss of sperm DNA caused by the extraction can be avoided by using "mild preferential lysis". Amplification by PCR (polymerase chain reaction) then yields sufficient DNA to be able to identify both components in the mixture.

Population genetics and forensic efficiency data of 4 AMPFLP's

Family studies were carried out in a population sample from north west Germany using 4 amplifiable VNTR polymorphic systems D1S80 (MCT118), ApoB, D17S30 (YNZ22) and COL2A1. Separation was carried out in polyacrylamide gels and visualised using silver staining. In family studies (n = 30) no evidence of new mutations was found. The population study of unrelated individuals (mothers and putative fathers) showed that all 4 systems were highly polymorphic and similar to other population studies. The combined exclusion chance was calculated to be approximately 99% and the combined discrimination index 1.5.10(-4). The Hardy-Weinberg equilibrium was checked by forming groups of alleles and no significant deviations could be found in all systems.