Optimized oligonucleotide probes for DNA fingerprinting

DNA fingerprinting of renal cell carcinoma with special reference to tumor heterogeneity

Genomic alterations in renal cell carcinoma were investigated by DNA fingerprinting using the simple repetitive oligonucleotide probe (CAC)s. Nine of ten tumors showed somatic changes in the fingerprint pattern compared with constitutional DNA. The most consistent changes were deletions and/or decrease in intensity of a band. When using two or three samples from different parts within the tumor, up to three different cell clones could be detected. These results indicate that DNA fingerprinting analysis can be a useful technique for the study of genomic alterations and tumor heterogeneity in renal cell carcinoma.

Abundance and polymorphism of simple repetitive DNA sequences in Bmssica napus L

The Brassica napus genome has been investigated by DNA fingerprinting with six synthetic oligonucleotide probes complementary to simple repetitive sequences, namely (GATA)4, (GACA)4, (GGAT)4, (CA)8, (CT)8 and (GTG)5. While all sequence motifs were found to be present in the B. napus genome, their organization and abundance varied considerably. Among the investigated probes, (GATA)4 revealed the highest level of intraspecific polymorphism and distinguishes not only between cultivars but even between different individuals belonging to the same cultivar. In contrast, (GTG)5, (GACA)4 and (GGAT)4 produced relatively homogeneous fingerprint patterns throughout different cultivars, while hybridization to (CT)8 and (CA)8 resulted in only a few weak bands superimposed on a smear. The isoschizomeric pair Hpa II and Msp I revealed the presence of methylated cytosines in the vicinity of (GATA)m repeats. The applicability of simple repetitive sequence polymorphisms as molecular markers for Brassica species is discussed.

Genetic and population study of a Y-linked tetranucleotide repeat DNA polymorphism with a simple non-isotopic technique

A polymorphic microsatellite (Y-27H39) based on a (GATA)n repeat was recently discovered on the short arm of the human Y chromosome. We have used a simple technique based on polymerase chain reaction amplification and native polyacrylamide gel electrophoresis followed by highly sensitive silver staining to study the inheritance, the genetic stability and the allele frequency distribution of this polymorphism in the Brazilian population. We have analyzed 100 randomly chosen Caucasian Brazilian father-son pairs with established paternity. Five alleles, four base-pairs apart, were easily distinguishable. Their frequencies were: A (186 bp), 0.19; B (190 bp), 0.49; C (194 bp), 0.24; D (198 bp), 0.07; E (202 bp), 0.01. In all father-son pairs, there was complete allelic concordance. From these data, the probability of discrimination for forensic cases and the average probability of exclusion for paternity cases were both calculated to be 0.66.

Testing deficiency paternity cases with a Y-linked tetranucleotide repeat polymorphism

Because a son's genotype at a Y-linked locus uniquely specifies his father's genotype at that locus irrespective of the maternal contribution, Y-linked polymorphisms show increased exclusion power over autosomal polymorphisms in paternity cases involving a male child. This advantage is even more obvious when the alleged father is deceased or otherwise unavailable for testing. In this situation, any individual connected by patrilineage to the alleged father may be tested in his place. The usefulness of the Y-linked tetranucleotide repeat locus Y-27H39 in deficiency cases was evaluated in a set of 41 families that had a deceased alleged father and that had been tested at GENE/MG with multilocal and unilocal DNA fingerprinting probes. In sixteen of these cases the proband (child tested) was male and there were male relatives. In the thirteen cases in which paternity was included, Y-27H39 would contribute significantly to the paternity index. In one of three cases in which there was exclusion by fingerprinting probes there was also exclusion by Y-27H39. Thus, Y-27H39 is useful in deficiency paternity cases and will be specially valuable in situations where autosomal polymorphisms have limited power, such as when there is only one male living relative of the deceased father. However, our experience is that Y-linked probes can only be applied in approximately 40% of cases.

Detection, cloning, and distribution of minisatellites in some mammalian genomes

The chromosomal distribution of minisatellites (cloned and/or detected using natural or synthetic tandem repeats) is strikingly different in man and mouse. In man, the vast majority is clustered in the terminal band of a subset of chromosome arms. Interestingly, the class of shorter tandem repeats called microsatellites is widespread along the chromosomes, suggesting that minisatellites can be created or maintained only in certain regions. In order to gain a better knowledge of these areas, we have studied a sub-telomeric cosmid from the pseudoautosomal region. Sixty kilobases of human genomic DNA starting approximately 20 kilobases from the human sex chromosomes telomere have previously been independently isolated in two cosmid clones (locus DXYS14) (Cooke et al., 1985); Rouyer et al., 1986). We have studied in more detail one of the two cosmids from this locus and found that it contains four different minisatellite structures representing 20 kilobases of the cosmid. These structures are unrelated to each other or to the minisatellite family described by Jeffreys et al. (1985). They display different degrees of polymorphism correlated with varying amounts of inner homogeneity. Combined with the previous description of an additional minisatellite (Cooke et al., 1985; Inglehearn and Cooke, 1990) in the contiguous cosmid, our observation shows that these structures may represent an important proportion of the DNA in sub-telomeric regions.

Paternity testing with the F10 multilocus DNA fingerprinting probe

Empirical analysis of 200 paternity cases by multilocus DNA fingerprinting with the F10 probe showed that it was capable of distinguishing fathers from non-fathers in every case. The average exclusion probability was 0.99998. A very effective discrimination parameter was the proportion of non-maternal (test) bands which cannot be detected in the alleged father (unassignable bands) among all test bands. Values below 0.2 were seen in true fathers while in all cases of non-fathers the values were above 0.35. Minisatellite mutations occurred at a rate of 0.004 per band per child. The distribution of band-sharing among first degree relatives and unrelated individuals showed only a small overlap. Thus, band-sharing of the F10 fingerprints should provide a useful statistic for testing genetic relationships in deficiency cases.

Oligonucleotide DNA fingerprinting: results of a multi-center study on reliability and validity

We report the results of an empirical study of 256 paternity cases referred to 7 different German laboratories for DNA fingerprinting with oligonucleotide probe (CAC)5/(GTG)5. All parameters characteristic of such multilocus DNA fingerprints were found to differ significantly between the contributing centres. Despite these differences, clear-cut decisions between paternity and non-paternity could be made in all but one case. Furthermore, we found no systematic deviation of the gel-phenotype distribution among trios from random expectation as derived from commonly adopted analytical models. Thus, we conclude that oligonucleotide DNA fingerprinting is a robust and reliable means for the resolution of paternity cases.

Self-reactive and antigen-specific T cell clones derived from a HLA-DR4+/DR5+ donor: T cell receptors and MHC-restriction patterns

The relationship of heat shock proteins and rheumatoid arthritis as well as the relevance of autoreactivity in this disease is unclear. T cells of six individuals (four expressing the DRB1*0401 allele, one harboring DRB1*0404 and one the DRB1*0407 allele) were cloned in the presence of 65kD mycobacterial heat shock protein (HSP60) in order to determine T cell receptors (TcR) used and the MHC class II restriction patterns of potentially relevant T cell clones (TcC). All TcC obtained were not specific for HSP60, but six TcC of one donor (HLA-DR4/HLA-DR5) were responsive towards autologous antigen-presenting cells. One TcC displayed authentic autoreactivity whereas five TcC reacted specifically to serum proteins. The amino acids (aa) of the MHC molecule, crucial for immune recognition were mapped to aa #71 or #86 of either maternal or paternal origin. The strictly autoreactive TcC did not recognize transfected L cells implicating specificity for self-peptides not presented by L cells or the involvement of adhesion molecules. Correlations between autoreactivity and TcR V(D)J sequences or N nucleotides of various "autoreactive" TcC were not evident.

On the potential of simple repetitive DNA for fingerprinting in clinical, forensic, and evolutionary dynamic studies

The purpose of this review is to discuss critically the practical meaning of a specific genome component, simple repetitive desoxyribonucleic acid (DNA) sequences as clinical and forensic and diagnostic and research tools. Previously, multilocus DNA fingerprinting was the major technology employed to visualize such simple repeat sequences. This technique enables many polymorphic loci to be simultaneously detected thus yielding vast amounts of information. With the advent of enzymatic DNA amplification via the polymerase chain reaction (PCR), individual simple repeat loci can be demonstrated, theoretically even from single DNA molecules and so a wealth of additional approaches have also become feasible. In general investigating, small, known, single copy parts of genomes have not posed truly insurmountable problems if enough material was available. There have even been a few (anecdotal) reports on the amplification of simple repeats from ancient DNA (see, e.g. [30]. Here we would like to after a solid basis for an earnest discussion of the applications of these simple repetitive sequences using various methodological approaches relevant for clinical diagnosis, setting aside the obvious unsolved mysteries of their biology.

Diagnosis of transfusion-associated graft-versus-host disease by genetic fingerprinting and polymerase chain reaction

A patient with Hodgkin's disease (clinical stage IIIB) received chemotherapy and total nodal irradiation. After the transfusion of filtered packed red cells, this patient developed transfusion-associated graft-versus-host disease (TA-GVHD). The genetic fingerprint of the patient's peripheral blood lymphocytes (PBLs) differed completely from that of her other body tissues. Normally, after transfusion, only the patient's own genetic fingerprints are observed in the PBLs, as exemplified in more than 10 control cases in which the transfused blood had not been filtered before transfusion. No signal bands corresponding to those of the blood donor could be demonstrated in samples of the patient's tissue DNA. Moreover, chimerism was detected in the hybridization pattern of the patient's PBLs on the ninth day after the onset of symptoms. Polymorphic simple repeats in the HLA-DRB gene after amplification by polymerase chain reaction were also investigated, which confirmed the fingerprinting results. The advantages of these methods for the diagnosis of TA-GVHD include the rapid and unequivocal diagnosis as well as the fact that there is no need for the relatives to be HLA typed.

PCR amplification products are of limited use for the study of DNA/protein interaction

Conventional methods for labeling double-stranded DNA lead to high specific activity. Yet they often alter the target DNA sequence to such an extent as to prevent a meaningful protein/DNA interaction analysis. Therefore we tried to establish a polymerase chain reaction (PCR)-based method which allows radiolabeling to high specific activity and should maintain the protein binding capability of small double stranded DNA fragments. By using PCR it is possible to label double stranded DNA to high specificity, but the protein binding capability of such DNA is drastically reduced.

Characterization of hypervariable locus-specific probes derived from a (CAC)5/(GTG)5 multilocus fingerprint in various Eurasian populations

Population genetic studies were performed using oligonucleotide probes (Hz1103, Hz4103, and Hz4201) that recognize three hypervariable loci (D11S859, D9S128 and D22S265) in the human genome. DNA from 17 Eurasian population samples including 37 monozygotic twin pairs were digested with HinfI and hybridized with Hz4103. Allele frequency distribution profiles and high degrees of heterozygosity were similar in each ethnic group. Among 804 unrelated individuals tested, we detected one case of mosaicism caused by a somatic recombination event in a monozygotic twin. In addition, samples of DNA from three ethnic groups (Germans, Assamese Hindus and Thais) and from German and Thai families were restricted with MboI and probed with Hz1103, Hz4103, and Hz4201. The results showed considerable degrees of heterozygosity and locus-specific allele distribution profiles, rather than interpopulation differences. Among 262 meioses (12 three-generation families with a total of 131 children) analyzed, a single recombination event was observed following hybridization with the DNA probe Hz4201.

Oligonucleotide and Amplification Fingerprinting of Wild Species and Cultivars of Banana (Musa spp.)

DNA oligonucleotide and amplification fingerprinting have been successfully used to detect genetic polymorphisms in 15 representative species and cultivars of the genus Musa, comprising AA, AAA, AAAA, AAB, ABB, and BB genotypes. In-gel-hybridization of Hinf I-digested genomic banana DNA to the 32P-labeled synthetic oligonucleotides (GATA)4, (GTG)5, and (CA)8 revealed considerable polymorphisms between Musa species and cultivars. The fingerprint patterns proved to be somatically stable and did not show differences between individual plants of 'Grand Nain' (AAA genotype). Dendrograms based on oligonucleotide fingerprint band sharing data proved to be consistent with most of the known features of the history of banana and plantain cultivation and evolution, respectively. DNA samples from the same banana species and cultivars were also amplified by PCR using single or pairwise combinations of short oligonucleotide primers. Amplification products were separated on agarose or polyacrylamide gels and visualized by ethidium bromide or silver staining, respectively. Polymorphic patterns were obtained with some but not all primers. By using the CCCTCTGCGG primer in simplex and/or duplex PCR, the induced mutant 'GN60A' was clearly recognized from its original variety 'Grand Nain'. Both fingerprint techniques allowed the detection of bands characteristic for the A and B genome. This DNA fingerprinting technology has potential application in several areas of Musa improvement.

Dissecting (CAC)5/(GTG)5 multilocus fingerprints from man into individual locus-specific, hypervariable components

Individual components of multilocus fingerprints from man produced by (CAC)5/(GTG)5 oligonucleotides have been scrutinized to characterize their peculiar properties. Successful cloning and changes occurring during the propagation of recombinant simple repetitive DNA in prokaryotic hosts are described. The isolated locus-specific probes were characterized with respect to their formal (and population genetic) properties and their usefulness for individualization and linkage studies. The localization was determined on chromosomes 8, 9, 11, and 22. Repeat flanking sequences were characterized and analyzed for their coding potential because of significant open reading frames and apparent evolutionary conservation among vertebrates. The organization of the repeats and their flanking regions in the human genome is discussed with respect to the sequence (fine) architecture that developed during evolution. Classical "minisatellite" sequences were not detected near hypervariable (cac)n/(gtg)n repeats. The single-copy probes described herein are a convenient complement to the oligonucleotides employed for multilocus fingerprinting. Many practical applications are apparent.

Biostatistical basis of individualization and segregation analysis using the multilocus DNA probe MZ 1.3: results of a collaborative study

A collaborative study using the multilocus minisatellite DNA probe MZ 1.3 was carried out to investigate segregation information, mutation rate, DNA fragment frequencies as well as band sharing characteristics. The fingerprint patterns of 393 children as well as 694 unrelated individuals were analysed after digestion of DNA with the restriction enzyme HinfI. A mutation rate of 1% per meiosis or 0.04% per band was found with a mean number of 26 bands/individual. It was shown that maternal and paternal fragments are inherited in equal proportions. Population frequencies of restriction fragments demonstrated a distribution with increasing frequencies in the small fragment size range below 10 kb as well as the absence of very common or very rare fragments. Our data can be used to calculate simple exclusion probabilities based on the number of non-maternal bands in the child.

Fingerprinting plant genomes with oligonucleotide probes specific for simple repetitive DNA sequences

Oligonucleotides hybridizing to simple repetitive DNA patterns are highly informative as probes for DNA fingerprinting in all investigated animal species, including man. Here we demonstrate the applicability of this technique in higher plants. The oligonucleotide probes (GTG)5 and (GATA)4 were used to investigate the differences in DNA fingerprint patterns of the following angiosperm species: Triticum aestivum, Secale cereale, Hordeum vulgare, Beta vulgaris, Petunia hybrida, Brassica oleracea, and Nicotiana tabacum. Two species, Hordeum vulgare as a monocot and Beta vulgaris as a dicot, were analyzed in more detail. Their genomes differ considerably in both amount and organization of the simple repetitive sequences (GATA)n, (GACA)n, (GTG)n, and (CT)n due to the evolutionary distance of these two species. Furthermore, several lines and cultivars of Beta vulgaris and Hordeum vulgare can clearly be distinguished on the basis of their highly polymorphic patterns of these repetitive sequences.

Oligonucleotide fingerprinting of plant and fungal genomes: a comparison of radioactive, colorigenic and chemiluminescent detection methods

Digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences were introduced into nonradioactive fingerprint analysis of plant and fungal DNA. The fragment patterns, obtained by blot hybridization of TaqI-restricted DNA from chickpea (Cicer arietinum) and its fungal pathogen Ascochyta rabiei with digoxigenated probes and either a colorigenic or a chemiluminescent detection method, were compared to those obtained with 32P-labeled probes. In combination with alkaline phosphatase and its chemiluminescent substrate 3-(2'-spiroadamantane)-4-methoxy-4-(3"-phosphoryloxy)phenyl- 1,2-dioxetane (AMPPD) digoxigenated oligonucleotides yielded clear-cut fingerprints with high signal-to-background ratios within several minutes of exposure to X-ray films. The chemiluminescence reaction remained stable for at least two weeks. A comparison of banding patterns obtained by radioactive versus digoxigenin-based hybridization and detection techniques revealed substantial differences in the relative signal intensities of bands. Both nonradioactive techniques show a tendency to "equalize" band intensity differences. Whereas 32P-labeled oligonucleotides are also applicable to in situ hybridization with DNA immobilized in dried agarose gels, gel hybridization did not work efficiently with digoxigenated probes and either substrate.

Early stages of sex chromosome differentiation in fish as analysed by simple repetitive DNA sequences

Animal sex chromosome evolution has started on different occasions with a homologous pair of autosomes leading to morphologically differentiated gonosomes. In contrast to other vertebrate classes, among fishes cytologically demonstrable sex chromosomes are rare. In reptiles, certain motifs of simple tandemly repeated DNA sequences like (gata)n/(gaca)m are associated with the constitutive heterochromatin of sex chromosomes. In this study a panel of simple repetitive sequence probes was hybridized to restriction enzyme digested genomic DNA of poeciliid fishes. Apparent male heterogamety previously established by genetic experiments in Poecilia reticulata (guppy) was correlated with male-specific hybridization using the (GACA)4 probe. The (GATA)4 oligonucleotide identifies certain male guppies by a Y chromosomal polymorphism in the outbred population. In contrast none of the genetically defined heterogametic situations in Xiphophorus could be verified consistently using the collection of simple repetitive sequence probes. Only individuals from particular populations produced sex-specific patterns of hybridization with (GATA)4. Additional poeciliid species (P. sphenops, P. velifera) harbour different sex-specifically organized simple repeat motifs. The observed sex-specific hybridization patterns were substantiated by banding analyses of the karyotypes and by in situ hybridization using the (GACA)4 probe.

A gel retardation assay system for studying protein binding to simple repetitive DNA sequences

Simple repetitive DNA sequences have been regarded as mere "junk" present in all eukaryotic genomes. In fact, mixed simple repeat (gt)n(ga)m sequences are present in major histocompatibility complex MHC-DRB genes for long evolutionary times, including such distant animals as artiodactyla and man. We describe herein an unsophisticated method which reveals that at least certain simple repetitive (gt)n(ga)m sequences bind nuclear proteins and show characteristics of a specific DNA-protein interaction via gel retardation.

A genetic factor model for the statistical analysis of multilocus DNA fingerprints

A novel concept is described for the statistical analysis of multilocus DNA fingerprints. Utilizing this method, it is shown by simulation that the application of multilocus DNA fingerprints to paternity testing is robust against deviations from idealistic assumptions made about underlying models and parameters. Partial homozygosity, allelism and linkage at the DNA loci involved, as well as variations in estimates of band-sharing probabilities were studied for effects on the resulting paternity probabilities. None of the above-mentioned phenomena appear to change these values to an extent relevant for decision making in paternity cases.

Two different multi-locus probes MZ1.3 and (CAC)5 show nearly the same RFLP pattern

The RFLP patterns revealed by 2 different multi-locus probes MZ1.3 and (CAC)5 were compared using 4 different restriction enzymes AluI, MboI, HaeIII, HinfI. Irrespective of the restriction enzyme the fingerprints obtained with MZ1.3 and (CAC)5 were almost identical. The MZ1.3 RFLP pattern showed some extra bands which were absent in the (CAC)5 fingerprint.

On the statistics of the "genetic fingerprint"

In analogy to the polygene determined morphological features, the DNA-fingerprint is also not suitable for statistical processing. Statements about the individuality are merely speculative. Frequencies of genes cannot be found, since it is impossible to determine which combinations of bands belong to one gene locus. Hence the DNA fingerprint enables the recognition of exclusions from paternity; it does not, however, allow a statistical analysis, no matter which method be employed.

Uncommon chromosomal mosaicism in chorionic villi

Three cases of unusual chromosomal mosaicism are reported for which the cytogenetic data show inconsistent findings between CVS and AC or fetal tissue, and which cannot be explained simply by non-disjunction. For case 1, in CVS the karyotype was 46,XY, whereas lymphocytes and fibroblasts revealed 69,XXY. DNA fingerprinting indicated one paternal and two maternal chromosome sets, the latter most probably due to omission of maternal meiosis II. For case 2, in CVS mos 46,XX/47,XX,+ mar de novo was observed. Amniotic fluid cells had the karyotype 46,XX. The origin of the marker chromosome might be explained by at least two events of unknown order (a somatic chromosome/chromatid deletion and non-disjunction of the homologous chromosome). In case 3 (CVS: mos 46,XY/46,XY,19q+ de novo; amniotic fluid cells, lymphocytes, and fibroblasts: 46,XY), the surplus of chromosome material in 19q+ might be explained on the basis of a somatic translocation. The idea of a chimera is less convincing, as the mosaic finding is restricted to one tissue. Furthermore, there was no hint of a vanishing twin. Hitherto, no case of structural chromosome mosaicism in CVS has been reconfirmed in fetal tissues.

Determining consanguinity by oligonucleotide fingerprinting with (GTG)5/(CAC)5

Simple tandemly organized (GTG)n/(CAC)n sequences are spread throughout the human chromosomes. The most informative DNA fingerprints for the testing of pedigrees and/or paternity were obtained with the simple triplet repeat probe (GTG)5 or its complement (CAC)5. These hypervariable simple-repeat fragments are stably inherited in a Mendelian fashion. Using these highly discriminating probes, all human individuals could, theoretically, be differentiated, except for genetically identical monozygotic twins. Examples from actual case work are reported and pertinent advantages of this methodology are discussed.

Distribution of the IS elements ISS1 and IS904 in lactococci

A broad distribution of the lactococcal IS elements ISS1 [1] and IS904 [2] in several lactococcal plasmids and chromosomal DNA was observed. Hybridization of the ISS1 and IS904 oligonucleotide gene probes with DNA of lactococcal phages showed that none of these tested bacteriophages contained one of the IS elements. On the transductionally shortened lactose plasmid pTD1 an insertion sequence homologous to ISS1 was identified closely downstream to the P-beta-galactosidase gene. Sequence analysis of ISS1/pTD1 showed 82% homology in the deduced amino acid sequence to the putative transposase of ISS1, ISS1W, ISS1N, and IS946.

Individual-specific DNA fingerprinting in man using the oligonucleotide probe (GTG)5/(CAC)5

Restriction fragment length polymorphisms (RFLPs) associated with interspersed simple repetitive DNA arise from DNA fragment lengths that contain variable numbers of the repeated motifs. Using restriction enzymes with different 4 base pair recognition sites and the simple triplet repeat hybridization probe, (GTG)5/(CAC)5, DNA multilocus fingerprints can be obtained in man. Only the DNAs of monozygous twins show indistinguishable banding patterns. Since the bands are inherited according to Mendelian laws, DNA fingerprints can be used for identification of individuals and paternity analysis. The discriminatory power in the DNA fingerprinting technique in forensic science is demonstrated and examples of paternity testing are given.

Differentiation of species and strains among filamentous fungi by DNA fingerprinting

We have analyzed 11 strains and clones, representing five species (Penicillium janthinellum, P. citrioviridae, P. chrysogenum, Aspergillus niger, Trichoderma harzianum) and three genera of filamentous fungi, for the presence of hypervariable loci in their genomes by hybridization with simple repeat oligonucleotides and the DNA of phage M13. The oligonucleotide probes (CT)8, (GTG)5 and (GACA)4, as well as M13 DNA, are informative probes for fingerprinting in all genera and species tested. The probe (GATA)4 produced informative fingerprints only with the genomic DNA of A. niger. There was no similarity between the fingerprints originating from fungi of different genera and also little similarity between the fingerprints of different species belonging to the same genus. Fingerprints of strains of the same species differed only slightly from each other. Fingerprints of clones originating from one strain were identical. The results indicate that DNA fingerprinting is a powerful method to differentiate species and strains of filamentous fungi.

Coamplification of simple repetitive DNA fingerprint fragments and the EGFR gene in human gliomas

DNA fingerprints were generated by the oligonucleotide probe (GTG)5 from surgically removed tissue and/or primary cell culture of 36 intracranial tumors (31 gliomas, 1 medulloblastoma, 4 metastatic carcinomas) and compared with the constitutional banding pattern obtained from the peripheral blood leukocytes of each patient. A multitude of somatic changes was detected and found to reflect the chromosome alterations identified by parallel karyotype analysis. Gain and/or loss of bands or significant band intensity shifts could be demonstrated in the fingerprints of more than 80% of the tumors investigated. This included a highly amplified fingerprint fragment in five independent gliomas (four of them had double minutes, dmin) which appeared not individual- but tumor-specific (2.4 kilobases, kb, after HaeIII digestion). Rehybridization with the oligonucleotide probes (GT)8 and (GATA)4, respectively, revealed additional amplified fingerprint fragments in the tumor DNA of these patients. While a (ca/gt)n fragment (2.6 kb. HaeIII) was also found to be amplified in all five cases, one band detected with (GATA)4 (1.4 kb, HaeIII) represented a unique feature for one of these tumors only. Amplification of the epidermal growth factor receptor (EGFR) gene via Southern blot hybridization was revealed only in those tumors showing the amplified DNA fingerprint fragments as well. Thus in many gliomas the amplification unit harbors two simple repetitive DNA fingerprint loci, (cac/gtg)n and (ca/gt)n, in addition to the EGFR gene.

DNA fingerprinting in domestic animals

DNAs of several species of domestic animals digested with the restriction endonucleases HinfI, AluI and HaeIII were hybridized with different synthetic probes. DNA fingerprint patterns were found in each investigated species by at least two of these probes. Furthermore, two probes gave sex-specific banding patterns in the chicken. Some applications of DNA fingerprinting in domestic animals are discussed.

Routine applications of DNA fingerprinting with the oligonucleotide probe (CAC)5/(GTG)5

The use of DNA fingerprinting with synthetic oligonucleotides is illustrated for practical applications familiar in clinical diagnostics: pre- and postnatal zygosity determination and the monitoring of bone marrow transplantation. A simple method for non-radioactive detection is described which may be interesting for many diagnostic laboratories.

Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences

The existence of hypervariable DNA sequences in nuclear genomes, and the use of appropriate "fingerprinting" probes to detect them, has gained widespread scientific interest, and also led to multiple applications in diverse areas. Two years ago, the new technique of "DNA fingerprinting" was also introduced into the analysis and characterization of plant genomes, initially by using human or M13 minisatellites as probes. In the present article, we demonstrate the applicability for plant DNA fingerprinting of oligonucleotide probes specific for simple repetitive DNA sequences. We show that various levels of intra- and interspecific polymorphisms can be detected; the information to be gained depends on the optimal combination of probe and species. Variety-specific patterns were obtained in several cases. Some probes revealed variability between individuals. Somatic variability was not observed. Different DNA isolation and purification procedures were tested in order to introduce a fast and easy-to-perform isolation method suitable for a large variety of plant species. Nonradioactive fingerprinting was performed using digoxigenated oligonucleotides as probes. Banding patterns obtained with radioactive and digoxigenin-based labeling techniques proved to be of similar quality.

Identification of variable simple sequence motifs in 19q13.2-qter: markers for the myotonic dystrophy locus

Variable simple sequence motifs (VSSMs), or microsatellites, were used for the genetic delimitation of the myotonic dystrophy (DM) region at 19q. Three simple sequence motifs were identified in and around the ERCC1 DNA-repair gene at 19q13.2-13.3 and one in the vicinity of the RRAS gene at 19q13.3-qter. A (TG)n repeat, situated within the ninth intron of the ERCC1 gene, was converted into a highly informative multiallelic marker using PCR-mediated DNA amplification and high-resolution gel analysis. The structurally similar sequence motif in the RRAS gene yielded a marker system with only two alleles. Use of these VSSMs for linkage analysis and haplotyping in a selected set of DM families revealed that the DM gene is distal but close to the ERCC1 locus and can be excluded from the CKM-ERCC1 interval at 19q13.2. The order for RRAS and other distally located markers was established as DM-D19S50-[RRAS,KLK]-D19S22-ter.

Forensics of birds of prey by DNA fingerprinting with 32P-labeled oligonucleotide probes

Paternity tests on confiscated families of eight species of birds of prey were carried out successfully by DNA fingerprinting with 32P-labeled oligonucleotide probes. Variations in the number of hybridized fragments, depending on the species of birds, are observed using the same probe, as well as differences of polymorphism by hybridizing the DNA samples with several oligonucleotide probes.

Hybridization and polymerase chain reaction amplification of simple repeated DNA sequences for the analysis of forensic stains

We have evaluated oligonucleotide hybridization and amplification techniques with regard to quantity and quality of genomic DNA that is under investigation in practical forensic case work. In order to obtain sufficient information from analyzing stain material, we use hypervariable simple repeat sequences for individualization, which occur in all eukaryotic genomes. For the analysis of larger amounts of stains (greater than 500 ng DNA) the multilocus probes (CAC)5/(GTG)5* are superior because of their discrimination potential--provided that the hybridizing DNA is of high molecular weight. The less discriminating probes (CT)8 and (GACA)4 are more sensitive (minimal amount: 100ng DNA) and still informative when the DNA is degraded. To increase the sensitivity of forensic stain analysis in special cases we have used the polymerase chain reaction technique to amplify hypervariable simple (gt)n/(ga)m repeat structures from the intron 2 of HLA-DRB genes. Largely independent of the starting amount of DNA and independent of the degradation status, we were able to generate discriminating DNA fragments, which can be used to type (i) microstains and (ii) totally degraded material including human mummy DNA.

Highly instable (GATA)n-containing sequences of the mouse during the cloning process

Mouse DNA fingerprints were obtained by HaeIII digestion of genomic DNA and in-gel hybridization with the (GATA)4 oligonucleotide probe. In order to obtain locus-specific probes that hybridize with only one fragment of the (GATA)4 DNA fingerprint, a genomic library of size-selected inserts was constructed using a system of direct subcloning from the phage clones. During the cloning procedure, the phage as well as the plasmid insert DNAs changed primarily within their repetitive DNA but also within adjacent nonrepetitive sequences, as was demonstrated for several clones by in-gel hybridization with the (GATA)4 probe as well as by sequence analysis. Isolated subclones varied within their (GATA)n repeats, resulting in different insert lengths. Several "metastable" as well as stable (GATA)4-positive subclones could be isolated. Also, vector sequences were affected by alterations during the cloning process. These phenomena are discussed within the context of possible mechanisms for cloning artifacts.

Detection of single and multiple polymorphic loci by synthetic tandem repeats of short oligonucleotides

Loci containing tandem repeats of short sequences are sometimes associated with a high level of polymorphism due to variations in the number of repeats. The different variants can be easily characterized by Southern blotting when the repeats span a range from a few hundred bases to a few kilobases, and probes derived from such tandem repeats constitute convenient genetic markers. These structures, usually called minisatellites, are best documented in the human genome, where their number has been estimated to be at least 1500. However, their role and mode of evolution are poorly understood. We are developing tools to evaluate the number of such redundant sequences in a genome and to gain access to new polymorphic loci. Our strategy is based on the use of polymers of oligonucleotides as DNA probes for hybridization on Southern blots. In a previous report, we made polymers with random units of 14 bp and showed that they detect multiple polymorphic loci on human genomic DNA. At present, we are testing the effect of an increase in the complexity of the polymer, as obtained by the use of a longer random unit, and the effect of slight sequence modifications to a particular tandem repeat sequence. In addition, some of these synthetic probes can detect a single polymorphic locus and directly provide new genetic markers.

Monitoring genomic alterations with a panel of oligonucleotide probes specific for various simple repeat motifs

Germline and somatic instability of the human genome was studied, using synthetic oligonucleotides specific for simple repeat motifs. The following probes were used: (GTG)5, (GACA)4, (GATA)4, (CT)8, (TTAGGG)3, (GT)8, (GAA)6 and (GGAT)4. Each of them is unique with respect to the target regions recognized in the genome. Thus compilation of the various fingerprint data provides a complex map of the genome (and its deviations). While the fingerprints of differentiated somatic tissues never showed any alterations, in tumor tissues (namely gliomas) many changes could be detected. Most of the latter reflect secondary karyological aberrations. In nearly one third of the gliomas, drastically amplified and apparently monomorphic DNA fragments were identified. This marker should make it possible to deal with causal pathogenetic mechanisms as well as novel diagnostic strategies.

Oligonucleotide fingerprinting with (CAC)5: nonradioactive in-gel hybridization and isolation of individual hypervariable loci

The first topic to be treated in this paper is the nonradioactive DNA fingerprinting by means of in-gel hybridization with digoxigenated (CAC)5. Besides the fact that time-consuming Southern blotting can be avoided, the dried agarose is an excellent matrix to produce background-free nonradioactive DNA fingerprints. There is no tendency of either the oligonucleotide probe or the antibody towards unspecific binding to the dried agarose. Prehybridization and blocking steps are therefore superfluous. Furthermore, we will discuss what effect the degree of crosslinking of the antibody-enzyme conjugates has. The second topic concerns the isolation and characterization of locus-specific probes from a human (CAC)5 fingerprint. The isolation and characterization of one variable probe, by screening complete genomic libraries, is described and discussed. This probe is compared to a hypervariable single-copy probe, isolated from a size-enriched genomic library. The sequence of the repeat flanking locus-specific probe is presented and a semi-specific, adaptor-mediated polymerase chain reaction was designed to amplify (CAC)n/(GTG)n flanking sequences.

Genome scanning by two-dimensional DNA typing: the use of repetitive DNA sequences for rapid mapping of genetic traits

The existence of repetitive DNA sequences offers the possibility to assess the mammalian genome for individual variation in its entirety rather than at one or only a few sites. In order to fully explore the various sets of mammalian repeat sequences for this purpose, analytical tools are required which allow many if not all individual members of sets of repetitive elements to be resolved and identified in terms of location and allelic variation. We have applied and further developed an electrophoretic system, two-dimensional DNA typing, which may fulfill these requirements. The two-dimensional system combines separation of DNA fragments by size in a neutral gel, with separation by sequence composition in a denaturing gradient gel. By hybridization with minisatellite- and simple-sequence core probes and by inter-repeat polymerase chain reaction techniques, it is possible to obtain individual--and even chromosome-specific separation patterns that consist of hundreds of spots. Computerized image analysis and matching of such spot patterns allows the rapid assessment of multiple polymorphisms, spread over the genome, to monitor genetic variability in populations. When coupled to databases of polymorphic DNA markers with a known genomic location, two-dimensional DNA typing can greatly accelerate the mapping of genetic traits in humans, animals, and plants.

Chromosomal organization of simple repeated DNA sequences used for DNA fingerprinting

Stretches of short, simple DNA sequences are widespread in all eukaryote genomes studied so far. Simple sequences are thought to undergo frequent expansion and deletion due to intrinsic genomic mechanisms. Some of the simple sequences were used successfully to detect hypervariable loci in various genomes. Hybridization experiments using synthetic probes not only revealed the informative simple repeats suitable for DNA fingerprinting in a particular species, but also reflected the wide range of distribution of the simple sequences among eukaryotes. The organization of these simple repetitive sequences at the chromosomal loci was investigated using in situ hybridization with chemically synthesized, pure oligonucleotide probes. Both biotin- and digoxigenin-attached probes detected specific chromosomal sites that are enriched in the respective simple-repeat blocks. Depending on the organism and probe used, accumulation of simple DNA sequences at individual or multiple sites on the chromosomes of different vertebrates could be demonstrated. The simple repetitive DNA sequences are located in different chromosomal regions (e.g., heterochromatin on the sex chromosomes, nucleolus organizer regions, and R-band sites), which are constrained considerably during evolution.

Nonradioactive labeling of oligonucleotides in vitro with the hapten digoxigenin by tailing with terminal transferase

A procedure for the nonradioactive labeling of oligonucleotides with the hapten digoxigenin (DIG) has been developed. The label is introduced by enzymatic tailing of the 3'-end. Two different modified nucleotides were applied. DIG-dUTP allows the synthesis of hapten-modified oligonucleotides with longer tails containing several DIG molecules, whereas the novel compound DIG-ddUTP leads to the addition of only a single DIG hapten. The efficiency of the labeling reactions with respect to variation of the different parameters was analyzed and data on application of labeled oligonucleotide probes to different blot formats are shown.

Oligonucleotide fingerprinting using simple repeat motifs: a convenient, ubiquitously applicable method to detect hypervariability for multiple purposes

A panel of simple repetitive oligonucleotide probes has been designed and tested for multilocus DNA fingerprinting in some 200 fungal, plant and animal species as well as man. To date at least one of the probes has been found to be informative in each species. The human genome, however, has been the major target of many fingerprinting studies. Using the probe (CAC)5 or (GTG)5, individualization of all humans is possible except for monozygotic twins. Paternity analyses are now performed on a routine basis by the use of multilocus fingerprints, including also cases of deficiency, i.e. where one of the parents is not available for analysis. In forensic science stain analysis is feasible in all tissue remains containing nucleated cells. Depending on the degree of DNA degradation a variety of oligonucleotides are informative, and they have been proven useful in actual case work. Advantages in comparison to other methods including enzymatic DNA amplification techniques (PCR) are evident. Fingerprint patterns of tumors may be changed due to the gain or loss of chromosomes and/or intrachromosomal deletion and amplification events. Locus-specific probes were isolated from the human (CAC)5/(GTG)5 fingerprint with a varying degree of informativeness (monomorphic versus truly hypervariable markers). The feasibility of three different approaches for the isolation of hypervariable mono-locus probes was evaluated. Finally, one particular mixed simple (gt)n(ga)m repeat locus in the second intron of the HLA-DRB genes has been scrutinized to allow comparison of the extent of exon-encoded (protein-) polymorphisms versus intronic hypervariability of simple repeats: adjacent to a single gene sequence (e.g. HLA-DRB1*0401) many different length alleles were found. Group-specific structures of basic repeats were identified within the evolutionarily related DRB alleles. As a further application it is suggested here that due to the ubiquitous interspersion of their targets, short probes for simple repeat sequences are especially useful tools for ordering genomic cosmid, yeast artificial chromosome and phage banks.

A human XY female with a frame shift mutation in the candidate testis-determining gene SRY

The primary decision about male or female sexual development of the human embryo depends on the presence of the Y chromosome, more specifically on a gene on the Y chromosome encoding a testis-determining factor, TDF. The human sex-determining region has been delimited to a 35-kilobase interval near the Y pseudoautosomal boundary. In this region there is a candidate gene for TDF, termed SRY, which is conserved and specific to the Y chromosome in all mammals tested. The corresponding gene from the mouse Y chromosome is deleted in a line of XY female mutant mice, and is expressed at the expected stage during male gonadal development. We have now identified a mutation in SRY in one out of 12 sex-inversed XY females with gonadal dysgenesis who do not lack large segments of the short arm of the Y chromosome. The four-nucleotide deletion occurs in a sequence of SRY encoding a conserved DNA-binding motif and results in a frame shift presumably leading to a non-functional protein. The mutation occurred de novo, because the father of the sporadic XY female that bears it has the normal sequence at the corresponding position. These results provide strong evidence for SRY being TDF.

Stain analysis using oligonucleotide probes specific for simple repetitive DNA sequences

The use of oligonucleotide fingerprinting is evaluated in practical forensic work, using both artificially and systematically produced stains as well as actual case work material. The probes (CAC5/(GTG)5 are superior because of their individualizing potential in comparatively fresh specimens with little DNA degradation, whereas (GACA)4, still produces substantial information when high molecular weight DNA is lacking. The overall limitations and the advantages of this technology are discussed in detail and compared to the classical minisatellite probes.

Heterogeneities in the distribution of (GACA)n simple repeats in the karyotypes of primates and mouse

Tandemly organized simple repetitive sequences are widespread in all eukaryotes. The organization of the simple tetrameric (GACA)n sequences at chromosomal loci has been investigated using in situ hybridization with chemically pure oligonucleotide probes. Both biotin- and digoxigenin-attached (GACA)4 probes reveal specific hybridization signals over the short arms of all acrocentric autosomes in man. In the other examined primates the NOR-bearing autosomes could be detected by in situ hybridization with (GACA)4, and a major concentration of the GACA simple repeats could be observed on the Y chromosome in the gibbon and mouse: the hybridization site in the gibbon Y chromosome coincides particularly with the silver-stainable NOR. In the past, accumulations of (GACA)n sequences were demonstrated mainly on vertebrate sex chromosomes. Therefore, the organization of GACA simple sequences is discussed in the context of their evolutionary potential accumulation and the possible linkage with the primate rDNA loci.