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PubMed1996

Marker pattern instabilities as a major cause of reproducibility problems in two-dimensional DNA fingerprinting.

Two-dimensional (2-D) DNA fingerprinting is a promising technique for multilocus analysis of eukaryotic genomes. It has been successfully applied to the detection of DNA variation in tumors, to linkage analyses and to genomic comparisons of inbred mouse strains. However, there are still problems with inter-gel comparisons of 2-D DNA typing patterns as documented by the inter-gel reproducibility rates reported in the literature, which range from 84 to 98%. The basis for standardization in almost all of these studies has been a set of lambda fragments (digested separately with the restriction enzymes HaeIII, RsaI, Bg/I) that produces a spot pattern scattered across the gel. These spots are used as markers for gel comparisons. Since we noticed considerable variations in the marker spot patterns, we evaluated the properties of the lambda marker using both computer simulation and an empirical analysis of forty independent consecutive gels from our laboratory. We explain the instabilities of the spot pattern on the basis of the melting properties of the individual lambda fragments. A subset of spots is presented that has been stable in all our experiments. Only this set of spots should be used for gel standardization purposes until a new, completely reproducible marker becomes available. Finally, suggestions for an improved marker system are made.

Bacteriophage lambda↗

PubMed1989

Analysis of DNA fingerprinting data in cases of disputed paternity.

DNA fingerprinting is proving to be of great use in the establishment of the relatedness between individuals. Models are presented to assess the probabilities of DNA fingerprints as a means of establishing the paternity of a disputed offspring. The simplest models make a variety of unrealistic assumptions and an outline is presented of how the assumptions of fingerprint band population frequency equality and mutation rate constancy can be relaxed to produce a more realistic and powerful model.

DNA Fingerprinting↗

PubMed1996

DNA fingerprinting of benign and malignant breast lesions.

Paired blood and breast tissue samples from 96 patients undergoing surgical excision of a breast lesion were subjected to DNA fingerprint analysis using the minisatellite probes 33.6 and 33.15. The 'fingerprints' of the blood and breast DNA were compared. DNA fingerprint changes seen were classified as band additions, band deletions or changes in band intensity. Significantly more DNA fingerprint changes were seen in malignant than in benign lesions (probe 33.6, P<0.01; probe 33.15, P=0.01; both probes, P = 0.04). The frequency of the changes detected in the breast cancers was unrelated to tumour grade or the presence of invasion. DNA ploidy was measured in 70 of the breast carcinomas. DNA fingerprint changes were seen in 41 of these, but flow cytometry detected aneuploidy in only 29 tumours (P=0.04). The DNA fingerprinting technique is unlikely to be useful in differentiating between benign and malignant breast lesions as changes were detected in one of the fibroadenomas studied. However, it may be a useful technique in screening tumour DNA for abnormalities suitable for more detailed analysis.

Breast Diseases↗

PubMed1988

DNA fingerprints: the importance in forensic medicine. II. The significance of examining DNA polymorphisms of placental tissues for the purpose of paternity determination during the early stages within the first trimester.

Investigation of genomic polymorphisms detected by a minisatellite named tentatively "Myo", which is expected to correspond to the minisatellite in human myoglobin gene of Jeffreys et al., gives distinct and different aspects of chorionic villus and the decidual membrane in the same placenta. The chorionic villus, which is regarded as the extraembryonal tissue, represents the essential embryonal DNA fingerprint pattern, while the decidual membrane reveals the maternal one. A comparison between the DNA fingerprints from the chorion villus and from the blood sample of the suspected father provides the possibility of setting a paternity determination which can be achieved during the first trimester of a pregnancy.

Base Composition↗

PubMed1992

DNA fingerprinting in the Chinese with an oligonucleotide probe (GTG)5.

DNA fingerprinting is a very powerful tool that enables specific identification of individuals. In order to study fingerprinting patterns in the Chinese, the oligonucleotide probe designed by Epplen et al was used. Peripheral blood leukocyte DNA was digested with restriction enzyme Hinf I and probed by (GTG)5. Normal females and males were tested; all revealed very different DNA fingerprints. Most of the discernible bands in the gel were polymorphic; there was no specific association between any polymorphic band and the sex of the individual tested. In situ gel-hybridization was used with the oligonucleotide probe, and after electrophoresis, all procedures could be completed within one working day. Three patients who had received bone marrow transplants from their respective siblings had the same fingerprints as their donors. The inheritance of all bands from either the father or mother proved parents' authenticity. DNA fingerprinting with a oligonucleotide probe is obviously a useful technique. Clinical application may include engraftment monitoring, zygosity determination and paternity testing.

Base Sequence↗

PubMed2002

Spontaneous and bleomycin-induced genomic alterations in the progeny of Drosophila treated males depends on the Msh2 status. DNA fingerprinting analysis.

Deficiency in DNA mismatch repair (MMR) confers instability of simple repeated sequences and increases susceptibility to cancer. Some of the MMR genes are also implicated in other repair and cellular processes related to DNA damage response. Supposedly, lack of their function can lead to a global genomic instability, besides microsatellite instability (MSI). To study the spontaneous and induced genomic instability in germ cells, related to the Msh2 status, DNA alterations in the progeny of individual crosses of Drosophila deficient in one or two copies of the Msh2 gene, were analysed by the arbitrarily primed polymerase chain reaction (AP-PCR). The results indicate that the progeny of homozygous parents for the normal Msh2 allele (+/+) presents a significantly lower frequency of genomic alterations than those from heterozygous (+/-) or mutant homozygous (-/-) parents. In addition, the DNA damage transmitted to the progeny, after the adult parental males were exposed to bleomycin, indicates that whereas the induction of mutations related to MSI depends on the lack of the Msh2 function, the induction of other mutational events may require at least one functional Msh2 allele. Thus, the results obtained with heterozygous individuals may have special relevance for cancer development since they show that a disrupted Msh2 allele is enough to generate genomic instability in germ cells, increasing the genomic damage in the progeny of heterozygous individuals. This effect is enhanced by mutagenic stress, such as occurs after bleomycin exposure.

Animals↗

PubMed1997

Characterization of leptospiral serovars by randomly amplified polymorphic DNA fingerprinting.

Randomly amplified polymorphic DNA (RAPD) fingerprinting of 14 laboratory strains of leptospiral serovars (serovars australis, autumnalis, ballum, bataviae, canicola, grippotyphosa, hardjoprajitno, hebdomadis, icterohaemorrhagiae, javanica, pomona, pyrogenes, panama, and tarassovi) was carried out by using a pair of primers. Each serovar had a unique and distinct fingerprint pattern. DNAs of other bacterial species, including Escherichia coli, Pasteurella multocida, Salmonella spp., Pseudomonas spp., and Klebsiella spp., did not show any amplification. RAPD fingerprinting was found to be a rapid and sensitive method for serovar identification when it was compared to DNA restriction enzyme analysis, which produced a larger number of bands that made it more difficult to compare serovars.

Base Sequence↗

PubMed1994

A rapid and simple DNA fingerprinting method using RFLP and SSCP analysis of the hypervariable noncoding region of human mitochondrial DNA.

A simple method for identification of individuals and maternity testing has been developed. This technique includes PCR amplification of the 199-bp hypervariable portion of the noncoding region of human mtDNA, digestion with RsaI and subsequent SSCP analysis of restriction fragments with DNA silver staining. Using this approach we have analysed the DNA fingerprint patterns of the family members. The fingerprints of maternally related individuals appeared to be identical in three generations, while maternally unrelated members of the family showed differences in their fingerprints, either in SSCP or both RFLP and SSCP patterns. Sequencing data have confirmed the results obtained. Further DNA fingerprinting analysis of 19 unrelated mother-child pairs by means of the method described revealed complete identity of the fingerprint patterns within the pairs. The probability of a random fingerprint match for two maternally unrelated individuals was estimated as 8%.

Adult↗

PubMed1992

DNA fingerprinting in non-human populations.

DNA fingerprinting of non-human populations is beginning to fulfill its early promise, and in the past year there has been a flush of papers on mammalian breeding systems. However, many people, particularly field workers, believe that progress in this area has been slow. Attention is now focused on two amenable alternatives: microsatellite polymorphisms and randomly amplified polymorphic DNA. Of these, it is probable that microsatellites hold the key to rapid, efficient and highly informative screening of the genetic variability that exists within natural populations.

Animals↗

PubMed1998

Somatic DNA alterations in breast carcinomas of different lymph-node status by DNA fingerprint analyses.

The purpose of this study was to screen for somatic changes in invasive breast tumors by multilocus DNA fingerprints comparing normal (blood) and malignant tissue samples from 34 patients. The comparison of lymph node-positive and node-negative breast carcinomas was of primary interest. After restriction enzyme digestion with HinfI and HaeIII, altered banding patterns were detected by using the oligonucleotide probe (GTG)5 in 7 of 34 (20.5%) and in 3 of 34 (8.8%) tumors after hybridization with (GACA)4. The overall frequency of changes thus amounted to 29.4%. Because long (GACA)n repeat motifs, generating predominant DNA fingerprint bands, are localized on the short arms of the human acrocentric chromosomes, sequences that are important in breast carcinogenesis may be present in these regions. The overall methylation status of the DNA does not appear to be responsible for DNA fingerprint differences, as can be demonstrated with the restriction endonuclease HaeIII. DNA fingerprint differences did not correlate with tumor grade, stage, and hormone receptor status. Tumors with lymph-node metastases expressed DNA fingerprint differences more frequently.

Aged↗

PubMed1997

PCR-based DNA fingerprinting of Staphylococcus haemolyticus to investigate nosocomial infections.

OBJECTIVE: To apply PCR-based DNA fingerprinting in a clinical microbiology laboratory to investigate nosocomial infections with Staphylococcus haemolyticus. METHODS: DNA fingerprints were generated by PCR on 99 S. haemolyticus isolates using different primer combinations based on ERIC, REP or arbitrarily chosen simple repeat sequences. RESULTS: Primer combinations REP1+(GTC)6 and ERIC1+ERIC2 had sufficient discrimatory power and were chosen to analyze the clinical isolates. DNA fingerprint patterns from strains isolated from the patients nursed in the same hospital ward in the period 1991--94 were approximately 90% similar to each other. One staff member, sampled in 1991, carried a strain with a similar fingerprint. CONCLUSIONS: PCR based DNA fingerprinting is a suitable method to perform in a clinical laboratory. An S. haemolyticus strain appeared to be endemic in the hospital ward and had most probably been transmitted from patient to patient. S. haemolyticus may carry glycopeptide resistance and needs attention as a causative agent of nosocomial infections.

Journal Article↗

PubMed2006

DNA fingerprinting in the criminal justice system: an overview.

DNA fingerprinting is a powerful technology that has revolutionized forensic science. No two individuals can have an identical DNA pattern except identical twins. Such DNA-based technologies have enormous social implications and can help in the fight against crime. This technology has experienced many changes over time with many advancements occurring. DNA testing is a matter of serious concern as it involves ethical issues. This article describes various trends in DNA fingerprinting and the current technology used in DNA profiling, possible uses and misuses of DNA databanks and ethical issues involved in DNA testing. Limitations and problems prevailing in this field are highlighted.

Criminal Law↗

PubMed1991

Chromosomal DNA fingerprint patterns produced with IS6110 as strain-specific markers for epidemiologic study of tuberculosis.

Mycobacterium tuberculosis isolates were studied by comparing chromosomal DNA fingerprint patterns produced by digestion of chromosomal DNA with BamHI, followed by agarose electrophoresis and hybridization with radiolabeled probes of insertion sequence IS6110. DNA fingerprints of 14 isolates from separate members of five households or closely associated individuals were compared. Marked differences were observed when unrelated isolates were compared. There were no or minimal differences in the restriction fragment patterns generated from isolates of any one household or associated group. Among related isolates, the only noticeable difference was an additional fragment of IS6110 in the fingerprint pattern of one isolate. Insertional activity was also suggested when restriction fragment patterns of H37Rv DNA isolated in 1987 and 1990 were compared. In a similar manner, M. tuberculosis reference strain Erdman was compared to a clinical isolate from an individual working with that strain. These isolates had identical DNA fingerprints which were distinct from all other isolates, verifying laboratory-acquired infection. Chromosomal DNA fingerprint patterns produced with IS6110 are excellent stain-specific markers for the epidemiologic study of tuberculosis.

DNA Fingerprinting↗

PubMed1993

Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology.

DNA fingerprinting of Mycobacterium tuberculosis has been shown to be a powerful epidemiologic tool. We propose a standardized technique which exploits variability in both the number and genomic position of IS6110 to generate strain-specific patterns. General use of this technique will permit comparison of results between different laboratories. Such comparisons will facilitate investigations into the international transmission of tuberculosis and may identify specific strains with unique properties such as high infectivity, virulence, or drug resistance.

Base Sequence↗

PubMed1995

Interstrain polymorphisms of isoenzyme profiles and mitochondrial DNA fingerprints among seven strains assigned to Acanthamoeba polyphaga.

Interstrain polymorphisms of isoenzyme profiles and mitochondrial (Mt) DNA fingerprints were observed among seven strains of Acanthamoeba isolated from different sources and morphologically assigned to A. polyphaga. Mt DNA fingerprints by eight restriction endonucleases (Bgl II, Sca I, Cla I, EcoR I, Xba I, Kpn I, Sal I, and Sst I) revealed considerable interstrain polymorphisms. Isoenzyme profiles revealed considerable interstrain polymorphisms for acid phosphatase, lactate dehydrogenase, and glucose-6-phosphate dehydrogenase while those for glucose phosphate isomerase, leucine aminopeptidase, and malate dehydrogenase showed similarity. Despite of the interstrain polymorphisms, the isoenzyme profiles and Mt DNA fingerprints of the strain Ap were found to be identical with those of the strain Jones. Mt DNA fingerprinting was found to be highly applicable for the strain identification, characterization, and differentiation.

Acanthamoeba↗

PubMed1994

Minisatellite DNA markers in the chicken genome. I. Distribution and abundance of minisatellites in multilocus DNA fingerprints.

This paper reports the detailed characterization of multilocus minisatellite DNA fingerprints in the chicken. Results are presented of DNA fingerprint segregation analyses carried out in three chicken pedigrees, calculating the number of detected loci, testing for Mendelian inheritance, and cosegregation among fingerprint bands. Two pedigrees (families 1 and 2) were analysed using the Jeffreys probes 33.6 and 33.15 only, and one pedigree (family 3) was analysed using 33.6, 33.15, 3' alpha-globin HVR and M13 protein III gene repeat. Mean band transmission frequencies in families 1 and 2 were near to the Mendelian expectation of 0.5 and no mutations were observed. Family 3 showed transmission frequencies slightly exceeding 0.5. Linkage among bands was higher than observed in some other avian species, with each allele represented by a mean of 1.48 HaeIII fragments. Cosegregation of heterozygous parental fragments representing distinguishable loci followed the expected binomial distribution. The number of minisatellites detectable by the four probes was estimated to be 217. The pattern of cosegregation among those minisatellite loci was tested against that expected for different levels of recombination through the use of a simulation model. We conclude that most minisatellites are unlinked and probably widely dispersed in the chicken genome.

Animals↗

PubMed1996

A comparative study of different PCR-based DNA fingerprinting techniques for typing of the Acinetobacter calcoaceticus-A. baumannii complex.

Different PCR-based DNA fingerprinting techniques were evaluated for typing 26 clinical isolates belonging to the Acinetobacter calcoaceticus-A. baumannii complex. Seven isolates belonged to a previously defined outbreak while 19 isolates were unrelated epidemiologically. The PCR-based DNA fingerprinting techniques used were: (i) repetitive extragenic palindromic (REP) PCR; (ii) enterobacterial repetitive intergenic consensus (ERIC) PCR; (iii) randomly amplified polymorphic DNA with M13 forward primer; (iv) restriction analysis of the amplified 16S rRNA gene (ARDRA-16S); and (v) restriction analysis of an amplified region containing the 16S-23S rRNA spacer region and part of the 23S rRNA gene (ARDRA 23S + spacer). The discrimination index for the PCR-based DNA fingerprinting techniques was: 0.99 for REP; 0.94 for ERIC; 0.87 for M13; 0.60 for ARDRA-16S digested with Hpa II and <0.50 for ARDRA 23S + spacer. It was concluded that REP-PCR possessed high discriminatory power and reproducibility in comparison with the other PCR-based DNA fingerprinting techniques, and is a simple and rapid typing method for use in epidemiological studies of isolates belonging to the A. calcoaceticus-A. baumannii complex.

Acinetobacter↗

PubMed1990

Characterization of human glioblastoma cell lines in vitro and their xenografts in nude mice by DNA fingerprinting.

Human gliomas were grown as permanent tissue cultures and xenografts in nude mice. DNA fingerprint patterns from two human gliomas were established using two different hypervariable multilocus probes [( GTG]5 and 33.15). In general the cell lines investigated showed an overall stability in the DNA fingerprint pattern. However, differences in the DNA fingerprint patterns were shown to occur depending upon the above mentioned parameters.

Animals↗