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PubMed1995

Vertical transmission of Citrobacter diversus documented by DNA fingerprinting.

OBJECTIVE: To confirm the vertical transmission of Citrobacter diversus from a mother to her infant and to evaluate the epidemiologic usefulness of a new automated procedure for analysis of polymerase chain reaction (PCR)-generated DNA fingerprints. DESIGN: Repetitive element-based PCR (rep-PCR) analysis of C diversus isolates from the blood and amniotic fluid of a mother and the blood of her infant was performed. Unrelated C diversus isolates also were characterized and compared with the isolates from mother and infant. DNA fingerprints were generated by gel electrophoresis of PCR products derived from either unlabeled standard repetitive sequence-based oligonucleotide primers or fluorescent primers. The standard rep-PCR fingerprints were analyzed by visual inspection. The fluorescent primers were used in fluorophore-enhanced rep-PCR (FERP), and the FERP DNA fingerprints were analyzed by an Applied BioSystems (ABI) Model 373A laser scanning unit equipped with Genescan 672 software (Applied Biosystems, Inc, Foster City, CA). SETTING AND PATIENTS: A mother and her newborn infant, both with invasive disease due to C diversus, in an urban tertiary-care hospital. RESULTS: The DNA fingerprints of the maternal blood, amniotic fluid, and infant blood isolates of C diversus were identical by both visual inspection of ethidium bromide-stained agarose gels and computer-aided analysis of FERP patterns. These strains appeared to differ from all but one control isolate, which had been collected 7 years earlier in the same city in which the infant was born. CONCLUSIONS: Vertical transmission of C diversus from mother to infant can occur in utero. Automated analysis of rep-PCR-generated DNA fingerprints derived using fluorescent primers is an objective means for comparing isolates of C diversus and in all likelihood would be useful for other species of bacteria that possess repetitive elements.

Adult↗
PubMed1992

DNA fingerprinting of freeze-dried tissues.

DNA profiling is usually unproblematic when carried out on material sampled shortly after death. Prolonged postmortem intervals and improper storage cause significant DNA degradation, however there are instances where DNA analysis becomes necessary months after the autopsy. In such cases the investigator may be able to revert to material initially stored for toxicological purposes. In some cases such specimens undergo freeze-drying before storage. We have therefore tested DNA fingerprinting of freeze-dried postmortem material. It was found that freeze-drying is a suitable method for preserving tissue samples for DNA profiling.

DNA Fingerprinting↗
PubMed1992

On the probability of matching DNA fingerprints.

Forensic scientists commonly assume that DNA fingerprint patterns are infrequent in the general population and that genotypes are independent across loci. To test these assumptions, the number of matching DNA patterns in two large databases from the Federal Bureau of Investigation (FBI) and from Lifecodes was determined. No deviation from independence across loci in either database was apparent. For the Lifecodes database, the probability of a three-locus match ranges from 1 in 6,233 in Caucasians to 1 in 119,889 in Blacks. When considering all trios of five loci in the FBI database, there was only a single match observed out of more than 7.6 million comparisons. If independence is assumed, the probability of a five-locus match ranged from 1.32 x 10(-12) in Southeast Hispanics to 5.59 x 10(-14) in Blacks, implying that the minimum number of possible patterns for each ethnic group is several orders of magnitude greater than their corresponding population sizes in the United States. The most common five-locus pattern can have a frequency no greater than about 10(-6). Hence, individual five-locus DNA profiles are extremely uncommon, if not unique.

Black People↗
PubMed1991

DNA fingerprinting; a biotechnology in business.

Since its discovery by Professor Alec Jeffreys, first published in 1985, DNA fingerprinting has never been far from the headlines. Cellmark, as the leading commercial DNA fingerprinting enterprise, has had the challenge of establishing its business in this high profile environment. The challenge for such a business has had three elements. Firstly and primarily to establish a laboratory system that consistently provides results to the highest standards possible. Secondly to communicate the science to its broad customer base which ranges from the general public to the experts of legal, scientific and governmental systems. Then finally there is the challenge of setting up the business in the context of the volatile, venture-capital based biotechnology market where the requirements for assured quality spar with those for cut prices. Given this backdrop it is not surprising that DNA fingerprinting has had its detractors, yet the consensus of opinion is that this technology has become a near routine business with the challenges effectively met and the success that was hoped for.

Biotechnology↗
PubMed1998

Use of DNA fingerprinting to detect genotoxic effects.

The effects of environmental pollutants on organisms may be monitored in a number of ways and at different levels. In the case of genotoxic chemicals, the effects on the DNA may be monitored using a number of biomarker assays capable of detecting phenotypic changes as a result of mutation, gross chromosomal abnormalities, unscheduled DNA synthesis, DNA adducts (e.g., by 32P postlabeling or by ELISA) and DNA strand breaks (e.g., by the alkaline unwinding assay or the comet assay); the sensitivity and specificity of these assays are variable. Recent developments in molecular biology such as DNA fingerprinting and gene amplification by the polymerase chain reaction (PCR) offer new possibilities for detecting DNA damage. In this laboratory, whether an alternative biomarker assay (using DNA fingerprinting by arbitrarily primed PCR) can reveal differences in the DNA fingerprints of individuals from control and polluted areas was investigated. The results indicate that DNA fingerprinting by arbitrarily primed PCR offers a useful alternative biomarker assay for detection of the genotoxic effects of environmental pollutants.

Animals↗
PubMed2000

A prospective evaluation of the clinical value of nation-wide DNA fingerprinting of tuberculosis isolates in Denmark.

SETTING: Denmark, a country with a low incidence of tuberculosis (TB). OBJECTIVE: To evaluate the value of the nation-wide DNA fingerprinting of Mycobacterium tuberculosis isolates performed in Denmark since 1992. DESIGN: Prospective study of consecutive patients with culture-verified TB from five large TB Departments in Denmark during a 7-month period in 1998. Results of IS6110 RFLP and spoligotyping were compared to those in the nation-wide Danish DNA-fingerprint database which covers approximately 95% of all culture-verified TB cases from 1992 onwards. Questionnaires asking about contact tracing and epidemiological links were sent to the patients' treating physicians. RESULTS: Of the 177 patients included in the study, 57 were Danes, one was from Iceland, 111 were immigrants, and eight were from Greenland. Responses to the questionnaires were obtained from 163 patients (92%). Four cases of unsuspected transmission were detected: one of nosocomial spread of TB, one of occupational acquisition of TB and two of transmission in an international school, leading to further contact tracing among 75 schoolchildren. These four cases were all the result of short-term contacts. In 22 cases, contact with one or more TB patient(s) was reported. In six of these, the DNA-fingerprint result revealed that the presumed contact could not be the source of infection, even though in two of the cases the known TB contact was from the household. CONCLUSION: Nation-wide DNA fingerprinting of TB isolates provides information that could not have been obtained otherwise, and contribute to the understanding of TB transmission in Danish society. In some cases the results lead to further contact tracing. Short-term contact can apparently result in transmission of TB.

Adult↗
PubMed1989

DNA fingerprinting of spontaneously hypertensive and Wistar-Kyoto rats: implications for hypertension research.

Probes to hypervariable minisatellite regions of DNA identify multiple loci scattered over the autosomal chromosomes and produce a complex Southern blot pattern of fragments termed a DNA 'fingerprint'. As concern has been raised that different stocks of spontaneously hypertensive rats (SHR) and Wistar-Kyoto rats (WKY) may not be biologically identical, we have compared the DNA of SHR and WKY from several sources using two such probes which identify different sets of minisatellite sequences. While the DNA fingerprints of SHR from the various sources were identical, variability was observed in those of WKY, indicating genetic heterogeneity between different WKY stocks. In animals from one of the commercial suppliers even inter-rat variability in DNA fingerprints was seen, suggesting genetic heterogeneity within that single colony. These observations indicate that experimental results obtained using WKY from different sources may not be directly comparable and could provide an explanation for some of the conflicting data that exist on the comparative characteristics of SHR and WKY. In separate studies, direct comparisons both of the DNA fingerprints of SHR and WKY and of SHR and stroke-prone spontaneously hypertensive rats (SHRSP) showed multiple differences between the strains. The polymorphisms seen could provide useful linkage markers in locating the chromosomal sites of the genetic loci responsible for raised blood pressure in the SHR and the propensity to strokes in the SHRSP.

Animals↗
PubMed1996

Analysis of production brewing strains of yeast by DNA fingerprinting.

Production brewing strains of the yeast Saccharomyces cerevisiae were analysed by DNA fingerprinting, using a Southern blotting and hybridization procedure and employing the Ty1-15 transposon as a probe. The ability to differentiate readily between strains was very dependent on the restriction enzyme used to digest the DNA prior to Southern blotting and hybridization; the enzymes EcoRI, PstI and SalI were found to be particularly useful in this respect. The method was applicable to the differentiation of both ale and lager yeasts, and was sufficiently sensitive to distinguish between very closely related strains. DNA fingerprinting by this approach confirmed, for example, that a flocculent strain isolated during a production-scale fermentation with a lager yeast was genotypically different from the parent.

Base Sequence↗
PubMedDate not supplied

The use of biotyping and DNA fingerprinting in typing Candida albicans from hospitalized patients.

The application of typing procedures for the purpose of strain differentiation among isolates of Candida albicans obtained from hospitalized patients has been limited. We have applied biotyping and DNA restriction fragment analysis (DNA fingerprinting) by using EcoRI to the study of C. albicans isolates obtained from hospitalized patients. A total of 68 isolates from 15 patients were studied. Thirteen subtypes were identified by biotyping, 8 by DNA fingerprinting, and 21 by a combination of the biotyping and DNA fingerprinting approaches (composite subtype). Both techniques were highly reproducible. In examining the strain variation among isolates obtained from multiple anatomic sites over time, we found that similar, if not identical, strains were recovered from the oropharynx, urine, stool, and blood in a given patient, and these strains persisted. Only rarely did two patients share the same composite subtype suggesting sporadic nosocomial transmission. The combination of biotyping and DNA fingerprinting improved strain discrimination compared to either method alone. Further investigation with these and other epidemiologic typing methods will be necessary to enhance the understanding of the epidemiology and pathogenesis of candidiasis in hospitalized patients.

Bacterial Typing Techniques↗
PubMed2002

Application of DNA fingerprinting in medicolegal practice.

Fingerprinting is thought to establish the identify of an individual in forensic cases. The technique is extensively used for forensic purposes. Deoxyribonucleic acid (DNA) is the vehicle of generational transference of heritable unit. While arching markers for genetic disease professor Alec Jeffreys discovered that certain regions of DNA showed variations in the number of tandem repeats known as variable number of tandem repeats (VNTRs). Thus DNA fingerprint was named by observing the number of repeated sequences which differ from individual to individual. The structure of DNA is quite flexible, within the nucleus of each cell resides an identical copy of the individual's genetic material, DNA. The coding regions of the genomic DNA are known as genes. The DNA fingerprinting in forensic science has generated considerable excitement in the criminal justice community. DNA fingerprinting can be applied to identify an individual in criminal and civil cases. Polymerase chain reaction has revolutionised molecular biology it has an ability to amplify (usually fewer than 3000 bp) a particular sequence of DNA into million of copies in a very short period. Consequently only a very tiny amount of an organism's DNA needs to be available originally. This property of polymerase chain reaction has enabled to analyse many forensic samples particularly which are degraded. Microsatellite DNA or commonly as short tandem repeats are scattered throughout the human genome and occur on an average of every 10,000 nucleotides. Microsatellite markers are considered to be the most powerful genetic markers. Collection, preservation and handling are the integral part of DNA fingerprinting analysis. There are various methods to isolate DNA from different biological materials but presently most of the laboratories prefer using FTA paper. The age of humans can be estimated by using DNA based on telomere shortening.

Clinical Medicine↗
PubMed1997

Assessment of genomic damage in colorectal cancer by DNA fingerprinting: prognostic applications.

PURPOSE: Here we evaluate the prognostic significance of the relative value of genomic damage assessed by DNA fingerprinting in colorectal cancer. MATERIALS AND METHODS: Sixty-three tumor and paired normal mucosa samples were included in the study. Genomic damage was assessed by comparative analysis of paired normal and tumor tissue DNA fingerprints by the arbitrarily primed polymerase chain reaction (AP-PCR). Decreases and increases of intensity in bands were computed and referred to the total number of visualized bands per case. An index reflecting the genomic damage fraction (GDF), with separated values for losses and gains, was obtained for each tumor. This index was used to determine molecular and clinicopathologic correlates after exclusion of eight cases displaying microsatellite instability. RESULTS: Fifty-five cases were considered for the statistical analysis. The average fraction of altered bands per tumor was 0.287+/-0.121. When losses and gains were computed separately, the average fraction of changes was 0.126+/-0.113 and 0.161+/-0.120, respectively. Tumors lacking a ras mutation showed an increased GDF, primarily because of a higher fraction of gains. Tumors that were at advanced Dukes' stages and that were poorly differentiated also displayed a higher GDF. Finally, disease-free survival was significantly diminished in tumors with a GDF greater than 0.314 (P < .001). The prognostic significance of the GDF was independent of Dukes' stage (Cox multivariate analysis, P = .005). CONCLUSION: The degree of genomic damage assessed by unbiased DNA fingerprinting correlates with genotypic, phenotypic, and clinical variables in colorectal carcinoma and may be useful in assessing prognosis in colorectal cancer.

Aged↗
PubMed1993

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.

Carcinoma, Renal Cell↗
PubMed1995

DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism is useful for yeast typing.

Random amplified polymorphic DNA (RAPD) analysis was applied to genomic DNA from nineteen yeast strains belonging to the genera Saccharomyces and Zygosaccharomyces. Results obtained with five primers indicated that this technique is a powerful tool for yeast differentiation and identification. The data were consistent with those derived from restriction fragment length polymorphism (RFLP) using two S. cerevisiae DNA probes. We conclude that RAPD fingerprinting, combined with the analysis of RFLP, can provide unambiguous type assignment in yeasts.

DNA, Bacterial↗
PubMed1996

Ethical and legal issue raised by DNA fingerprinting in France.

As soon as DNA identification tests have been introduced as a new powerful tool in criminalistics and in paternity testing, this new technology has immediately aroused a mixture of ethical concerns, suspicion and interest among scientists and non-scientists. The major concerns about the so called 'DNA fingerprints' were related first to the possible constitution of data based by the police agencies for the purpose of identifying and investigating individuals as potential criminal suspects, and secondly to the risk of a widespread use without safeguards for private investigation as establishing paternity or the typing of a person for insurance companies. In this context, and in order to preserve civil liberties and the respect of individual privacy, the national Consultative Bioethics Committee advised, as early as 1989, the French government that DNA identification should be strictly limited to judicial use and performed by accredited laboratories. After a long debate, this recommendation has finally been adopted in July, 1994 by the French Parliament. As a result, France is presently the only member state of the European Union with such restricted legislation. This is not without raising difficulties in the implementation of the law, especially in the field of paternity testing where the demand is growing and can be satisfied in any other neighbour country.

Bioethics↗
PubMed1998

A comparative genetic analysis of the Irish greyhound population using multilocus DNA fingerprinting, canine single locus minisatellites and canine microsatellites.

Pairwise analysis of HinfI/33.6 DNA fingerprints from a total of one hundred and fifty-three Irish greyhounds of known pedigree were used to determine band-share estimates of unrelated, first-degree and second-degree relationships. Forty-eight unrelated Irish greyhounds were used to determine allele frequencies for three single-locus minisatellites, and following a preliminary screen, eight of the most polymorphic tetra-nucleotide microsatellites from a panel of 15. The results indicated that both band-share estimates by DNA fingerprinting and microsatellite allele frequencies are highly effective in resolving parentage in this greyhound population, while single-locus minisatellites showed limited polymorphism and could not be used alone for routine parentage testing in this breed. The present study also demonstrated that, to obtain optimal resolution of parentage, sample sets of known pedigree status are required to determine the band-share distribution and/or microsatellite allele frequencies.

Animals↗
PubMed1995

Characterization of a DNA sequence that detects repetitive DNA elements in the Asian rice gall midge (Orseolia oryzae) genome: potential use in DNA fingerprinting of biotypes.

We have isolated based on reverse genome hybridization, and sequenced a DNA clone, pNZE25, from a partial genomic library of the Asian rice gall midge Orseolia oryzae (Wood-Mason) (O.o.). Clone pNZE25 is highly A+T rich (67%), lacks any open reading frame and does not display homology to sequences in GenBank. Clone pNZE25 detects a 120-bp repeat in the O.o. genome, as seen from the generation of a 120-bp ladder after Southern analysis of HinfI-digested genomic DNA. When used to probe O.o. genomic DNA digested with DraI, HaeIII or AluI, pNZE25 generates individual specific DNA fingerprints on target DNA isolated from gall midge biotypes collected from different parts of India.

Animals↗
PubMed1997

Retrospective detection of laboratory cross-contamination of Mycobacterium tuberculosis cultures with use of DNA fingerprint analysis.

In 1992-1993, we investigated possible cross-contamination of Mycobacterium tuberculosis cultures as part of a study of tuberculosis in Arkansas by using DNA fingerprint analysis. Of patients whose isolates were matched, those for whom smears were negative and only one culture was positive were identified from laboratory records. Clinical, laboratory, DNA fingerprint, and epidemiological data were reviewed. Of 259 patients, nine (3.5%) were judged to be due to cross-contamination. None of these patients had a clinical course consistent with tuberculosis. All nine specimens were processed with another isolate with a matching DNA fingerprint, and epidemiological connections were not identified among any of the patients. To avoid erroneous diagnoses and unnecessary therapy and public health investigations, specimens from patients with tuberculosis whose smears are negative and only one culture is positive should be investigated for cross-contamination. An inconsistent clinical course and a DNA fingerprint that matches those of other culture-positive specimens processed concurrently, coupled with the lack of an epidemiological connection, suggest cross-contamination.

Adult↗
PubMed1991

DNA fingerprinting and electrophoretic karyotype of environmental and clinical isolates of Candida parapsilosis.

The endonuclease restriction pattern (DNA fingerprinting) and the electrophoretic karyotype of 16 Candida parapsilosis isolates from environmental and clinical sources were investigated. DNA from both whole cells and separated mitochondria was digested with enzymes, including EcoRI, BamHI, KpnI, BglII, HpaII, PvuII, and HindIII. Regardless of their source and pathogenic properties, all isolates showed a uniform, reproducible, and overlapping whole-cell DNA fingerprinting with each endonuclease digest. Mitochondrial DNA fragments were, in all cases, major contributors to the total cellular DNA restriction pattern. In contrast, the electrophoretic karyotype generated by rotating field gel electrophoresis (RFGE) or contour clamped homogeneous field electrophoresis (CHEF) showed a remarkable polymorphism among the isolates. This polymorphism concerned the smaller molecular size section of the karyotype (range, 1.8 to 0.7 Mb), where at least two to five chromosomal bands could be consistently detected by both RFGE and CHEF. Larger (greater than or equal to 3.0 to 1.9 Mb) chromosome-sized DNA bands (four in CHEF and three in RFGE) were quite distinct and common to all isolates. Thus, seven karyotype classes could be defined, on the basis of both the number and size of putative chromosomes. The three categories of isolates (soil, vaginal, and hematological) were not randomly distributed among the seven classes. In particular, the four hematological isolates had a karyotype pattern which was clearly distinct from that shown by the three environmental isolates, and of the nine vaginal isolates only one shared a class with isolates from another source (soil). Although tentative, the classification was totally consistent with the independent and reproducible results obtained by the two pulse-field electrophoretic techniques employed. It is suggested that the electrophoretic analysis of the karyotype might be particularly useful for epidemiological and pathogenicity studies on biotypes of C. parapsilosis.

Candida↗