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PubMed1996

[DNA-fingerprinting and tuberculosis].

DNA-fingerprinting or RFLP (Restriction Fragment Length Polymorphism) is a molecular biological technique which allows differentiation between tuberculosis strains. The technique is based on the occurrence of repetitive elements in the mycobacterial genome and is a powerful tool in epidemiological studies. DNA-fingerprinting is also of value in tracking the spread of infection in patients with tuberculosis. The latter is illustrated in two case stories.

Adult↗

PubMed1991

Two-dimensional DNA-fingerprinting in animals.

DNA-fingerprinting has become, during the last five years, an important method of genetic analysis in medicine, veterinary medicine and other disciplines. The power of this technique, especially for genetic linkage analysis, may be enhanced in humans by using the two dimensional DNA-fingerprinting method. Here we show that this procedure can successfully be applied to different animal species, e.g. pig, dog and mouse. Optimal conditions, however, have to be determined for each species tested. With the use of marker systems as well as computer programs it will be possible to evaluate complex two-dimensional spot patterns in a short time and with high reliability.

Animals↗

PubMed1993

Assessment of DNA fingerprinting for determining genetic diversity in sheep populations.

Genomic DNA, prepared from 12 animals from four sheep flocks, was digested with either HaeIII or HinfI and probed with three DNA fingerprinting probes. Mean DNA fingerprint band sharing and band frequency calculated for each flock were used to estimate genetic diversity. Each of the DNA fingerprinting systems showed the same trend in diversity within the sampled flocks, and greater diversity between the flocks than within the flocks. DNA fingerprinting therefore provides a useful measure of genetic diversity in sheep.

Analysis of Variance↗

PubMed1998

Use of DNA fingerprinting to assess tuberculosis infection control.

BACKGROUND: DNA fingerprinting establishes the genetic relatedness of Mycobacterium tuberculosis isolates and has become a powerful tool in tuberculosis epidemiology. OBJECTIVE: To use DNA fingerprinting to assess the efficacy of current tuberculosis infection-control practices. DESIGN: Retrospective molecular and descriptive epidemiologic study. SETTING: A 700-bed urban public hospital that follows the Centers for Disease Control and Prevention (CDC) guidelines for tuberculosis infection control. PATIENTS: 183 patients who had positive cultures for M. tuberculosis from 1 April 1995 to 31 March 1996. RESULTS: 173 of 183 M. tuberculosis isolates from the study period underwent DNA fingerprinting. Fingerprinting revealed that five isolates represented false-positive cultures and that 91 (54%) of the remaining 168 isolates were in 15 DNA fingerprinting clusters, which ranged in size from 2 to 29 isolates. Risk factors for clustering were birth in the United States, African-American ethnicity, homelessness, substance abuse, and male sex. Retrospective epidemiologic analysis of inpatient and outpatient visits by the 91 patients who had clustered isolates revealed only one possible instance of patient-to-patient transmission. CONCLUSIONS: The DNA fingerprinting of all M. tuberculosis isolates from a 1-year period revealed one possible instance of nosocomial transmission and five false-positive M. tuberculosis cultures. However, these results did not lead to changes in infection-control practices or in clinical care. The study findings do not support the use of DNA fingerprinting for nosocomial tuberculosis surveillance, but they suggest that compliance with the CDC tuberculosis infection-control guidelines may control patient-to-patient transmission in high-risk urban hospitals.

Chicago↗

PubMed1989

DNA fingerprints revealing common and divergent human DNA methylation patterns.

We compared DNA fingerprints of different cell populations from the same individuals, after separate digestion with the isoschizomers MboI and Sau3A. Methylation differences were observed within every individual when comparing fingerprints of Sau3A- with MboI-digested DNA, and of Sau3A-digested sperm with somatic DNA. In some cases, differences were also detected between fingerprints of Sau3A-digested somatic DNA originating from various cell sources. Methylation patterns common to all cell populations examined, including the germline, were observed with a higher frequency than divergent ones. These 'common methylations' are most likely to find their origin during early embryogenesis.

DNA↗

PubMed1987

Detection of somatic changes in human cancer DNA by DNA fingerprint analysis.

Minisatellite DNA probes which can detect a large number of autosomal loci dispersed throughout the human genome were used to examine the constitutional and tumour DNA of 35 patients with a variety of cancers of which eight were of gastrointestinal origin. Somatic changes were seen in the tumour DNA in ten of the 35 cases. The changes included alterations in the relative intensities of hybridising DNA fragments, and, in three cases of cancers of gastrointestinal origin, the appearance of novel minisatellite fragments not seen in the corresponding constitutional DNA. The results of this preliminary study suggests that DNA fingerprint analysis provides a useful technique for identifying somatic changes in cancers.

Breast Neoplasms↗

PubMed1998

Subtyping of Streptococcus dysgalactiae and Streptococcus uberis isolated from bovine mammary secretions by DNA fingerprinting.

Streptococcus dysgalactiae and Streptococcus uberis isolated from mammary secretions of cows from Tennessee and New Zealand were subtyped using polymerase chain reaction-based DNA fingerprinting. Such DNA fingerprinting using primer 8.6d (5'-GTAACGCC3') resulted in categorizing 116 S. dysgalactiae isolates into 25 different subtypes, with 17 subtypes observed in isolates from Tennessee and eight in isolates from New Zealand. All S. dysgalactiae DNA fingerprint profiles, regardless of origin, contained 700- and 330-base pair fragments. The majority of S. dysgalactiae isolates (73%) from Tennessee belonged to two subtypes. The remaining 23 isolates belonged to 15 different DNA fingerprint subtypes. Streptococcus dysgalactiae isolates from New Zealand (n = 32) were grouped into eight different subtypes; 66% belonged to two subtypes. A characteristic feature of S. dysgalactiae isolates from New Zealand was the presence of a 270-base pair DNA fragment seen infrequently in S. dysgalactiae isolates from Tennessee. When primer OPE-4 (5'-GTGACATGCC-3') was used, DNA fingerprinting differentiated S. uberis from Tennessee (n = 28) and New Zealand (n = 30) into 20 subtypes; 14 subtypes were observed in isolates from Tennessee, and six in isolates from New Zealand. All S. uberis DNA fingerprint profiles, regardless of origin, contained 1100-, 640-, and 450-base pair fragments. A characteristic feature of S. uberis isolates from New Zealand was the presence of a 300-base pair DNA fragment seen infrequently in S. uberis isolates from Tennessee. The most common subtypes of S. dysgalactiae and S. uberis from Tennessee herds were isolated in milk from lactating cows during monthly herd surveys, in milk from cows with clinical mastitis, and in mammary secretions from cows during the periparturient period, and thus were not confined to one particular stage of lactation. These data suggest that S. dysgalactiae and S. uberis from New Zealand are distinct from those isolated from the USA, and that DNA fingerprinting can be used as an epidemiological tool to differentiate streptococci and identify important sources of these mastitis pathogens on dairy farms.

Animals↗

PubMed1995

Parallel genome analysis by one- and two-dimensional DNA fingerprinting in human gliomas.

The detection of DNA variation in cancers is an important step in elucidating the mechanism of tumorigenesis. Using the strategy of multipoint genome analysis we detected many differences between glioma-derived and constitutional DNA by customary DNA fingerprinting with simple repetitive oligonucleotide probes. Amplification of the epidermal growth factor receptor (EGFR) gene has been found to be easily detectable as new or highly intensified bands in one-dimensional (1-D) DNA fingerprints of glioblastoma DNA generated with probes (GTG)5 or (GT)8. However, in most low-grade astrocytomas, 1-D DNA fingerprinting has failed to reveal any genomic abnormalities. In these cases a two-dimensional (2-D) technique was successfully employed that is based on size separation in neutral gels followed by sequence-dependent separation in denaturing gradient gels and hybridization with several mini- and microsatellite core probes. The hundreds of spots visualized with this technique were used to detect subtle changes probably occurring as the initial steps of tumorigenesis in human gliomas. On average, five of the approximately 580 spots generated by probes CAC and 33.6 were found to be altered in tumor DNA; 80% of the alterations were spot losses, the rest being spot gains or amplifications. Computer-based image analysis using an external lambda marker provided a stringent way to compare spot patterns generated by 2-D DNA fingerprinting. In comparisons performed between typing patterns generated on the same gel, 99% of truly identical spots were confirmed by the software. In intergel comparisons 84% of identical spots were matched on the basis of the marker information alone.

Base Sequence↗

PubMed2003

Detection of universal variable fragments as markers for genetic studies. A novel technology for DNA fingerprinting.

A novel DNA technology enables the detection of universal variable fragments (UVF), thus revealing genetic variation without a priori sequence information. The detection of UVF markers is based on two amplifications of genomic DNA with the polymerase chain reaction. In the first amplification, two short oligonucleotide primers produce a large number of fragments. One primer is based on a microsatellite sequence, whereas the second primer can have any sequence. In the second amplification, the length of the primers is increased in order to decrease the number of amplicons. This enables the selection of polymorphic fragments. Restriction digestion can be used to further increase the number of polymorphisms. Until now, we have demonstrated UVF in several different species. In addition, with the present study we have contributed to the linkage map of the rabbit by localizing 11 UVF markers on different linkage groups. Mendelian inheritance was shown in this linkage study through a backcross of two inbred rabbit strains. The power of the UVF technique is based on the selection for microsatellite variation in combination with the detection of single-nucleotide polymorphisms. UVF thus offers the possibility of increasing the clustering of markers and localizing genes in species for which sequence information is either not present or only scarcely present.

Animals↗

PubMed1995

Epidemiology of tuberculosis by DNA fingerprinting.

In recent years, deoxyribonucleic acid (DNA) probes have become available to study the epidemiology of tuberculosis by DNA fingerprint techniques. These methods make it possible to distinguish different strains of Mycobacterium tuberculosis. Currently, DNA fingerprinting is integrated with conventional epidemiological approaches to improve understanding of the spread of tuberculosis. This molecular approach has led to the investigation of a wide variety of epidemiological issues, such as adequate identification of outbreaks, tracing of nosocomial infections in hospitals, and investigation of the relative contribution of newly acquired versus reactivated infections in different populations. This paper reviews the potentials of DNA fingerprinting for studying the epidemiology of tuberculosis, and the lessons learned from this strategy. In addition, future prospects for molecular epidemiology will be discussed.

Contact Tracing↗

PubMed1999

New applications of low-C0tDNA as a DNA fingerprint probe.

New applications of low-C0t DNA are reported as probes for genetic identification and genome characterization. These fast and intermediately reannealing fractions have sometimes either been discarded in genomic library construction to enhance the probability of finding single copy genes, or they are used as resources for identifying individual repetitive sequences. In addition, they are used as blockers to enhance hybridization signals. C0t-1 DNA serves as a probe for DNA fingerprinting of human yeast artificial chromosomes. We have isolated low-C0t DNA from bacteria, fungus, plant, mussel, chicken, rat and fish from the sheared genomic DNA of the respective species. Low-C0t DNA is labeled to generate DNA fingerprints and for in situ hybridization. Individual specific DNA fingerprint profiles are observed and species-specific DNA fragments can be identified in bacteria, fungus, plants (Ginseng and Amaranthus) and mussel. When low-C0t DNA probes from rat, chicken and fish were employed, only smear profiles and no distinct DNA banding patterns were evident. In these species, individual clones can be used as a probe for DNA fingerprinting containing repetitive sequences after subcloning. The advantage of this approach is to quickly develop a useful probe for DNA fingerprinting for genetic identification and analysis without sequencing knowledge a priori. This represents an innovative approach to the use of these repetitive components of the genome.

Animals↗

PubMed1995

Use of DNA fingerprinting for human population genetic studies.

DNA fingerprinting techniques have been used in population genetic studies on many different kinds of organisms. Here, we present new applications for multilocus DNA fingerprint probes in population studies and demonstrate the applicability of DNA fingerprinting to human population genetics, using M13 phage DNA as a probe. The new approach, which is based on a factor method of numerical coding of nonquantitative data (factor correspondence analysis-FCA), shows good agreement between population position, as indicated by the three principal factors, and ethnogenetic proximity.

Azerbaijan↗

PubMed1999

Changes in methylation patterns identified by two-dimensional DNA fingerprinting.

Two-dimensional DNA fingerprinting (2-D fingerprinting) is a sensitive tool for genomic difference analysis between tumor DNA and constitutive DNA of glioma patients. Numerous differences were found even in low-grade gliomas. They can be interpreted as deletions, amplifications, rearrangements, HaeIII restriction site mutations, tandem repeat instabilities, or methylation differences. The influence of methyl groups on the melting behavior of double-stranded DNA fragments in a denaturing gradient gel was demonstrated by analyzing the migration of lambda-phage DNA fragments in 2-D fingerprint gels. A characteristic intensity shift between two neighboring spots in several glioma samples was identified and verified by rehybridization of 2-D filters with a cloned DNA fragment corresponding to the lower spot in 10 out of 11 pilocytic astrocytomas. We hypothesized that this shift may be related to an alteration in the methylation pattern of the tumor DNA. This was specifically tested by analyzing the underlying 750 bp genomic fragment (including 21 CpG dinucleotides) with bisulfite treatment of agarose-embedded DNA. A methylation grade of 88% in tumor DNA as compared to 96% in blood DNA was found. Although only one CpG is located in the melting domain of the cloned fragment, this particular CpG is methylated in all blood samples, but mostly demethylated in the tumor samples. In conclusion, we demonstrate that 2-D fingerprinting may be a powerful tool for the detection of DNA methylation changes in genomic difference analysis.

Astrocytoma↗

PubMed1995

An informativity index for multilocus DNA fingerprints.

An informativity index for multilocus DNA fingerprints, r, was developed. It is based upon the Shannon information that a paternal DNA fingerprint conveys about the offspring phenotype pattern. Both simulation and empirical data reveal that the index r is strongly correlated with the mean log likelihood ratio (paternity vs. nonpaternity) expected in trio cases of true paternity. Since r can be estimated from DNA fingerprints of unrelated individuals in advance, it will provide an easy means to assess the potential utility of a given probe/enzyme combination in kinship testing.

Animals↗

PubMed1993

Comparison of DNA fingerprinting and serotyping for identification of avian Pasteurella multocida isolates.

The DNA fingerprint profiles and serotypes of 63 avian Pasteurella multocida field isolates, 13 attenuated vaccine isolates (propagated from vaccines manufactured by five companies), and 16 somatic reference strains were compared. DNA fingerprinting established the relationship of isolates that could not be distinguished by serotyping. Of the 76 isolates, 28 DNA fingerprint profiles and 12 somatic types were recognized. One isolate was nonreactive with 16 reference somatic and 5 reference capsule-type antisera. Thirty-one field isolates and seven vaccine isolates were identified as capsule type A. Twenty-nine field isolates and six vaccine isolates were nonencapsulated. Three field isolates were capsule type F. Isolates of capsule types B, D, and E were not found. One field isolate, identified as somatic type 7, had a DNA fingerprint identical to that of the somatic reference type 6 profile. Twelve field isolates had profiles identical to the somatic reference type 3 strain profile; 11 of these were identified as somatic type 3, 4, and 1 was identified as somatic type 3. The DNA fingerprint profiles of 50 field isolates and 13 attenuated vaccine isolates did not match profiles of the 16 somatic type reference strains. Twenty-five DNA fingerprint profiles were recognized from 30 of these field isolates. The DNA fingerprint profiles of 20 field isolates and 13 attenuated vaccine isolates were identical. Three somatic types (3; 3,4; and 4,16) were identified from the field isolates, and two somatic types (3 and 3,4) were identified from the attenuated vaccine isolates. DNA fingerprinting is useful for accurate identification and epidemiologic study of P. multocida isolates.

Animals↗

PubMed1993

Application of DNA fingerprinting to enforcement of hunting regulations in Ontario.

DNA fingerprinting has been used in investigations of 40 cases of infractions of hunting regulations involving white-tailed deer (Odocoileus virginianus) and moose (Alces alces) in Ontario. In most of these cases, individual-specific DNA fingerprints obtained with the Jeffrey's 33.15 multilocus probe were used to link the animal remains found at the illegal kill site to blood and tissue samples of the dead animal associated with a suspect. DNA fingerprints from 27 white-tailed deer and 19 moose were obtained in order to establish the level of band-sharing in DNA fingerprints among unrelated individuals in each species. We also determined the levels of band-sharing among animals from the same region and calculated the probability of two individuals sharing the same DNA fingerprint. Details are presented from cases in which the evidence was presented and accepted by Ontario courts.

Animals↗

PubMed1988

DNA fingerprints of Streptococcus pyogenes are M type specific.

DNA from group A streptococci of various M and T types was cleaved with endonucleases to produce a DNA fingerprint. Comparison of DNA fingerprints proved to be a very useful tool for studying the epidemiology of isolates from various outbreaks of streptococcal disease. Patterns of DNA fragments from HindIII digests of samples of total DNA were conserved among strains of the same M serotype yet were easily distinguished from those of different M serotypes. Different M types were associated with specific restriction enzyme profiles. DNA fingerprints of strains of the same M type were stable enough to establish a clonal relationship between strains obtained from an isolated outbreak of disease or strains endogenous to people geographically isolated by continent. Strains of the same serotype from different continents had very similar, but distinguishable, restriction profiles. Those strains unable to be typed with standard typing sera were also amenable to comparison because they yielded unique fingerprints.

Africa↗

PubMed1990

Genetic heterogeneity of Porphyromonas (Bacteroides) gingivalis by genomic DNA fingerprinting.

This study describes the use of total genomic DNA fingerprinting with the use of restriction endonucleases to characterize clinical isolates of Porphyromonas gingivalis (Bacteroides gingivalis) obtained from patients with periodontitis or with root-canal infections. The majority of independent isolates had a unique DNA fingerprint, indicating extensive genetic heterogeneity within this species. Twenty-nine distinct DNA fingerprints were found among the 33 isolates investigated. This is in contrast to biotyping and serotyping, where only one type and three types, respectively, have been reported. The observed heterogeneity indicates that DNA fingerprinting is a sensitive measure of genetic dissimilarity between P. gingivalis isolates and is able to characterize individual isolates. These results have ecological implications, indicating that there is considerable natural diversity in the global population of P. gingivalis, and that there are likely to be relatively large numbers of genetically distinct clonal lines. Furthermore, DNA fingerprinting is a sensitive and powerful tool for longitudinal and cross-sectional epidemiological studies. This technique provides far greater discrimination between isolates than either biotyping or serotyping, and will be most helpful in, for example, the analysis of distribution of clonal lines within one periodontal patient, or the analysis of the transmission to and turnover of strain populations within a patient population, since the probability of two strains with the same DNA fingerprint being found by chance is small.

Bacteroides↗