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PubMed1988

Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells.

Hypervariable minisatellites can be amplified from human DNA by the polymerase chain reaction, using primers from DNA flanking the minisatellite to amplify the entire block of tandem repeat units. Minisatellite alleles up to 5-10 kb long can be faithfully amplified. At least six minisatellite loci can be co-amplified from the same DNA sample and simultaneously detected to provide a reproducible and highly variable DNA fingerprint which can be obtained from nanogram quantities of human DNA. The polymerase chain reaction can also be used to analyse single target minisatellite molecules and single human cells, despite the appearance of spurious PCR products from some hypervariable loci. DNA fingerprinting at the level of one or a few cells therefore appears possible.

Alleles↗
PubMed2002

[IS6110-restriction fragment length polymorphism based DNA fingerprinting in molecular epidemiology of tuberculosis].

OBJECTIVE: To identify the IS6110-restriction fragment length polymorphism (RFLP) DNA fingerprinting patterns of some clinical isolates of Mycobacterium tuberculosis (MTB) isolated from Ningxia, Beijing and Shanghai in recent years, and to observe their epidemiological characteristics. METHODS: Chromosomal DNA of MTB was digested with endonuclease PvuII, then electrophoresed on agarose gel plate and transferred capillarilly to a nylon filter and hybridized with 245 bp fragment of IS6110 which labeled using random primer fluorescein labeling kit. The RFLP patterns of Southern hybridization were inspected autofluorographically and the chromosomal DNAs of MTB were thereby typed. RESULTS: Most of 103 isolates of MTB shared 8 approximately 21 copies. Some of them were clustered. Strains isolated from Ningxia and Beijing had similar DNA fingerprinting patterns. One zero copy strain and one single copy strain were found among isolates from Shanghai. CONCLUSIONS: IS6110-RFLP based typing is feasible for MTB molecular epidemiological study in China. Most of isolates of MTB show analyzable patterns. Isolates of MTB from Ningxia and Beijing have close genomic relation.

China↗
PubMed1991

DNA fingerprints of sheep using an M13 probe.

The bacteriophage M13 DNA was used to detect hypervariable minisatellites in several families of Booroola sheep as well as Merino and Suffolk sheep. Digestion of sheep DNA gave rise to three to eight fragments with different restriction enzymes demonstrating considerable polymorphism between the different breeds. The length of informative DNA fragments varied in size from 6 to 20kb. The DNA fingerprints generated were individual specific and allowed for differentiation between closely related animals. The pattern obtained with sheep DNA was different from that observed with humans and other vertebrates in the proportion of high molecular weight DNA fragments present. Pedigree analysis of DNA patterns of dams and their offspring for several sets of twins and triplets showed a clear distinction between individuals and failed to reveal the presence of monozygosity.

Animals↗
PubMed1999

The properties of human DNA fingerprints produced by polymeric monocore probes (PMC probes).

The properties of human DNA fingerprints detected by multilocus polymeric monocore probes (PMC probes) have been investigated. The PMC probes were produced by the polymerase chain reaction with two partly complementary oligonucleotides homologous to various minisatellite or microsatellite core sequences (Ijdo J, Wells RA, Baldini A, Reeders ST. Nucleic Acids Res 1991;19:4780). It has been shown that these probes possess increased sensitivity, they detect considerably more hypervariable fragments in genomic DNA thus exhibiting advantages over the corresponding oligonucleotides and natural polycore minisatellite probes. Variation in the DNA fingerprints of different individuals produced by these probes indicates that the probability of accidental identity is very low (< 10(-12)). According to the data of cross-hybridization with PMC probes of various specificity, several distinct families can be distinguished among G-rich hypervariable sequences of the human genome.

Bacteriophage M13↗
PubMed1995

Application of DNA fingerprinting to the taxonomy of European blackberry species.

Thousands of blackberry species (Rubus subgenus Rubus) have been described from Central and Northern Europe. These species are usually polyploid and pseudogamous. Since apomixis is only facultative, the species have retained the possibility to produce some offspring by sexual recombination. Hybridization of restriction-enzyme-digested DNA samples to the M13, (AC)/(TG) and 33.15 probes has yield valuable information on the occurrence and distribution of genetic variation in Rubus. Intraspecific variation proved to be very restricted, with identical DNA fingerprints sometimes being exhibited by Swedish, Danish and German populations of the same species. By comparison, interspecific variation was usually pronounced, suggesting that most species have been derived through genetic recombination. Speciation through interspecific hybridization was demonstrated in one case. Several critical taxa were investigated; some of these proved to have unique DNA fingerprints, whereas others appear to be identical with previously described species. Evaluation of raspberry cultivars, obtained through several generations of vegetative propagation or with various in vitro techniques, failed to detect any DNA fingerprint variation, suggesting that the fingerprints are somatically stable. Blackberry seedlings, obtained by pollinating various species as well as interspecific hybrids with pollen from yet other species, were successfully evaluated with DNA fingerprinting to determine the relative proportions of the apomictic and sexual seed set.

DNA Fingerprinting↗
PubMed1990

DNA-fingerprint changes compared to karyotypes in acute leukemia.

Chromosomal analysis is routinely used in follow-up studies of acute leukemia, but it cannot be used in patients who do not have karyotypic abnormalities in blastic phase (10-46% of all cases). Recently we have demonstrated that unspecific DNA-fingerprint (DNA-F) changes can be detected in blastic phase of leukemia by DNA-F analysis. These changes can be used as molecular markers of the disease and in the follow-up studies of acute leukemia karyotyping and DNA-F analysis are complementary. The comparative analyses of leukemia samples with both these methods could help to localize minisatellite loci in chromosomes and reveal new DNA areas related to leukemia. New, more specific probes targeted to specific chromosomes could consequently be developed. We compared the DNA-F to the karyotypes of 50 acute leukemia patients. In blastic phase, 19 patients had DNA-F alterations and 31 patients abnormal karyotypes, 12 patients had both DNA-F alterations and karyotypic abnormalities. DNA-F changes were detected in six of the 16 patients with normal karyotypes and 19 patients with normal DNA-F had abnormal karyotypes at the time of diagnosis. Eleven patients showed neither DNA-F changes nor abnormal karyotypes in blastic phase. Three acute myeloid leukemia (AML) patients with DNA-F changes in blastic phase had trisomy eight as a sole abnormality or combined with balanced translocation, which suggests that there might be AML associated minisatellite locus in chromosome 8. In other cases the karyotypes were complicated and no clear evidence of the relationship of DNA-F changes with other chromosomes could be found.

Acute Disease↗
PubMed1986

An outbreak of group B meningococcal disease: tracing the causative strain of Neisseria meningitidis by DNA fingerprinting.

Following an outbreak of meningococcal disease in three schoolchildren in a small community in northern Norway, DNA fingerprinting, serotyping with monoclonal antibodies, serogrouping, and sulfonamide sensitivity testing were applied for characterization and tracing of the causative agent. The three case isolates were genomically indistinguishable, sulfonamide-resistant, serogroup B, serotype 15 meningococci. Throat specimens were collected from 552 healthy contacts, including all children below age 17 and their parents. Among the 36 carrier isolates (carrier rate, 6.5%) 13 showed DNA fingerprints identical, or almost identical, to the index pattern. All of these 13 isolates were sulfonamide resistant, 12 were of serotype 15, and 8 were of polysaccharide serogroup B (5 were nongroupable). These closely related isolates were almost exclusively recovered from schoolchildren of 2 of 15 small villages, one of which included the homes of two of the patients. The remaining 23 carrier isolates were nonresistant, non-type 15 meningococci of widely differing DNA restriction patterns. Our results confirm that DNA fingerprinting has potential as an efficient tool in practical meningococcal epidemiology.

Adolescent↗
PubMed2004

DNA fingerprint changes in tuberculosis: reinfection, evolution, or laboratory error?

BACKGROUND: DNA fingerprint patterns of Mycobacterium tuberculosis strains vary within individuals and between epidemiologically linked individuals because of pattern evolution, new infections, and laboratory error. We explored the importance of these factors. METHODS: Cultures from individuals in northern Malawi who had been diagnosed with tuberculosis (TB) during 1996-2001 were fingerprinted with restriction fragment-length polymorphism (RFLP). Probable laboratory error was inferred by use of dates or isolated positive cultures. Pattern evolution was explored within and between individuals, and the relative importance of relapse and reinfection was estimated in individuals with recurrent TB. RESULTS: RFLP results were available for 930 isolates from 806 individuals. The maximum laboratory-error rate was 3.9%. Pattern evolution was more common in linked individuals (17%) than on relapse (11%) or during treatment (3%). Twenty individuals had recurrent TB after completing treatment: in human immunodeficiency virus (HIV)-positive individuals, 7 of 12 recurrences were due to reinfection, compared with 0 of 8 in HIV-negative individuals (P=.01). CONCLUSIONS: The rate of DNA fingerprint-pattern evolution is not linear, and rates of change calculated from repeat cultures within individuals may not be applicable to transmission between individuals. The high proportion of recurrence due to reinfection found in HIV-positive individuals suggests that secondary prophylaxis and/or antiretroviral treatments are needed for such individuals.

Adolescent↗
PubMed1995

[Genomic DNA fingerprints of Legionella pneumophila serogroup 2 strains as an epidemiologic marker].

Using pulsed-field gel electrophoresis, DNA fingerprints of eleven Legionella pneumophila isolates of serogroup 2 were generated. It was shown that two strains from a patient suffering from pneumonia as well as three environmental strains isolated from the shower in the hotel where the patient stayed 5 days before his illness were identical. Six strains of the same serogroup isolated from other sources were clearly separated. Thus, DNA fingerprints by pulsed-field gel electrophoresis are excellent epidemiological markers for the rarely occurring serogroup 2 of Legionella pneumophila.

Antibodies, Monoclonal↗
PubMed1998

Measurement of genetic variation within and between Japanese quail lines using DNA fingerprinting.

The objective of the present experiment was to study genetic variation within and among well-defined Japanese quail lines by DNA fingerprinting. The Japanese quail lines included a randombred control line (R1) and lines developed from R1 by divergent selection over 30 generations for 4-wk BW (HW, LW) and total plasma phosphorus (TPP) (HP, LP), a measure of yolk precursor in the blood. In addition, two sublines (HW-HP, HW-LP) of HW, developed in the ninth generation, were included in the analysis. Males of the sublines were selected for increased 4-wk BW whereas females were selected for increased (HW-HP) or decreased (HW-LP) TPP. Sixteen individual DNA samples per line were digested with HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs designed to measure band sharing (BS). Within lines, BS ranged from 0.384 to 0.525. The BS within the R1 line was less than that of all selected lines, except for the HP and LP lines, indicating that, in general, selection had increased genetic homogeneity within the selected lines. Between lines, BS was less than within lines and the R1 line had the highest average level of BS (0.278) with the other lines. The BS between lines for the selected lines ranged from 0.230 to 0.308 with an average of 0.265. In the comparison of the R1 line with the selected lines, it appeared that selection for increased TPP or decreased BW may have influenced BS levels. The relationships of the HW line with its sublines (HW-HP and HW-LP) were not accurately predicted by the DNA fingerprinting technique used. All lines were separated, as indicated by the genetic distance between lines.

Animals↗
PubMed1992

DNA fingerprinting survey of various human tumors and their metastases.

DNA fingerprinting with the minisatellite probes 33.6 and 33.15 was used to screen for genetic abnormalities in primary tumors of a variety of organs and, where appropriate, their metastases, obtained from 32 patients. The constitutional DNA of each host, obtained from blood leukocytes or normal tissue, was used to produce control, individual-specific fingerprints for comparison with those of their tumor. Fingerprints obtained with probe 33.6 showed differences between tumor and host fingerprints in 69% of patients and those produced with 33.15 in 55%. The most common change was loss or reduction in the intensity of one or more bands, but the appearance of new bands, not present in the fingerprint of the constitutional DNA, was also noted in several tumor DNA samples. The findings are interpreted as indicating loss or rearrangement of expressed sequences in the chromosomal regions adjacent to the hypervariable tandem repeat intron arrays which are detected by these probes. In three patients further differences were identified between primary tumors and their metastatic deposits. With this technique it is possible to perform simultaneous multilocus screening of the genome and the present results show that it has potential for identification of as yet unknown abnormalities in DNA constitution, which may be of pathogenetic significance.

Autoradiography↗
PubMed1993

The formal analysis of multilocus DNA fingerprints.

A description is given of a novel method for the formal analysis of multilocus DNA fingerprints, the so-called 'genetic factor model'. Using this model, multilocus DNA fingerprints can be shown to be a robust means for both paternity testing and pedigree reconstruction.

Computer Simulation↗
PubMed1993

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.

Base Sequence↗
PubMed1990

Application of DNA fingerprinting to parentage and extended family relationship testing.

For the purpose of applying DNA fingerprinting to parentage or other extended blood relationship testing, we have developed a general system for estimating blood relationship between a set of individuals. This system can be used for any blood relationship testing, even if critical family members are unavailable. A general formula for calculating the probability of such relationships based on Bayes' theorem has been devised and the ability of DNA fingerprinting produced by Jeffrey's polycore probe to determine the relationships has been evaluated.

Bayes Theorem↗
PubMed1993

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.

Base Sequence↗
PubMed1991

DNA fingerprinting in reptiles: Bkm hybridization patterns in Crocodilia and Chelonia.

The simple tetranucleotide repeat GATA (GACA) occurs in all eukaryotes so far studied. In many species, the arrangement of these sequences varies considerably among individuals. Thus GATA (GACA) type probes produce DNA fingerprints when hybridized with restricted DNA from different individuals within a species. Banded krait minor (Bkm) satellite DNA (related to sequences originally recovered from the W chromosome of the banded krait and consisting essentially of a series of GATA repeats) is found in a wide spectrum of vertebrates and invertebrates. We used the Bkm 2(8) clone to evaluate the occurrence of this satellite in DNA from five species of Crocodilia and six species of Chelonia, including the sea turtles Chelonia mydas and Lepidochelys kempi. Well-resolved DNA fingerprints were obtained. Among the crocodilians, fewer restriction fragments were generated and fewer of the fragments were polymorphic, than among the chelonians, consistent with the view that the crocodilians are less divergent within species. The Bkm 2(8) clone can accordingly be used to advantage in individual, familial, and population studies, and perhaps in the evaluation of taxonomic relationships in these animals. This is of potential value in endangered species such as C. mydas and L. kempi.

Alligators and Crocodiles↗
PubMed1998

Paternity assessment in rhesus macaques (Macaca mulatta): multilocus DNA fingerprinting and PCR marker typing.

Establishing kinship relations in primates using modern molecular genetic techniques has enhanced the ability to scrutinize a number of fundamental biological issues. We screened 51 human short tandem repeats (STRs) for cross-species PCR amplification in rhesus macaques (Macaca mulatta) and identified 11 polymorphic loci with heterozygosity rates of at least 0.6. These markers were used for paternity testing in three social groups (M, R, and S) of rhesus macaques from Cayo Santiago, Puerto Rico. Several consecutive birth cohorts were analyzed in which approximately 200 males were tested for paternity against more than 100 mother/ infant pairs. Despite a combined exclusion rate of more than 99.9% in all three groups, some cases could not be solved unequivocally with the STR markers and additional testing of the MHC-associated DQB1 polymorphism. A final decision became possible through multilocus DNA fingerprinting with one or more of the oligonucleotide probes (GATA)4, (CA)8, and (CAC)5. Paternity assessment by multilocus DNA analysis with probe (CAC)5 alone was found to have limitations in rhesus macaques as regards the number of potential sires which might be involved in a given case. Multilocus DNA fingerprinting requires large amounts of DNA, and the ensuing autoradiographic patterns present difficulties in comparisons across gels and even within the same gel across remote lanes. Computer-assisted image analysis was incapable of eliminating this problem. Therefore, a dual approach to DNA typing has been adopted, using STR markers to reduce the number of potential sires to a level where all remaining candidates can be tested by multilocus DNA fingerprinting on a single gel, preferably in lanes adjacent to the mother/infant pair.

Animals↗
PubMed1991

Use of DNA fingerprinting in paternity analysis of closely-related Exmoor ponies.

DNA fingerprinting techniques were used to try to resolve the parentage of an Exmoor pony foal. Three young Exmoor ponies, one female and two males, shared a paddock and the female subsequently became pregnant. The two possible sires were three-quarter siblings and were also half-siblings to the dam. Southern hybridisation of Exmoor pony DNA with human mini-satellite probes resolved the disputed parentage in spite of the fact that there was a 70 per cent band share between the individuals involved. Colt M6 was 2.06 times more likely to be the father than an uncle, and Colt M3 was 477 times more likely to be an uncle than the father.

Animals↗