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PubMed1987

Differential diagnosis of genetic disease by DNA restriction fragment length polymorphisms.

DNA restriction fragment length polymorphisms (RFLPs) are used for diagnosis of genetic disease in families known to be affected by specific disorders, but RFLPs can be also useful for the differential diagnosis of hereditary disease. An RFLP pattern represents the inheritance of chromosomal markers in a family, and such a pattern may be compatible with the inheritance of a certain disorder in that family. Probabilities to find such a pattern if the disorder were present and if it were absent can be combined with the prior probabilities of disease considered in the differential diagnosis on the basis of previous clinical and laboratory data. Bayes' theorem is used to calculate the posterior probabilities of the diseases in question. This approach is illustrated in a family suffering from either spinal muscular atrophy (an autosomal recessive disease) or Becker muscular dystrophy (an X-chromosomal disorder). Probabilities to exclude a certain disorder can be calculated in advance, as some RFLP patterns are not compatible with the presence of that disorder.

Bayes Theorem↗

PubMed1999

[Epidemiological study of microepidemics of tuberculosis by restriction fragment length polymorphism analysis].

Restriction fragment length polymorphism (RFLP) analysis was performed with 13 events considered as microepidemics of tuberculosis occurred in Osaka prefecture from July 1995 to July 1998. In 7 out of 13 events, isolates from patients involved in each event showed identical RFLP patterns, hence these events were verified as microepidemics. Out of 7 microepidemics, three were intrafamily infection, the other three occurred in work places and the remaining one was in a school occurred among students. The total number of patients who were involved in microepidemics was 19 and their ages distributed in the wide range from 18 to 69 years old, but 11 were at twenties or forties. The total delay in case-finding was 2 months in the shortest case, and more than 14 months in the longest. In the remaining 6 of 13 events, the isolates from patients were showed different RFLP patterns, although they were suspected as microepidemics. Furthermore, in the 2 microepidemics, one isolate showed different RFLP pattern from the other isolates involved in each events. These facts suggest that there could be many overlooked sources of tuberculosis infection in Osaka.

Adolescent↗

PubMed2005

Culture-independent microbial community analysis with terminal restriction fragment length polymorphism.

Terminal restriction fragment length polymorphism is a polymerase chain reaction (PCR)-based technique that has been used to effectively interrogate microbial communities to determine the diversity of both phylogenetic and functional markers. It requires the isolation of community DNA and knowledge of the target sequence. PCR amplification, performed with fluorescently labeled primers, is followed with restriction digestion and size selection on automated sequencing systems. The fluorescent tag identifies the terminal fragment, and the length polymorphism of the terminal fragments reveals a fraction of the phylogenetic diversity within the target sequence. Because the technique has high-throughput capabilities, it performs well in surveys where a large number of samples must be interrogated to ascertain spatial or temporal changes in community structure.

Bacteriolysis↗

PubMedDate not supplied

[Molecular typing by amplified fragment length polymorphism and PCR-restriction fragment length polymorphism , biotyping and antimicrobial susceptibility of Campylobacter jejuni].

Molecular typing systems have provided invaluable information for tracking infectious agents through the food chain. These tools have been essential for understanding the epidemiology of gastrointestinal infectious diseases, therefore providing essential and evidence-based information for appropriate interventions and preventative measures. Two such molecular typing techniques based on the polymerase chain reaction (PCR) that have been applied to the epidemiology of foodborne pathogens are, amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) analysis. Campylobacter is responsible for one of the most common bacteria foodborne gastrointestinal infections affecting humans, especially in developed countries. The object of this paper is to apply AFLP and RFLP analysis of the flagellin (flaA) gene to 18 isolates of Campylobacter jejuni from human sporadic cases in Italy. Results of these analyses were compared to the phenotypes of these isolates based on biotyping and antimicrobial resistance determinations. All isolates were typable by the four methods. The RFLP procedure was performed with DdeI and HinfI enzymes, and 12 and 8 distinct profiles respectively were recognised. AFLP analysis was more discriminatory, and recognised 16 different profiles. Results from AFLP were reproducible and applicable for definitive characterisation of C. jejuni isolated from different outbreaks. PCR-RFLP of the flaA gene represents a useful tool only to compare isolates within a single outbreak.

Anti-Bacterial Agents↗

PubMed1990

Nucleic acid probe characterizes Leptospira interrogans serovars by restriction fragment length polymorphisms.

Restriction endonuclease analysis (REA) of genomic DNA can discriminate between many Leptospira interrogans serovars. However, several serovars have similar restriction endonuclease digestion patterns which prohibits accurate identification. This investigation expands previous REA studies of L. interrogans to include serovars in serogroup Tarassovi. Most serovars in this serogroup had characteristic digestion patterns by which they could be identified. However, four of the serovars in this serogroup had similar digestion patterns, thus preventing serovar identification by REA alone. To discriminate between these serovars REA was supplemented with Southern blot analysis. The DNA from each serovar showed similar but unique patterns when hybridized with a probe synthesized from a repetitive sequence element cloned from L. interrogans serovar hardjo type hardjo-bovis. The applicability of this technique to characterize other serogroups was assessed. One hundred sixty six of 190 serovars screened by Southern blot analysis contained sequences which hybridized with the repetitive element probe under conditions of relaxed stringency. These results suggest that Southern blot analysis using this probe will be a valuable supplement for typing L. interrogans.

Animals↗

PubMed2003

Identification of Mycobacterium avium genotypes with distinctive traits by combination of IS1245-based restriction fragment length polymorphism and restriction analysis of hsp65.

One-hundred eight Mycobacterium avium isolates from pigs, humans, birds, and bovines were typed by the IS1245-based restriction fragment length polymorphism (RFLP) method and PCR-restriction enzyme analysis (PRA) of hsp65. Nine clusters of isolates showing more than 80% similarity in their RFLP profiles were detected. The largest cluster (cluster B) included 32 of 79 pig isolates (40.5%), 3 of 25 human isolates (12%), and 1 of 2 bovine isolates, comprising 33% of all isolates. The second largest cluster (cluster A) included 18 pig isolates (22.8%) and 6 human isolates (24%). Six smaller clusters included six pig isolates (clusters C and D), four and two human isolates (clusters E and F, respectively), two pig isolates (cluster I), and two pig isolates plus one bovine isolate and the avian purified protein derivative strain (cluster H). Cluster G represented the "bird-type" profile and included the bird isolate in this series, one pig isolate, plus reference strain R13. PRA revealed four allelic variants. Seventy-seven isolates were identified as M. avium PRA variant I, 24 were identified as M. avium PRA variant II, 6 were identified as M. avium PRA variant III, and 1 was identified as M. avium PRA variant IV. Except for three isolates from cluster B, each of the RFLP clusters was associated with a single PRA pattern. Isolates with unique (nonclustered) RFLP profiles were distributed between PRA variants I and II, and there was one unique isolate of PRA variant IV. These observations are consistent with divergent evolution within M. avium, resulting in the emergence of distinct lineages with particular competence to infect animals and humans.

Animals↗

PubMed1988

Close correlation between restriction fragment length polymorphism of the L-MYC gene and metastasis of human lung cancer to the lymph nodes and other organs.

Restriction length fragment polymorphism of the L-MYC gene was examined in DNAs from lung cancer tissues and normal tissues of 51 Japanese patients with lung cancer. In individual patients, no difference was seen between the restriction length fragments of the two alleles of L-MYC [6-kilobase (kb) and 10-kb fragments in EcoRI digests] in lung cancer tissues and normal tissues. But a striking correlation was found between the restriction length fragment polymorphism pattern of L-MYC and the extent of metastasis, particularly to the lymph nodes at the time of surgery: Patients with only the L band (10 kb) had few lymph node metastatic lesions, whereas patients with either the S band (6 kb) or the S and L bands almost always had lymph node metastatic lesion. A similar correlation was found between the presence of the S band and metastases to other organs. This correlation was particularly marked in cases of adenocarcinoma. These results indicate a clear genetic influence on metastases and a consequent poor prognosis for certain patients of lung cancer; L-MYC restriction length fragment polymorphism is thus shown to be a useful marker for predicting the metastatic potential of human lung cancer.

Adult↗

PubMed1987

A unique AT-rich hypervariable minisatellite 3' to the ApoB gene defines a high information restriction fragment length polymorphism.

A DNA restriction fragment length polymorphism has been found immediately 3' to the human apoB gene. Digestion of many different human DNAs at sites flanking the region and Southern blotting analysis reveal that this region can vary in length by approximately 300 base pairs with five alleles readily distinguishable. The length polymorphism is due to a unique AT-rich minisatellite that consists primarily of a 30-base pair tandem repeat with two structurally related subunit sequences, x (ATAATTAAATATTTT) and y (ATAATTAAAATATTT). In general, the sequences repeat in an x-y order. The AT-rich region also contains variant x and y sequences that result from C or G for A substitution. Sequence analysis of one large allele revealed the expected increased number of xy repeats. In addition, similar analysis of three different smaller alleles with the same apparent size on Southern blotting analysis showed that all were of slightly different size due to minor differences in the number of xy repeats. The heterogeneity of this AT-rich minisatellite provides the basis for a highly informative restriction fragment length polymorphism of the apoB gene and should be very useful in association and linkage analysis studies of the contribution of this locus to atherosclerosis susceptibility.

Alleles↗

PubMed1993

High lysozyme activity in a Norwegian bovine family co-segregates with a restriction fragment length polymorphism.

Analysis of restriction fragment length polymorphism (RFLP) of the lysozyme gene cluster was performed in a Norwegian bovine family segregating a single dominant Mendelian factor for high lysozyme activity in serum. An RFLP site with allelic bands of 16kb and 5.9 kb turned out to be linked to the locus for the high lysozyme activity factor with a lod score of 6.8 at a recombination fraction of 3.4%. This implies that we have revealed a genetic marker for the high lysozyme activity trait.

Abomasum↗

PubMed1999

Typing of hepatitis C virus by a new method based on restriction fragment length polymorphism.

A new restriction fragment length polymorphism (RFLP) analysis has been developed for hepatitis C virus (HCV) typing in the viral 5' non-coding region and contiguous core region. These genomic sequences were chosen for the relative nucleotide homology among different genotypes and for the presence of polymorphic sites. By employing two endonucleases (AccI and MboI) and, in some instances, a third one (EcoRII), we can unambiguously and reproducibly distinguish between genotypes and subtypes 1a, 1b, 1c, 2a, 2c, 2b, 3a, 3b, 4a, 5a and 6a. The method was applied for diagnosing two Italian groups of HCV-infected individuals reflecting a randomly collected population and a group of intravenous drug users. The accuracy of this method has been validated by comparison with INNOLiPA and by sequencing. Our approach represents an improvement over previous RFLP methods, since typing is accurate and simpler.

Base Sequence↗

PubMed1992

The inheritance of type I and type III von Willebrand's disease in Israel: linkage analysis, carrier detection and prenatal diagnosis using three intragenic restriction fragment length polymorphisms.

Three intragenic restriction fragment length polymorphisms (RFLPs) were used to study linkage and analyse the mode of inheritance in type I and type III von Willebrand's disease (vWD). In two families linkage was established between Sac I RFLPs and the inheritance of type I vWD. RFLP analysis of amniocyte DNA from a potentially affected foetus enabled us to establish a prenatal diagnosis of vWD in a third family with type I vWD. Linkage was also established in four families between the Sac I and two Taq I RFLPs and the inheritance of type III vWD. All type III probands were homozygotes and inherited the same mutant vWF allele from both parents. Heterozygous carriers from one type III family were phenotypically normal and could be detected only by linkage analysis, whereas carriers from the remaining three type III families were asymptomatic but had decreased values of vWF antigen and activity. RFLP-based linkage analysis of vWD alleles provides a way to improve the diagnostic precision, detect carriers, and may be useful for prenatal diagnosis of type III vWD.

Female↗

PubMed2005

T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles.

Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align (http://inismor.ucd.ie/~talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Align.

Bacteria↗

PubMed1993

Molecular characterization of human rotavirus VP4 genes by polymerase chain reaction and restriction fragment length polymorphism assay.

A restriction fragment length polymorphism (RFLP) assay was developed to examine the genetic variability and similarity of the VP4 genes of human rotaviruses. The VP4 genes of 14 human rotavirus strains, including VP4 serotype P1A strains (Wa, P, VA70), serotype P1B strain (DS-1), serotype P2 strains (M37, 1076, McN, ST3) and serotype P3 strains (AU-1, AU228, K8, PA151, PCP5, MZ58), and those of 2 feline strains (FRV-1 and Cat2) were reverse-transcribed and amplified by the polymerase chain reaction (PCR). The amplified VP4 cDNAs were then digested with a panel of restriction endonucleases (HindIII, NruI, HaeIII, and EcoRI), resulting in the identification of at least one enzyme with which digestion produced an RFLP profile specific for a particular P serotype. Of interest was the presence of two distinct RFLP patterns within the serotype P3 VP4 genes: one corresponding to the VP4 gene carried by the members of the AU-1 genogroup and the other corresponding to the VP4 genes carried by naturally-occurring reassortants between members of the AU-1 and other genogroups.

Animals↗

PubMed1996

Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes.

Conserved regions about 420 bp long of the pelADE cluster specific to Erwinia chrysanthemi were amplified by PCR and used to differentiate 78 strains of E. chrysanthemi that were obtained from different hosts and geographical areas. No PCR products were obtained from DNA samples extracted from other pectinolytic and nonpectinolytic species and genera. The pel fragments amplified from the E. chrysanthemi strains studied were compared by performing a restriction fragment length polymorphism (RFLP) analysis. On the basis of similarity coefficients derived from the RFLP analysis, the strains were separated into 16 PCR RFLP patterns grouped in six clusters, These clusters appeared to be correlated with other infraspecific levels of E. chrysanthemi classification, such as pathovar and biovar, and occasionally with geographical origin. Moreover, the clusters correlated well with the polymorphism of pectate lyase and pectin methylesterase isoenzymes. While the pectin methylesterase profiles correlated with host monocot-dicot classification, the pectate lyase polymorphism might reflect the cell wall microdomains of the plants belonging to these classes.

Base Sequence↗

PubMed1987

[Genetic monitoring of laboratory rat strains by restriction fragment length polymorphisms of mitochondrial DNA].

Restriction fragment length polymorphisms of rat mitochondrial DNA (mtDNA) were examined using various kinds of laboratory rat strains in Japan. The results show that mtDNA of laboratory rats, Rattus norvegicus, are highly polymorphic; at least 7 types, Aa, Ba, Bb, Cb, Dc, Eb, and Fa, were found with the use of 6 restriction enzymes, EcoR I, Hind II, Hha I, Hpa II, Taq I, and Hinf I. Types Aa, Ba, and Eb were distributed widely in several strains, whereas types Ba, Cb, Dc and Fa were limited to some specific strains. These results indicate that restriction fragment length polymorphisms of mtDNA can be applied to genetic monitoring of laboratory rat strains.

Animals↗

PubMed1994

Genetic heterogeneity of Pseudomonas aeruginosa clinical isolates revealed by esterase electrophoretic polymorphism and restriction fragment length polymorphism of the ribosomal RNA gene region.

The intra-species differentiation of Pseudomonas aeruginosa was analysed by comparing the polymorphism of esterases by conventional polyacrylamide-agarose gel electrophoresis, the physicochemical properties of the variants of the major esterase P3 and the restriction fragment length polymorphism of ribosomal RNA gene regions (ribotyping) to O-serotyping for several panels of strains selected from among a series of 257 clinical isolates and two references strains, (ATCC nos. 10145 and 27853). The electrophoretic variation of four main kinds of esterase (P1-P4) and 11 additional esterases distinguished by their spectra of hydrolytic activity with synthetic substrates and by their sensitivity to di-isopropylfluorophosphate, allowed the discrimination of 67 zymotypes. Thirty-two esterase P3 variants were characterized by their pI, electrophoretic mobilities and titration curve analyses. They were distributed into two groups which, by these molecular criteria, seem to be distantly related. Combination of the patterns resulting from HindIII, EcoRI and BclI restriction endonuclease digestions allowed the discrimination of 33 ribotypes among 134 strains. The strains exhibiting esterase P3 variants of group 2 presented a distinct ribotype and belonged to serotype (O)12. They could constitute a distinct group within the species. For the majority of the strains, the absence of correlation between zymotype, ribotype and serotype argues for a high level of heterogeneity within P. aeruginosa and indicates that the parallel use of the first two methods represent a potential tool for epidemiological study.

DNA, Ribosomal↗

PubMed1987

Neutrality tests of highly polymorphic restriction-fragment-length polymorphisms.

The allele frequency data of Baird et al. were tested using Ewens-Watterson sampling theory for goodness of fit to the infinite-alleles model of neutral evolution. Although probes of both the HRAS-1 and D14S1 loci identify highly diverse restriction-fragment-length polymorphisms, the observed values of gene identity (F) and the common allele frequency (C) are not significantly different from the neutral expectation. Allele frequency distributions show a tendency toward a deficit in diversity for HRAS-1 and a slight excess diversity for D14S1. The direction of these departures is consistent with potential selective effects of the Harvey-ras oncogene and hitchhiking of the D14S1 locus to closely linked immunoglobulin genes. Direct chi 2-tests of goodness of fit of the observed and expected allele frequency distributions reveal significant departures in the caucasoid and Hispanic HRAS-1 distributions but not in any of the other tests.

Alleles↗

PubMed1993

Association of restriction fragment length polymorphism in alcohol dehydrogenase 2 gene with alcohol induced liver damage.

OBJECTIVE: To investigate the role of genetically determined differences in the enzymes of alcohol metabolism in susceptibility to liver damage from misusing alcohol. DESIGN: Use of pADH36 probe to study PVU II restriction length fragment polymorphism in alcohol dehydrogenase 2 gene in white alcohol misusers and controls. SETTING: Teaching hospital referral centres for liver disease and alcohol misuse. SUBJECTS: 45 white alcohol misusers (38 with alcoholic liver disease) and 23 healthy controls. MAIN OUTCOME MEASURES: Alcohol misuse, the presence and severity of alcoholic liver disease, alcohol dependency, and family history of alcohol misuse. RESULTS: A two allele polymorphism (A and B) was identified. In control subjects the allele frequencies were 85% for A and 15% for B compared with 37% and 63% respectively in alcohol misusers (p < 0.001). B allele was significantly associated with severe liver damage (p < 0.05) as well as alcohol dependency and family history of alcohol misuse compared with controls. CONCLUSION: Inherited variation in enzymes of ethanol metabolism may contribute to the pathogenesis of alcohol induced liver damage. This supports the presence of a genetic component in alcohol misuse.

Adult↗