Enhanced detection of mutations in BRCA1 exon 11 using restriction endonuclease fingerprinting-single-strand conformation polymorphism

A novel approach to mutation screening in the large exon 11 (comprising 3427 bp) of the human BRCA1 gene is presented. Restriction endonuclease fingerprinting single-strand conformation polymorphism (REF-SSCP) is based on repeated detection of DNA sequence variants in different restriction endonuclease fragments, and we evaluated the method using blood samples from 25 Norwegian patients with hereditary breast/ovarian cancer. We compared REF-SSCP to constant denaturant gel electrophoresis (CDGE) and to the protein truncation test (PTT). REF-SSCP detected 12 different DNA variants. Four of these were not detected by CDGE, and only one variant detected by CDGE was missed by REF-SSCP. PTT detected 4 of these 13 variants. REF-SSCP was subsequently applied to a second patient series (Swedish, n=20). A total of 14 different DNA variants were detected by REF-SSCP, 6 of which were truncating mutations (PTT detected only 4). Nonsense and frameshift mutations that are putative breast/ovarian cancer mutations, were detected in 7 of the 25 Norwegian and 9 of the 20 Swedish patients.     

Multiple exon screening using restriction endonuclease fingerprinting (REF): Detection of six novel mutations in the L1 cell adhesion molecule (L1CAM) gene

Restriction endonuclease fingerprinting (REF) has been utilized to screen 19 of the 28 exons in the L1CAM gene using only 5 PCR reactions. The clustered exons were amplified and the PCR products were subjected to endonuclease digestion and subsequent gel electrophoresis to produce a highly informative fingerprint for each PCR product. An alteration in the fingerprint, when compared to a control, determined the specific DNA fragment containing the mutation. Sequencing of the corresponding exon and flanking region was done to determine the precise location of the mutation. Using this method we have identified 6 novel mutations in the L1CAM gene in 5 patients with X-linked hydrocephalus and 2 patients with MASA. One of the mutations was common to both a patient with HSAS and a patient with MASA. The utilization of REF will allow for easier and quicker detection of mutations in the L1CAM gene. This method should be applicable for screening other genes with multiple, clustered exons. Hum Mutat 11:222–230, 1998. © 1998 Wiley-Liss, Inc.     

Epidemiological fingerprinting of Enterobacter cloacae by small-fragment restriction endonuclease analysis and pulsed-field gel electrophoresis of genomic restriction fragments.

A cluster of infections caused by Enterobacter cloacae was observed among preterm neonates in a neonatal intensive care unit (NICU) of a pediatric hospital in Osnabrück, Germany. The presence of similar antimicrobial susceptibility patterns among the bacterial isolates prompted an investigation to determine whether a limited spread of a single strain existed. All 12 E. cloacae isolates from the NICU and 50 nonrelated strains were fingerprinted by small-fragment restriction endonuclease analysis (SF-REA) of EcoRI DNA digests. Selected isolates were further characterized by pulsed-field gel electrophoresis (PFGE) of NotI- or XbaI-generated genomic restriction fragments. Epidemiologically unrelated strains were clearly discriminated by both methods. Results achieved by SF-REA and PFGE revealed that of the 12 isolates from the NICU, 11 belonged to the same genotypic cluster. Since all reagents and equipment for both techniques are commercially available, DNA fingerprinting by SF-REA or PFGE is proposed as a useful tool in the microbiology laboratory for investigating the epidemiological relatedness of E. cloacae strains of clinical and environmental origin.     

Computerized restriction endonuclease analysis compared with O-serotype and phage type in the epidemiologic fingerprinting of Pseudomonas aeruginosa strains

Objective: To assess restriction endonuclease analysis (REA) of chromosomal DNA using Sal l enzyme, low-concentration (0.4%) agarose gels and digitalized data management of the REA patterns obtained for the typing of clinical Pseudomonas aeruginosa isolates.
Method: A group of 67 clinical unrelated isolates from 10 Spanish hospitals was used to study the discriminatory power, reproducibility and typeability of REA typing.
Results: A Sal l REA pattern consisted of a variety (1–10) of restriction bands in the range between 12.2 and 48.5 kb and an unresolvable smear of low-molecular-weight bands. Forty different Sal l REA patterns with an index of discrimination of 0.979 were obtained. Low tupeability (91.04%) was the major limitation of REA typing. Analysis of blinded subcultures of eight Pseudomonas aeruguinosa strains showed the reproducibility of REA typing to be 87.5%. Combined phenotypic typing (O-serotyping and phage typing) performed on the same group of strains showed comparable discrimination but much lower reproducibility. Isolates selected from five clusters of nosocomial infections in hospitals in the UK were typed by REA typing, and the results show high agreement when compared with conventional phenotypic typing methods in distinguishing between strains.
Conclusions: These data underline the usefulness of REA typing enhanced with digitalized data management for the epidemiologic subtyping of clinical Pseudomonas aeruginosa isolates.     

Application of small fragment restriction endonuclease analysis (SF-REA) to the epidemiological fingerprinting of Staphylococcus aureus.

Total cell DNA of 14 isolates of Staphylococcus aureus from patients of an intensive care unit (ICU) and 180 unrelated strains was examined by restriction endonuclease analysis (REA). EcoRI-generated DNA fragments were either subjected to conventional REA on agarose gels and stained with ethidium bromide or separated by polyacrylamide gel electrophoresis and visualised by silver staining (SF-REA). Both methods were compared for inter-strain discriminatory ability, reproducibility and handling. All DNA-cleavage patterns of unrelated strains clearly differed from each other when subjected to SF-REA. In contrast, all S. aureus isolates from the ICU gave identical restriction fragment patterns. These findings supported the suspicion of nosocomial infection in these patients. Conventional REA proved the identity of the ICU isolates, but it failed to differentiate between some of the unrelated strains. Therefore SF-REA of total cell DNA seemed to be superior. It has proved to be a very useful technique for studying the epidemiology of S. aureus in hospitals.     

Analysis of mutations in the genome of cold-adapted strains of influenza A virus using extended modification of polymerase chain restriction method

Cold-adapted influenza viruses A/Leningrad/13 4/17/5 7 (H2N2) (Len/17) and A/Leningrad/I 34/4 7/57 (H2N2) (Len/47) are used in Russia to prepare live reassortant cold-adapted influenza vaccines (LIV) for adults and children, respectively. Comparison between the nucleotide sequences of the Len/17 strain and the initial wild-type strain A/Leningrad/13 4/5 7 (H2N2) revealed ten nucleotide substitutions (eight of them encoding). Four additional substitutions (three encoding) were found in the genome of the Len/47 virus. Gene segment restriction site (PCR-restriction) analysis was used for identification of the genotype of reassortant influenza viruses. Conventional methods of PCR-restriction analysis detect only five encoding nucleotides substitutions in the internal genes of the Len/17 and seven substitutions in the internal genes of the Len/47 virus. An extended modification of the PCR-restriction method detect all encoding mutations in the internal genes of the Len/17 and Len/47 viruses (eight and eleven encoding substitutions, respectively). This method is advantageous for genome composition analysis of reassortant influenza vaccine strains and for investigating the genetic stability of LIV during replication in vaccines.     

Examination of mycoplasma gallisepticum strains using restriction endonuclease DNA analysis and DNA-DNA hybridisation

DNA from 10 Mycoplasma gallisepticum strains and one strain each of M. synoviae and M. gallinarum were studied by restriction endo-nuclease DNA analysis using endonucleases Eco RI, HindIII, BglII, BamHI, KpnI, and XhoI. Digestion patterns of DNA in agarose gels allowed easy differentiation of M. gallisepticum strains from different sources, while patterns obtained from one strain at the 6th and 100th in vitro passage levels were identical. The F strain and a field derivative obtained from a poultry farm where F strain vaccine had been previously used had almost identical patterns. This technique should be useful for comparing and differentiating M. gallisepticum strains in epidemiological and other studies. Strain differences were also noted by DNA-DNA hybridisation using a probe containing mycoplasma ribosomal RNA genes.     

Evaluation of restriction endonuclease fingerprinting of chromosomal DNA and plasmid profile analysis for characterization of multiresistant coagulase-negative staphylococci in bacteremic neonates.

A procedure was developed for restriction endonuclease fingerprinting (REF) of the chromosomal DNA of coagulase-negative staphylococci. A total of 48 isolates comprising 29 Staphylococcus epidermidis and 19 Staphylococcus haemolyticus isolates from blood and mucocutaneous sites of 15 premature neonates were characterized by REF, plasmid profile (PP) analysis, antimicrobial susceptibility testing, biotyping, and slime production. On the basis of REF analysis of chromosomal DNA, the 48 coagulase-negative staphylococcal isolates were subdivided into 10 subgroups, whereas PP analysis subdivided the strains into 20 distinct subgroups. REF analysis of total DNA (i.e., chromosome plus plasmid) resulted in the same 20 subgroups as were subdivided by PP analysis. The high discriminatory power of PP analysis was associated with the variability of plasmid content in coagulase-negative staphylococcal strains isolated during the outbreak. REF patterns were found to be stable both in vitro and in vivo. Isolates carried from 2 to 10 plasmids that ranged in molecular size from 0.9 to 39.5 megadaltons. Plasmids were disseminated among the coagulase-negative staphylococci, regardless of the genetic relatedness of their chromosomal DNAs. Hence, a lack of correlation existed between the grouping of isolates by REF analysis of chromosomal DNA and the grouping by PP analysis. There were one and two distinct chromosomal patterns among 4 of 4 blood cultures and 15 of 15 mucocutaneous cultures of S. haemolyticus, respectively. In contrast, a higher proportion of distinct chromosomal patterns was found for S. epidermidis in blood cultures (7 of 11 cultures) compared with those identified for isolates in mucocutaneous cultures (6 of 18 cultures). In summary, REF analysis of chromosomal DNA, rather than total DNA, is a useful marker for epidemiological investigations of coagulase-negative staphylococci. PP analysis can also be used to provide additional epidemiological information regarding the most recent genetic events.     

Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization

Genomic DNA was prepared from four reference strains of Mycobacterium paratuberculosis and 46 isolates of this organism from New Zealand, Australia, Canada, and Norway and also from two mycobactin-dependent "wood pigeon" strains. The DNA was characterized by restriction endonuclease analysis, both with and without DNA hybridization, with a probe specific to a repetitive DNA sequence in M. paratuberculosis. Both techniques differentiated M. paratuberculosis strains into two groups, but DNA hybridization revealed more differences between strains within the larger group. All the strains from cattle and many strains from other animals belonged to this group. The second group of nine strains included the Faroe Islands strain, all New Zealand sheep strains, and one New Zealand goat strain. Primary isolation of strains belonging to this group was difficult to achieve. DNA from acid-fast organisms harvested directly from intestinal tissues of sheep with Johne's disease was shown to have restriction and hybridization patterns identical to those of DNA obtained from M. paratuberculosis isolates cultured from the same tissues. Two Norwegian goat strains and the wood pigeon strains did not hybridize to the M. paratuberculosis probe and had restriction patterns very different from those of other M. paratuberculosis strains. The wood pigeon strains had restriction patterns very similar to those of strains of Mycobacterium avium, indicating that they should be classified as that species. The presence of two distinct groups of M. paratuberculosis strains and their predominant distribution in different host animals may be significant in management of mixed-animal farming operations.     

人类肠道病毒分子生物学分型鉴定方法的建立及应用

目的 建立人类肠道病毒（HEV）分子生物学分型鉴定方法,用于临床分离肠道病毒的分型鉴定.方法 根据已知各型别人类肠道病毒基因的核苷酸序列和文献资料,分别合成HEV种属特异性和分型鉴定引物;提取病毒RNA,采用逆转录聚合酶链反应（RT-PCR）扩增病毒cDNA,通过琼脂糖凝胶电泳和核苷酸序列分析,鉴定病毒并分型,并与血清中和试验相互验证.结果 采用种属特异性引物鉴定18株疑似HEV毒株,其中17株阳性;型特异性引物鉴定结果：18株病毒中4株为科萨奇病毒A24型,3株为科萨奇病毒B3型;科萨奇病毒B2、A9、A15型、埃可病毒3、6、7、9、11、14、33型和鼻病毒9型各1株,分型结果与中和试验相符.结论 建立的人类肠道病毒分子生物学分型鉴定方法,具有特异性强、敏感性高、快速简便等优点,可以直接鉴定并分型诊断人类肠道病毒感染,适用于人类肠道病毒感染的实验室诊断和流行病学研究.     

Simple, specific molecular typing of dengue virus isolates using one-step RT-PCR and restriction fragment length polymorphism

A one-step RT-PCR and one-enzyme RFLP was used to detect and distinguish among flaviviruses, including the four serotypes of dengue and the St. Louis Encephalitis, West Nile and Yellow Fever viruses in cultured virus samples or acute-phase human serum. Using a previously described RT-PCR, but novel RFLP procedure, results are obtained in 24 h with basic PCR and electrophoresis equipment. There is 95% agreement between RT-PCR/RFLP results and those achieved by indirect immunofluorescence assays, and 100% agreement between RT-PCR/RFLP results and gene sequencing. This method is more rapid than tests of cytopathic effect based on virus isolation in tissue culture, and simpler than real-time PCR. It does not require specialized equipment, radioisotopes or computer analysis and is a method that can be applied widely in the developing world. It allows for prompt determination of whether a flavivirus is the cause of illness in a febrile patient, rapid identification of dengue serotypes in circulation, and improved patient management in cases where prior dengue exposure make dengue hemorrhagic fever or dengue shock syndrome a risk.     

Identification of germline missense mutations and rare allelic variants in the ATM gene in early-onset breast cancer.

Epidemiological studies have shown an increased risk of breast cancer in obligate ataxia telangiectasia (A-T) heterozygotes. We analyzed 100 samples from young breast cancer patients for mutations in ataxia-telangiectasia mutated (ATM), the gene responsible for the autosomal recessive condition, A-T, to determine whether A-T heterozygosity predisposes such individuals to develop breast cancer. These patients were selected from families with a moderate or absent family history of breast cancer and included a subset of 16 radiosensitive patients. Forty-four germline sequence variants were detected by fluorescent chemical cleavage of mismatch of RT-PCR products. These included seven rare variants found in nine patients (three described for the first time), but no truncating mutations. Although three variants were detected in the radiosensitive subset, this was not statistically significant compared to the nonradiosensitive group. One variant, G2765S, is likely to be a missense mutation, but the other six variants probably represent rare polymorphisms. However, five of the seven rare germline variants detected showed loss of heterozygosity of the wild-type ATM allele for one or more markers close to the ATM locus in matched tumor DNA. This high rate of somatic inactivation of ATM may indicate either that these rare variants play a role in breast cancer development or alternatively that a neighboring tumor suppressor gene is important for tumorigenesis. We found germline truncating ATM mutations to be rare in these young breast cancer patients and therefore they are unlikely to play a role in the etiology of their disease. Genes Chromosomes Cancer 26:286-294, 1999.     

Estimation of DNA fragment size and generation of DNA restriction endonuclease maps using linear models

A method for the estimation of DNA fragment size and for the generation of DNA restriction endonuclease maps using linear models is discussed, and a computer program which utilizes the SAS (SAS Institute Inc., 1982) statistical package is presented.     

Characterization of unrelated strains of Staphylococcus schleiferi by using ribosomal DNA fingerprinting, DNA restriction patterns, and plasmid profiles.

The molecular characteristics of 31 unrelated strains of Staphylococcus schleiferi isolated from 13 hospitals between 1973 and 1991 were determined by ribosomal DNA fingerprinting by using a digoxigenin-labeled DNA probe, genomic DNA restriction patterns, and plasmid profiles. Only six strains harbored one or two plasmids. DNA restriction analysis, which was carried out with five endonucleases (EcoRI, HindIII, PstI, PvuII, and ClaI), did not allow us to discriminate between isolates. Ribotyping with HindIII, ClaI, or EcoRI enzymes generated six, seven, and nine distinct patterns, respectively. With the combination ClaI-EcoRI, 13 ribotypes were obtained among the 31 strains, suggesting a relative heterogeneity within the species. Moreover, all strains shared two or three common bands, according to the endonuclease used, which were relatively specific for S. schleiferi in comparison with the ribosomal banding patterns described for other coagulase-negative staphylococci. These results illustrate that ribotyping can be used for the epidemiological investigation of S. schleiferi isolates and possibly for taxonomic analysis in this species.     

Detection of the heteromorphic spectrum of heterochromatin in the human genome by in situ digestion using restriction endonuclease Alui

A battery of selective banding techniques has been utilized to identify the heteromorphic markers in the human genome. The recent addition of the AluI/Giemsa (G)-technique has helped not only in identifying the variable sites, but in characterizing their heteromorphic spectra. In the present investigation, we classified the pericentromeric heterochromatin by the AluI/G-technique by its size and position using 50 normal individuals and suggested the potential uses of this banding technique over earlier methods. © 1992 Wiley-Liss, Inc.     

Identification of nocardia species by restriction endonuclease analysis of an amplified portion of the 16S rRNA gene

Identification of clinical isolates of Nocardia to the species level is important for defining the spectrum of disease produced by each species and for predicting antimicrobial susceptibility. We evaluated the usefulness of PCR amplification of a portion of the Nocardia 16S rRNA gene and subsequent restriction endonuclease analysis (REA) for species identification. Unique restriction fragment length polymorphism (RFLP) patterns were found for Nocardia sp. type strains (except for the N. asteroides type strain) and representative isolates of the drug pattern types of Nocardia asteroides (except for N. asteroides drug pattern type IV, which gave inconsistent amplification). A variant RFLP pattern for Nocardia nova was also observed. Twenty-eight clinical isolates were evaluated both by traditional biochemical identification and by amplification and REA of portions of the 16S rRNA gene and the 65-kDa heat shock protein (HSP) gene. There was complete agreement among the three methods on identification of 24 of these isolates. One isolate gave a 16S rRNA RFLP pattern consistent with the biochemical identification but was not identifiable by its HSP gene RFLP patterns. Three isolates gave 16S rRNA RFLP patterns which were inconsistent with the identification obtained by both biochemical tests and HSP gene RFLP; sequence analysis suggested that two of these isolates may belong to undefined species. The PCR and REA technique described appears useful both for the identification of clinical isolates of Nocardia and for the detection of new or unusual species.     

Characterization of noncapsulate Haemophilus influenzae by whole-cell polypeptide profiles, restriction endonuclease analysis, and rRNA gene restriction patterns.

Thirty-four clinical isolates of noncapsulate Haemophilus influenzae representing isolates with either related or dissimilar patterns of whole-cell polypeptide profiles on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were further characterized by restriction enzyme analysis (REA) and rRNA gene restriction patterns. Total cellular DNA was extracted by a rapid, microcentrifuge-scale method and digested with BamHI, which gave a pattern of about 18 discrete bands. This confirmed the five closely related groupings suggested by SDS-PAGE. Isolates dissimilar by SDS-PAGE were also distinguishable by REA. However, there was no correlation between the degrees of similarity estimated from whole-cell polypeptide profiles and those obtained from REA for the dissimilar isolates. Therefore, inferences of genetic relatedness made on the basis of these data should be interpreted with caution. rRNA gene restriction patterns also confirmed the groupings suggested by the other two techniques. We conclude that the three methods were highly discriminatory and that whole-cell polypeptide patterns or REA with BamHI would be appropriate techniques for epidemiological studies of noncapsulate H. influenzae.