Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources
PubMed1994

Experience with cloned mitochondrial DNA analysis to forensic practice.

The sequencing method of the D-loop region of cloned mitochondrial DNA (mtDNA) together with multilocus and single locus DNA probe patterns was applied to identification of the dismembered and putrefied remains of a pregnant woman. The multilocus DNA fingerprinting was useful to identify whether or not 4 dismembered remains were from the body of the same person, whereas the single locus DNA analysis was useful to decide that the suspect was the father of the fetus. On the other hand, the sequencing method of the D-loop region of cloned mtDNA after amplification by polymerase chain reaction (PCR) was particularly advantageous to highly degraded and contaminated DNA specimens.

Base Sequence↗
PubMed1999

DNA analysis of malignant salivary gland carcinomas: comparison of different tissue preparations and measuring techniques.

This study correlates static and flow-cytometric analysis on paraffin-embedded and fresh material of salivary gland carcinomas. Nuclear suspensions for DNA analysis were prepared from paraffin-embedded and fresh material. Comparison of the results of static and flow cytometry on paraffin-embedded material revealed no significant correlation between DNA ploidy and S-phase value. The coefficients of variation were significantly lower for static than for flow cytometry (p < 0.05). Flow-cytometric analysis on fresh and paraffin-embedded material correlated well concerning DNA ploidy, but not for the S-phase. The coefficients of variation were significantly lower for the fresh than for the paraffin-embedded material (p < 0.001). Cytometric analysis on paraffin-embedded material of malignant salivary gland carcinomas should be critically evaluated. There is a need for flow-cytometric investigations on fresh material to clarify further the prognostic value of this method.

DNA, Neoplasm↗
PubMed1996

Functional integration of PCR amplification and capillary electrophoresis in a microfabricated DNA analysis device.

Microfabricated silicon PCR reactors and glass capillary electrophoresis (CE) chips have been successfully coupled to form an integrated DNA analysis system. This construct combines the rapid thermal cycling capabilities of microfabricated PCR devices (10 degrees C/s heating, 2.5 degrees C/s cooling) with the high-speed (< 120 s) DNA separations provided by microfabricated CE chips. The PCR chamber and the CE chip were directly linked through a photolithographically fabricated channel filled with hydroxyethylcellulose sieving matrix. Electrophoretic injection directly from the PCR chamber through the cross injection channel was used as an "electrophoretic valve" to couple the PCR and CE devices on-chip. To demonstrate the functionality of this system, a 15 min PCR amplification of a beta-globin target cloned in M13 was immediately followed by high-speed CE chip separation in under 120 s, providing a rapid PCR-CE analysis in under 20 min. A rapid assay for genomic Salmonella DNA was performed in under 45 min, demonstrating that challenging amplifications of diagnostically interesting targets can also be performed. Real-time monitoring of PCR target amplification in these integrated PCR-CE devices is also feasible. Amplification of the beta-globin target as a function of cycle number was directly monitored for two different reactions starting with 4 x 10(7) and 4 x 10(5) copies of DNA template. This work establishes the feasibility of performing high-speed DNA analyses in microfabricated integrated fluidic systems.

DNA↗
PubMedDate not supplied

Prognostic value of flow cytometric DNA analysis in non-small-cell lung cancer: rationale of sequential processing of frozen and paraffin-embedded tissue.

The objective of this study was to determine the prognostic information provided by flow cytometric DNA analysis in non-small-cell lung cancer. Lung samples of 132 consecutive patients submitted to surgery were prospectively processed. When no aneuploid populations were detected in fresh frozen samples, the process continued as a second step in paraffin-embedded tissue, consuming all the tumor available. The influence of ploidy on the postoperative outcome was studied by both a univariate and a multivariate analysis. Aneuploidy was found in 81 patients (61.4%). Fourteen patients showed no aneuploidy in fresh frozen samples; and only after further analysis in paraffin-embedded tissue was abnormal DNA detected. Overall, the 36-month survival was 69% for the diploid group and 24% for the aneuploid group (p = 0.0006). Including subjects submitted to complete tumor removal (stages I, II, and IIIA) in a multivariate analysis adjusted for TNM stage and histologic type, bearers of aneuploid tumors exhibited a higher risk of relapse (hazard ratio 2.65; CI 95% 1.5-4.66;p = 0.004) or death (hazard ratio 2.17; CI 95% 1.08-4.39;p = 0.032) than patients with diploid tumors. DNA ploidy resulted an independent prognostic factor of survival and tumor relapse in completely resected non-small-cell lung cancer. Sequential analysis of fresh and paraffin-embedded samples can help avoid the bias due to intratumoral DNA content heterogeneity. DNA ploidy could be an useful parameter in any future multifactorial analysis of outcome in such tumors.

Aneuploidy↗
PubMed1983

A detergent-trypsin method for the preparation of nuclei for flow cytometric DNA analysis.

A new modification of our detergent technique for the preparation of nuclei for flow cytometric DNA analysis is described. The attainment of low coefficients of variation of the peaks and of quantitative staining of nuclei from different tissues was a problem with the original method. This was solved in the new modification by trypsinization of the unfixed nuclei. The nuclei were stabilized by spermine. A simple procedure for long-term storage of samples at -80 degrees C was integrated into the method. The fluorescence of the nuclei was stable for at least 3 hours after staining. Light exposure protection of the samples was essential. No cell loss was caused by storage or staining. The method was successfully applied on samples including: (a) Normal tissues--human lymphocytes, granulocytes and spleen. Mouse lymphocytes, bone marrow, spleen, liver, kidney and thymus. (b) Human neoplasms--lung cancer, breast cancer, lymphoma, leukemia, bladder cancer and cancer of the oral cavity. (c) Human tumors in nude mice--breast cancer, lung cancer, melanoma and colon cancer. (d) Mouse ascites tumors--JB-1, L 1210, Ehrlich and P 383. It therefore seems well suited as a routine clinical procedure.

Animals↗
PubMed1995

Molecular characterisation of Escherichia coli O157:H7 isolates by pulsed-field gel electrophoresis and plasmid DNA analysis.

Foods of bovine origin have been identified as sources of Escherichia coli O157:H7. Genomic DNA of E. coli O157:H7 isolates from patients (six isolates), food samples (18 isolates from ground beef and six isolates from raw milk) and calf faecal samples (31 isolates) were characterised by pulsed-field gel electrophoresis (PFGE) and plasmid DNA analysis. These isolates originated from different locations in the USA during 1992 and 1993. Twenty-one distinct genomic profiles were generated from the 61 isolates by PFGE after digestion with the endonuclease XbaI. Four genomic profiles were identified among five patient isolates and the remaining patient isolate was not typable. Five different profiles were detected amongst the isolates from ground beef, one of which was associated with 13 ground beef isolates from an outbreak in the Pacific Northwest of the USA in 1993. The PFGE profile of five calf isolates from Washington and Wisconsin was identical to the profile of the ground beef isolates from the outbreak, suggesting that these isolates were related. Similarly, one PFGE profile accounted for three isolates from calf faeces and one from ground beef. Six raw milk isolates from Georgia were indistinguishable both from each other and from one isolate from calf faeces. Fourteen genomic profiles were identified among 31 calf faecal isolates from 18 different herds in 11 states. Only five plasmid profiles were identified among the 61 isolates. PFGE was shown to be a useful typing technique for E. coli O157:H7.

Animals↗
PubMed1992

Comparative DNA analysis of solid tumors by flow cytometric and image analyses of touch imprints and flow cell suspensions.

Comparative DNA analysis by flow cytometric (FCM) and image analyses (IA) has shown a high concordance rate. When present, discordance has been attributed to the presence of aneuploid cell populations detected only by IA, yet missed by FCM. This phenomenon has been explained by loss of aneuploid cells during FCM cell processing, differences in sampling area, or misinterpretation of the DNA histograms. To determine which factors are responsible for the discordance between IA and FCM, 82 fresh solid tumors from various sites were examined. Flow cytometric analysis was performed on cell suspensions isolated from the tumors, whereas IA was performed on touch imprints (IAT) and on cytosmears of the same cell suspension used for FCM (IAF). Comparison between IAT and IAF (IAT/IAF) assessed cell processing and sampling area differences, whereas IAF/FCM comparison assessed differences in apparatus and methodology as possible contributing factors to discordance. Furthermore, DNA histograms of IAT, IAF, and FCM were analyzed in the discordant cases to determine whether the discordance was due primarily to different cell populations detected (true discordance) or due to differences in histogram interpretation of the same cell populations (false discordance). IAT/IAF and IAF/FCM concordance rates (90% and 88%) were not significantly different from that of IAT/FCM (87%). False discordance accounted for most of the discordant cases in IAT/FCM comparison (six cases, 67%), whereas true discordance was seen in three cases. In all three truly discordant cases, the DNA-aneuploid cell populations detected only by IAT yet missed by FCM were also detected by IAF. This study demonstrates that discordance between IA and FCM is probably not due to cell loss during FCM cell processing or sampling area differences, but may be due to differences in assessing DNA ploidy in the interpretation of IA histograms and/or dilution of aneuploid cells by normal diploid cells in FCM.

Cell Separation↗
PubMed1992

[The clinical usefulness of flow cytometric DNA analysis in prostatic cancer].

Flow cytometry was used to measure the DNA content in archival paraffin-embedded prostatic cancer specimens from 54 patients with known outcomes. The specimens were obtained by transurethral resection of the prostate. DNA ploidy as a predictor of prognosis was compared with histological grade and clinical stage. Although no significant correlation between histological grade or clinical stage and ploidy pattern was demonstrated, an increased percentage of DNA aneuploid tumors was seen in higher histological grade and in advanced clinical stage. The survival rate calculated by Kaplan-Meier analysis showed that DNA ploidy pattern was a more reliable indicator to predict survival probability than histological grade or clinical stage. All patients with a near diploid pattern (11 patients) survived more than 5 years, whereas all those with an aneuploid pattern (21 patients) died within 3.5 years. Of 22 patients with a tetraploid pattern, 15 died of tumor progression within 5 years. The remaining 7 patients with favorable outcome had a relatively lower proliferation index (less than 65) in DNA histogram and none of them suffered from stage D disease. In conclusion, the results from this retrospective study suggest that flow cytometric DNA analysis in prostatic cancer would be useful as a means of providing prognostic information.

Aged↗
PubMed1999

Functional activated protein C resistance assays: correlation with factor V DNA analysis is better with RVVT-than APTT-based assays.

We compare results of factor V DNA analysis with three different clotting-based assays designed to detect activated protein C (APC) resistance (APCR), using samples from 958 patients undergoing assessment for thrombophilia. The original and most commonly used APTT-based procedure (generating an APTT ratio in presence versus absence of APC), showed the least correlation with DNA findings, with a large overlap between normals and heterozygotes. Using this procedure, over 40% of patients with a normal DNA pattern gave APTT ratio results within the heterozygotes' ratio range, and thus is a poor predictor for factor V DNA Leiden mutation (sensitivity 94.3%, specificity 47.0% [APC ratio cut-off: 3.1]; sensitivity 52.1%, specificity 92.9% [APC ratio cut-off: 2.0]). Two commercially available procedures (protein C impedance [PCI] test and protein C pathway [PCP] test), using modified Russell's viper venom time (RVVT) assays, showed less overlap between normals and heterozygotes than did the APTT-based method. Fewer than 10% of normal individuals gave PCI or PCP test ratio results that fell within the respective heterozygotes' ratio range (PCI: sensitivity 95.3%, specificity 96.0%; PCP: sensitivity 97.3%, specificity 82.4% [APC ratio cut-off: 1.6 and 1.9 respectively]). Use of previously described normalisation procedures (patient's APTT ratio over pooled normal plasma [PNP] APTT ratio) showed little improvement in discriminatory power (sensitivity 96.4%, specificity 44.8% [normalised APC ratio cut-off value: 0.97]; sensitivity 58.8%, specificity 90.1% [normalised APC ratio cut-off: 0.68]). Use of factor V-deficient plasma as sample diluent improved discrimination for all assays, but added considerable time and cost to the testing process. Furthermore, use of factor V-deficient plasma dilutions in the APTT-based test (sensitivity 97.1%, specificity 93.8% [APC ratio cut-off: 2.0]) did not substantially improve discrimination compared with either PCI or PCP performed without factor V-deficient plasma. Overall, a combination of RVVT- and APTT-based tests was found to provide excellent discrimination, particularly negative prediction, with respect to the likely factor V DNA result. Of 567 patients co-tested, all factor V DNA-normal patients (n = 299) gave both PCP-RVVT and APCR-APTT (not prediluted with factor V-deficient plasma) test ratio values > or = 2.2. In conclusion, it is important to recognise the limitation of plasma-based assays, in particular the APTT procedure, to discriminate the factor V mutation.

Factor V↗
PubMed1990

Microphotometric DNA analysis in moderate dysplasia of the uterine cervix. Correlation to the progression and regression of the lesion.

Nuclear DNA content was determined by microphotometry in 27 cases of moderate dysplasia of the uterine cervix. All these cases were followed from one to ten years to study the biological behavior of moderate dysplasia in relation to cervical carcinogenesis. Ten of them showed progression to carcinoma in situ during a period of one to six years (median 34.8 months) and 17 cases showed regression to inflammation and normalcy during a period of one to ten years (median 44.2 months). DNA analysis was performed both on initial cervical smear and on representative smears collected during follow-up. Amongst ten cases which progressed to malignancy, nine had aneuploid DNA pattern and one had polyploid DNA pattern throughout the follow-up period. Amongst 17 cases which regressed to inflammation, 11 had euploid and six polyploid DNA pattern. The observation that moderate dysplasia with aneuploid DNA value often develops into carcinoma in situ in contrast to dysplasia with euploid or polyploid DNA value strengthens the conception that DNA aneuploidy may be considered as 'high risk indicator' for cervical precancerous lesions.

Adult↗
PubMedDate not supplied

Prediction of dystrophin phenotype by DNA analysis in Duchenne/Becker muscular dystrophy.

Allele-specific molecular diagnosis of Duchenne and Becker muscular dystrophies (DMD and BMD) has been largely dependent upon muscle biopsy for dystrophin protein assay. We performed lymphocyte DNA mutation analysis by polymerase chain reaction on 14 boys presenting with a clinical picture compatible with DMD or BMD. DNA analysis revealed that 12 of 14 boys had a deletion of the dystrophin gene, thus establishing the diagnosis of DMD/BMD. Furthermore, genotypes for 9 of 12 deletion patients permitted prediction of the specific allelic disorder (i.e., DMD or BMD). Subsequent dystrophin testing confirmed all of the DNA-based diagnoses. We propose that DNA mutation analysis be included in the initial evaluation of patients suspected of having DMD/BMD, thus potentially eliminating the need for muscle biopsy in the majority of patients.

Biopsy↗
PubMed1989

Flow cytometric DNA analysis of primary and concurrent metastatic squamous cell carcinoma of the head and neck.

Adequate flow cytometric DNA analysis comparing primary and concurrent metastatic squamous cell carcinoma of the head and neck has not been done in the past. The purpose of this study was to define any differences between the primary and concurrent metastasis of each patient with respect to flow cytometric parameters and histologic grade. Paraffin-embedded archival specimens from 28 patients with primary and metastatic tumors were prepared into nuclei and analyzed by flow cytometry using human lymphocyte standards. The mean DNA index was 0.82 for primary tumors and 0.83 for the metastases. Aneuploidy was found in 68 percent of primary tumors and in 82 percent of metastases. The percentage of cells in the proliferative fraction was 40.4 in the primary tumors and 24.5 in the metastases. A direct correlation was found between the differentiation of the primary and metastatic tumors. No survival difference was discovered among the flow cytometric parameters and histologic grade. We conclude that there is no difference between the primary and concurrent metastasis in squamous cell carcinoma of the head and neck with regard to DNA index, aneuploidy, or histologic grade.

Aneuploidy↗
PubMed2003

[DNA analysis of a 500 year mummy sample].

OBJECTIVE: To accumulate experience for dated forensic matter analysis, for example, Mummy. METHODS: DNA are extracted by methods of phenol-chloroform and are purified by Wizard DNA clean-up system. The STRs locus are ampolification with Promega Powerplus 16 system. The mtDNA hypervariable region 1 (HV1) is amplificated by '3 pair primers'. The products were sequenced with 377 DNA sequencer. RESULTS: The STRs locus very distinctness and mtDNA sequence is correct. CONCLUSION: It is a valuable method for special forensic matters.

Base Sequence↗
PubMed1985

Subspecies differentiation of Moraxella bovis by restriction endonuclease DNA analysis (BRENDA).

A total of 94 strains of Moraxella bovis have been examined by bacterial restriction endonuclease DNA analysis (BRENDA). These strains comprised isolates from the U.S.A., the U.K., in Australia, and from a number of widely separated areas within New Zealand. The strains were classified into a total of 26 different types on the basis of their BRENDA patterns. Fourteen types were present among 34 strains from the U.S.A., eight types from 17 strains in the U.K. three types from five strains in Australia but only one type resulted from all 38 New Zealand strains. Moraxella liquifaciens, M. nonliquifaciens and an atypical Moraxella sp. isolated from cattle eyes in Australia were tested and produced BRENDA patterns clearly different from those of the Moraxella bovis strains. BRENDA, when used with the restriction endonuclease EcoR1, did not provide a means of distinguishing between avirulent, nonhaemolytic M.bovis, and the virulent haemolytic strains.

Journal Article↗
PubMed1992

Thymoma. The prognostic significance of flow cytometric DNA analysis.

The clinical course of patients with thymoma varies widely despite its histologically benign appearance. Treatment decisions are based on local invasion and the extent of resection. Because some patients have more aggressive tumors, the prognostic significance of flow cytometric (FCM) analysis of nuclear DNA content was examined. Adequate tissue from paraffin-embedded blocks was available for 25 patients. Using FCM, the percentage of cells in S-phase (%S) and the ploidy, based on the DNA index (DI), were determined. The mean patient age was 52 years, with a female-to-male ratio of 1.3:1 and a median follow-up of 64 months. Seventeen patients underwent total tumor resections, and 12 also received radiation therapy. Eight patients underwent subtotal resections, with five receiving radiation therapy (with or without chemotherapy) and three receiving chemotherapy alone. Based on invasion and intrathoracic dissemination, the tumors were classified into four stages. The mean %S was 5.6. There was no relationship observed between %S and patient outcome. The 5-year disease-free survival rate was 85% for the 16 patients with diploid (DI = 1) tumors and 33% for the 9 patients with aneuploid (DI more than 1) tumors (P less than 0.002). Similar significant differences were observed by stage and extent of surgery. For those who had total resection (n = 17), the disease-free survival rate was 89% when DI equaled 1 and 50% when DI was more than 1 (P = 0.01). Although the numbers studied were small, when stage, histologic findings, and type of surgery were subdivided by DI, a higher incidence of relapse was associated consistently with aneuploidy. The DI appears to be a useful prognostic parameter for identifying patients at high risk of relapse.

Adolescent↗
PubMed1995

Phylogenetic relationships of some Microsporum and Arthroderma species inferred from mitochondrial DNA analysis.

Thirty-eight strains of 12 Microsporum and 10 Arthroderma (Nannizzia) species were investigated by analysis of mitochondrial DNA with 6 restriction enzymes, and classified into 13 genetic groups. The phylogenetic tree of the 13 groups thus established was constructed. On the tree, M. audouinii, M. langeronii, M. rivalieri, M. distortum, M. equinum, M. ferrugineum and A. otae comprise one genetic group and are suggested to be the same species. A. gypseum, A. fulvum, M. duboisii, M. ripariae, A. incurvatum, A. persicolor and A. obtusum are clustered on one of five boughs of the tree indicating their close relation. A. racemosum and A. cajetani are also closely related.

Ascomycota↗
PubMed1990

DNA analysis of intracellular Campylobacter-like organisms associated with the porcine proliferative enteropathies: novel organism proposed.

Intracellular Campylobacter-like organisms are a consistent feature of the porcine proliferative enteropathies. The relationship between these organisms and known Campylobacter sp. previously associated with the disease was studied using restriction enzyme analysis and DNA-DNA blot hybridization techniques. BglII restriction enzyme fragment patterns of DNA of the Campylobacter-like organisms were fundamentally different from those of C. mucosalis, C. hyointestnalis, C. jejuni, and C. coli. Crude DNA preparations from Campylobacter-like organisms hybridized strongly with homologous preparations, weakly with porcine DNA and not at all with DNA from Campylobacter sp. Fragment specific DNA probes prepared from Campylobacter-like organisms only hybridized with homologous preparations. This work suggests that the intracellular Campylobacter-like organisms are not one of the known Campylobacter sp. It is possible that they are a novel, uncultured organism worthy of a new name, such as HC. intracellulare'.

Animals↗