PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “DNA analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 595 records · Page 33Linked to original sources

Medium-chain acyl-CoA dehydrogenase deficiency does not correlate with apparent life-threatening events and the sudden infant death syndrome: results from phenylpropionate loading tests and DNA analysis.

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most common inherited disorder of fatty acid metabolism and typically presents in early childhood as potentially fatal hypoketotic, hypoglycaemic crisis often associated with Reye-like symptoms. Re-investigations of cases of sudden infant death syndrome (SIDS) have revealed in some instances a deficiency of MCAD, suggesting that this metabolic disorder may lead to sudden infant death without prior clinical symptoms. In the present study, we examined 142 infants who had suffered from an apparent life-threatening event (ALTE) or were otherwise considered at risk for SIDS for MCAD deficiency by phenylpropionate loading. In no case excretion of phenylpropionylglycine, the hallmark of MCAD deficiency, was increased. In contrast, 3 out of 55 children with symptoms of metabolic disorders showed increased phenylpropionylglycine excretion, and in all three cases MCAD deficiency was confirmed by DNA analysis. In addition, we investigated 142 cases of sudden unexplained child death and 100 control subjects for the A985G mutation in the MCAD gene which is associated with about 98% of enzyme deficiencies. We found one case of heterozygosity each in the patient and control group. Our data indicate that MCAD deficiency is not a major cause of ALTE and, in agreement with results from similar studies in other countries, its frequency is not increased in children who died of SIDS.

Acyl-CoA Dehydrogenase↗

Ancient DNA analysis of human populations.

The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA.

Animals↗

Flow-cytometric DNA analysis and immunohistochemical measurement of Ki-67 and BUdR labeling indices in human brain tumors.

Cell proliferation potential was assessed by measuring the labeling indices of the monoclonal antibody Ki-67 and of 5-bromodeoxyuridine (BUdR), and the cellular deoxyribonucleic acid (DNA) content in 48 human brain tumors. The diagnostic and prognostic value of flow-cytometric DNA analysis was also evaluated using ethanol-fixed paraffin-embedded BUdR-labeled specimens; these were the same specimens as were used for measuring the BUdR and Ki-67 labeling indices. Both the Ki-67 and the BUdR labeling indices correlated with the degree of malignancy estimated from conventional histological preparations. The Ki-67 labeling index was 1.7 times greater than the BUdR labeling index. The relationship of DNA aneuploidy to the labeling indices or to morphology in cases of glioma was examined. All of the tumors with an aneuploid line corresponded to malignant glioma classified by histological criteria, although malignant glioma did not always show DNA aneuploidy. In addition, the cases with aneuploid lines showed high BUdR and Ki-67 labeling indices. The cell kinetic data, which indicate the biological character of tumors, allowed prediction of the prognosis of the patients with gliomas. In contrast, despite the presence of an aneuploid line, three of 13 meningiomas showed a benign histological pattern without an aggressive clinical course, and neither the Ki-67 nor the BUdR labeling index was high. These results indicate an unequivocal relationship between DNA aneuploidy and clinical behavior; in general, both labeling indices may prove to be objective indicators of the outcome of patients with brain tumors.

Aneuploidy↗

Hb-M "Hyde Park": a de novo mutation, identified by mass spectrometry and DNA analysis.

BACKGROUND: Structural hemoglobinopathies usually are inherited as autosomic dominant traits; de novo mutations are uncommon. Analytical and preparative procedures for the characterization of an abnormal hemoglobin are complex and time-consuming. Mass spectrometer analysis allows a rapid identification of the amino acid substitution. METHODS AND RESULTS: A cyanotic 7-year-old girl was found to have 16% methemoglobin. Laboratory data showed the presence of an abnormal hemoglobin, which was isolated by collecting the abnormal peak from DEAE and globin chains from CM52. The amino acid substitution was rapidly identified by FAB mass spectroscopic analysis, leading to the recognition of HbM Hyde Park. These data were confirmed by molecular analysis (Southern blot and DNA sequencing). Neither the parents nor a sister showed any abnormality; non-paternity was excluded by blood group serology and HLA typing. CONCLUSIONS: This is a case of HbM Hyde-Park arising as a de novo mutation. FAB mass spectroscopic analysis is a rapid and useful analytical method for identifying aminoacid substitution.

Blotting, Southern↗

Flow cytometric DNA analysis of placental-site trophoblastic tumors.

The placental-site trophoblastic tumor is a rare form of gestational trophoblastic neoplasia. Although originally considered benign, it is now apparent that this lesion can be associated with aggressive clinical behavior. Our study examined the DNA ploidy status and clinicopathologic features of four new cases of placental-site trophoblastic tumor. Three cases demonstrated diploid DNA stemlines with S-phase fractions ranging from 6% to 16%. These patients were alive and well at follow-up and had low-serum human chorionic gonadotrophin (hCG) levels. A fourth patient, who had a large tumor, demonstrated a tetraploid DNA peak with a prominent S-phase fraction. This patient exhibited an elevated serum hCG at limited follow-up. Flow cytometric DNA analysis may be a useful adjunct for the identification of placental-site trophoblastic tumors with malignant potential.

Adult↗

Presymptomatic diagnosis in Portuguese FAP families using intragenic RFLPs and (CA)n flanking markers by fluorescence based semiautomated DNA analysis.

Owing to the large size of the APC gene, responsible for familial adenomatous polyposis, direct screening for individual mutations is not a practical approach. In the present study we establish the methodology of fluorescence based semi-automated DNA analysis to perform presymptomatic diagnosis of members at risk from 11 Portuguese FAP families with three (CA)n markers flanking the APC gene, MBC, CB26, and YN5.64, and four intragenic RFLPs. Haplotypes were constructed on the basis of individual genotypes and their segregation through generations were followed. The study was informative for 12% of subjects using only intragenic RFLPs and increased to 90% when we used the three (CA)n flanking markers. We report two of the 11 families under study in our laboratory and show recombinant events leading to a precise localisation of the CB26 marker between D5S82 and the APC gene. In one family there was a loss of (CA) units of one allele of the CB26 marker from an unaffected mother to her son.

Adenomatous Polyposis Coli↗

Flow cytometric DNA analysis of specimen mammography-guided fine-needle aspirates of ductal carcinoma in situ.

Flow cytometric studies of screening mammography detected ductal carcinoma in situ (DCIS) are limited by the lack of fresh cell samples. We have performed flow cytometric DNA analyses of specimen mammography-guided fine-needle aspirates of 50 consecutive DCIS lesions detected by screening mammography. The comedo histologic subtype had an aneuploidy rate of 39% (9 of 23); noncomedo subtypes had an aneuploidy rate of 19% (5 of 27), p=ns. Noncomedo subtypes were more likely to have low (less than 2.2%) S-phase percentages, 59% (16 of 27) as compared to comedo, 9% (2 of 23), p<0.05. High and intermediate nuclear grade DCIS lesions had an insignificantly greater rate of aneuploidy, 35% (9 of 26) and 33% (4 of 12) respectively, as compared to low nuclear grade lesions, 8% (1 of 12), p=ns. Low and intermediate nuclear grade DCIS lesions had low S-phase percentage rates of 67% and 50% respectively, as compared to the high nuclear grade lesions low S-phase percentage rate, 15%, p=ns. Aneuploidy and lesser rates of low S-phase percentages were significantly associated with necrosis and apoptosis. Our data suggest that flow cytometric DNA analysis of mammographic lesion-specific, fresh cell samples obtained by fine-needle aspiration under specimen mammographic guidance can assess mammography-detected DCIS lesions when gross fresh tissue procurement is not possible.

Adult↗

[Serovar-distribution, drug-resistance, and DNA analysis of Salmonella strains isolated from sporadic diarrhea cases or healthy cases in Tama, Tokyo (1991-2000)].

Serovar-distribution and drug-resistance of a total of 421 Salmonella strains, which were 98 stains from sporadic diarrhea cases and 323 strains from healthy cases between 1991 and 2000 in Tama, Tokyo were investigated. In serological typing tests, the strains tested were classified into 26 different kinds of serovar in diarrhea cases, 58 in food handlers, and 25 in individuals for health care. Salmonella serovar Enteritidis (S. Enteritidis) was the most predominant serovar in three cases. Following, S. Typhimurium and S. Infantis in diarrhea cases, S. Hadar, S. Montevideo and S. Thompson in food handlers, or S. Typhimurium, S. Lichfield and S. Oranienburg in healthy individuals were frequent. The drug-resistance test using 9 drugs (CP, TC, SM, KM, ABPC, SXT, NA, FOM, and NFLX) showed that 57.1% of the strains from diarrhea cases and 36.8% from the healthy cases were resistant to one or the other of the drugs examined. Drug-resistance patterns of those showed 13 types in diarrhea cases and 25 types in healthy cases. Out of them, strains which showed a predominant and common pattern in both cases were SM resistant-S. Enteritidis and CP.TC.SM.ABPC resistant-S. Typhimurium. In addition, the latter strains were also resistant to sulfiso-xzole (SU). In DNA analysis by RAPD method of their strains, common DNA finger-prints were observed in both cases through out the investigation period.

DNA, Bacterial↗

Primary malignant melanoma of the oesophagus. Report of a case with flow cytometric DNA analysis.

Primary malignant melanoma is a very rare tumour of the oesophagus, and although this is the first case reported in a black patient in South Africa, the clinical, radiographic and histopathological features were characteristic of this malignancy. Primary oesophageal melanoma is a highly lethal tumour--fewer than 2% of patients are surviving 5 years after diagnosis. Flow cytometric DNA analysis of the resected specimen in this case revealed two populations of malignant cells, one of which had grossly abnormal DNA. Existence of two clones of malignant melanoma cells supports the observations that this tumour is biologically aggressive, radioresistant and almost always incurable.

DNA, Neoplasm↗

Autosomal dominant polycystic kidney disease: prenatal diagnosis by DNA analysis and sonography at 14 weeks.

A pregnant woman affected with autosomal dominant polycystic kidney disease (ADPKD) had a history of an affected fetus, diagnosed by sonography at 29 weeks of pregnancy. The proband's father was also affected. DNA analysis performed on chorionic villi at 11 weeks during a second pregnancy predicted an affected fetus, and sonographic examination at 14 weeks confirmed the diagnosis.

Adult↗

[Quantitative DNA analysis in epithelial ovarian cancer].

The tumor cell nuclear DNA content was measured in 27 cases of epithelial ovarian cancer. The proliferative activity of the tumor was correlated with the prognosis of the patients. The proportion of G0 and G1 cells of the tumors of the same histologic type varied among individuals. There was a close relationship between the proliferative activity of the tumor and the remission rate, duration of survival and mortality of the patients. The heterogeneity of the proliferative activity of the tumor cells may explain the difference of response to chemotherapy. It is suggested that the quantitative analysis of DNA content may be used as an theoretical and experimental basis for the individualization of treatment.

Cell Cycle↗

Random amplified polymorphic DNA analysis of genetic relationships among Acanthopanax species.

Random amplified polymorphic DNA (RAPD) analysis was used to determine the genetic relationships among seventeen species of the Acanthopanax species. The DNA isolated from the leaves of the samples was used as template in polymerase chain reaction (PCR) with twenty random decamer primers in order to distinguish plant subspecies at the level of their genomes. The RAPD patterns were compared by calculating pairwise distances using Dice similarity index, and produced to the genetic similarity dendrogram by unweighted pair-group method arithmetic averaged (UPGMA) analysis, showing three groups; a major cluster(twelve species), minor cluster (4 species) and single-clustering species. The results of RAPD were compatible with the morphological classification, as well as the chemotaxonomic classification of the Acanthopanax species. The Acanthopanax species containing 3,4-seco-lupane type triterpene compounds in their leaves corresponded to the major cluster, another species having oleanane or normal lupane type constituents to minor clusters, and one species not containing triterpenoidal compound to single-cluster.

Eleutherococcus↗

A comparison of Echinostoma trivolvis and E. caproni using random amplified polymorphic DNA analysis.

The random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) technique was applied to two closely-related echinostome species, Echinostoma trivolvis and E. caproni, demonstrate interspecific polymorphisms of genomic DNA. Band patterns generated using five individual primers showed that these two echinostomes were genetically distinct, although they share genomic DNA to some extent.

Animals↗

Vitis vinifera must varietal authentication using microsatellite DNA analysis (SSR).

A microsatellite DNA-based method for Vitis vinifera grape must authentication is presented. Five of the most important port wine producing grape cultivars (Tinta Roriz, Tinto Cão, Touriga Francesa, Touriga Nacional, and Tinta Barroca) were typed at four microsatellite loci described by Bowers et al. (Genome 1996, 39, 628-633) and Thomas and Scott (Theor. Appl. Genet. 1993, 86, 985-990). The corresponding 5 varietal musts and 26 must mixtures that result from the combination of the five varieties were also typed at the four loci. There were no differences between the corresponding leaf and varietal must profiles. All must combinations showed the expected band profiles corresponding to the sum of the varietal band profile components. Among the 26 must mixtures, 8 could be discriminated using the four loci.

DNA, Plant↗

Sensitive and specific detection of Xanthomonas campestris pv. pelargonii with DNA primers and probes identified by random amplified polymorphic DNA analysis.

The random amplified polymorphic DNA method was used to distinguish strains of Xanthomonas campestris pv. pelargonii from 21 other Xanthomonas species and/or pathovars. Among the 42 arbitrarily chosen primers evaluated, 3 were found to reveal diagnostic polymorphisms when purified DNAs from compared strains were amplified by the PCR. The three primers revealed DNA amplification patterns which were conserved among all 53 strains tested of X. campestris pv. pelargonii isolated from various locations worldwide. The distinctive X. compestris pv. pelargonii patterns were clearly different from those obtained with any of 46 other Xanthomonas strains tested. An amplified 1.2-kb DNA fragment, apparently unique to X. campestris pv. pelargonii by these random amplified polymorphic DNA tests, was cloned and evaluated as a diagnostic DNA probe. It hybridized with total DNA from all 53 X. campestris pv. pelargonii strains tested and not with any of the 46 other Xanthomonas strains tested. The DNA sequence of the terminal ends of this 1.2-kb fragment was obtained and used to design a pair of 18-mer oligonucleotide primers specific for X. campestris pv. pelargonii. The custom-synthesized primers amplified the same 1.2-kb DNA fragment from all 53 X. campestris pv. pelargonii strains tested and failed to amplify DNA from any of the 46 other Xanthomonas strains tested. DNA isolated from saprophytes associated with the geranium plant also did not produce amplified DNA with these primers. The sensitivity of the PCR assay using the custom-synthesized primers was between 10 and 50 cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

Genomic DNA analysis of rodent mycoplasmas.

Genomic DNA was compared between three typical species of rodent mycoplasmas, Mycoplasma pulmonis, M. arthritidis and M. neurolyticum, and between strains of these species. Each of the three species showed a distinct restriction endonuclease cleavage pattern of genomic DNA. The genetic heterogeneity of these species was revealed by total DNA hybridization as well. In addition, the restriction endonuclease cleavage pattern of genomic DNA was almost identical in three strains of M. pulmonis and in two strains of M. neurolyticum. The genetic hemogeneity among strains of the same species was revealed by total DNA hybridization as well. These data suggest that the genomic DNA sequence of each rodent mycoplasma species has a high degree of species specificity.

Animals↗

DNA fingerprinting of Streptococcus pyogenes from patients with recurrent pharyngotonsillitis by means of random amplified Polymorphic DNA analysis.

In recent years, several DNA fingerprinting methods have been tried for the epidemiological investigation of Streptococcus pyogenes isolates. We chose the Random Amplified Polymorphic DNA (RAPD) method for the typing of pre- and post-antibiotic treatment S. pyogenes isolates obtained from 14 patients with pharyngotonsillitis. Isolates from 4 patients had been collected 10 years earlier than from the others. Hence epidemiological connections between the strains were unlikely. Both pre- and post-antibiotic treatment isolates showed identical RAPD patterns, indicating that recurrences in these patients had been caused by homologous strains of S. pyogenes. It was possible by means of RAPD to differentiate between 12 different T-types and occasionally between clones of the same serotype of S. pyogenes. The RAPD method is an easier alternative to traditional DNA-typing techniques and provides quick results with minimal technical complexity.

Bacterial Typing Techniques↗

[Nuclear DNA analysis of hepatocellular carcinoma].

Retrospective DNA ploidy studies of paraffin-embedded blocks were performed by flow cytometry on 212 surgically resected hepatocellular carcinoma. One hundred and sixty-four of 212 specimens yielded evaluable DNA histograms. Eighty-three cases showed a DNA diploid pattern and 81 a DNA non-diploid pattern. The incidence of non-diploid pattern increased with the tumor size. (2cm; 15.4%, 2-5; 42.3%, 5-10; 70.8% greater than 10; 73.3%). The DNA pattern correlated with the backgrounds, the degree of vascular invasion, intrahepatic metastasis and serum AFP levels. Survival of patients with non-diploid pattern was significantly less than those with diploid patients in any different stage. Of thirty who survived three years with disease free condition, 20 patients showed diploid patterns. Though remaining 10 patients were non-diploid patterns, 9 were high DNA index more than 1.5. It is concluded that flow cytometric DNA ploidy study had prognostic value for patients with surgically resected hepatocellular carcinoma.

Carcinoma, Hepatocellular↗