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 289 records · Page 16Linked to original sources
PubMed1993

Identification of Gaucher disease carriers: glucocerebrosidase antigen and DNA analysis.

Detection of Portuguese carriers for Gaucher disease with urine samples as a source of enzyme was carried out using an immunological procedure employing an anti-glucocerebrosidase monoclonal antibody and by DNA analysis for the presence of the two glucocerebrosidase mutations most frequently found in Portuguese Gaucher patients. Patients, obligate and putative carriers, and individuals unrelated to patients were analyzed. It was found that the vast majority of carriers for the two tested mutations (N370S and L444P), as well as obligate carriers for as yet unidentified mutations, could be distinguished from control subjects with this relatively easy and economic immunological procedure. Furthermore, results obtained for control subjects suggested a high frequency of carriers for the N370S mutation in the Portuguese population. It is concluded that this procedure may be useful in mass screening for carrier detection prior to DNA analysis, particularly in the study of non-Ashkenazi populations in which a significant number of mutations associated with Gaucher disease remain unidentified.

Adolescent↗
PubMed2002

Methacarn fixation for genomic DNA analysis in microdissected, paraffin-embedded tissue specimens.

We recently found methacarn to be a versatile fixative for analysis of RNA and protein applicable for microdissected specimens from paraffin-embedded tissue (PET). In this study we investigated the performance of methacarn for genomic DNA analysis using microdissected rat tissues. We found that extensive portions of DNA up to 2.8 kb could be amplified by nested PCR using DNA templates extracted by a simple and rapid extraction procedure from a 1 x 1-mm area of cerebral cortex of a 10-microm-thick section. By nested PCR, a 522-bp fragment from a single cell could be amplified in 20% of cresyl violet-stained Purkinje cells, and the minimal number of cells required, as estimated using hippocampal neurons, was on the order of 10-20. Although tissue staining with hematoxylin and eosin affected the PCR, amplification of a 522-bp fragment was successful, with 150-270 cells by 35 cycles of single-step PCR. Immunostaining resulted in a substantial decrease of yield and degradation of extracted DNA. However, even after immunostaining, a 184-bp DNA fragment could be amplified with 150-270 cells by 35 cycles of PCR. The results thus demonstrate the superior performance of methacarn to that reported with formalin in genomic DNA analysis using microdissected PET specimens.

Acetic Acid↗
PubMed1990

Flow cytometric analysis of localized adenocarcinoma of the prostate: the use of archival DNA analysis in conjunction with pathological grading to predict clinical outcome following radical retropubic prostatectomy.

Fifty-four specimens from patients undergoing radical prostatectomy for clinically confined prostate cancer between 1983 and 1987 were reviewed to determine the potential for flow cytometric (FCM) analysis of DNA ploidy and replication rate to predict disease recurrence. Each specimen was deparaffinized for FCM analysis and the pathology slides were reviewed by a single pathologist. FCM characteristics were correlated with pathological grade and stage, and both were correlated with disease status. In this series of patients, routine FCM analysis of DNA ploidy and replication rate failed to significantly enhance the ability of standard histopathological grading to predict disease recurrence in patients having clinically localized prostate cancer. Aneuploid tumors pathologically confined to the prostate did not appear to negatively affect prognosis.

Adenocarcinoma↗
PubMedDate not supplied

Cytophotomeric DNA-analysis of aspirated cells from prostatic carcinoma.

In the present study material obtained from prostatic lesions by transrectal aspiration biopsy was subjected to a comparative morphologic and cytophotometric DNA analysis. Based on the morphologic pattern, the clinical material was divided into benign lesions (prostatic hyperplasia), suspected prostatic malignancy and highly, moderately and poorly differentiated prostatic carcinoma. The cytochemical analysis, based on quantitative cytophotometric measurements of Feulgen stained nuclei, showed that cell nuclei from benign lesions (prostatic hyperplasia) exhibited the normal diploid amount of DNA. Contrary to this, cell populations from prostatic malignancies, were characterized by various degrees of heteroploidy, i.e. the existence of cells with nuclear DNA quantities increased above the normal diploid level. A general correlation between degree of heteroploidy (frequency of heteroploid cells) and degree of clinical malignancy seemed to exist; high grade malignant prostatic carcinoma (poorly differentiated) exhibited a pronounced degree of heteroploidy with more or less distinct aneuploid stemlines, whereas low-grade prostatic carcinomas (highly differentiated) were more similar to benign cell populations, in showing a large proportion of cells with a diploid DNA quantity suggesting the existence of diploid or near diploid stemlines. Cases morphologically classified as moderately differentiated prostatic carcinoma, which previously have been shown to exhibit individual variations in degree of clinical malignancy, also showed large individual variations in degree of hetyroploidy. Approximately half of these cases had cytochemical DNA characteristics similar to that of highly differentiated prostatic carcinoma in showing a modal DNA value in the diploid region, while the other half showed cytochemical characteristics similar to that of poorly differentiated prostatic carcinoma, i.e. aneuploid DNA distributions. However, no morphologiifferentiated prostatic carcinoma. In conclusion it can be stated that the present investigation suggests the possibility that quantitative cytochemical DNA analysis may be used in combination with, and offer additional information to, morphologic analysis in the malignancy grading of prostatic carcinoma. A future clinical follow-up, now in progress, will hopefully give a more definite answer to that idea.

Biopsy, Needle↗
PubMed1997

DNA analysis by flow cytometry in early gastric cancer.

OBJECTIVES: Flow cytometric analysis of a paraffin-embedded block of tissue provides rapid and accurate means of analyzing the DNA content of a tumor. The aim of this study was to clarify the clinical significance of flow cytometric findings in early gastric cancer(EGC). Thus we conducted this study to investigate whether DNA contents of tumor cells can correlate with known prognostic indices in patients with EGC. METHODS: The flow cytometric DNA analysis was performed with paraffin-embedded specimens from tumors of 107 patients with EGC. Flow cytometric analysis was performed using a FACScan (Becton Dickinson). In constructing the histogram, 30,000 cells were scanned from each section and results were scored. The S-phase fraction was obtained according to the CellFit cell cycle analysis (Becton Dikinson). Frequencies of aneuploidy in tumors with various clinical and pathologic parameters were compared using the chi-square test. Mean SPF/PI valuse were compared by the student t-test. RESULTS: Diploidy pattern was observed in 80 (75%) cases while aneuploidy was seen in 27(25%) cases. Aneuploidy was more frequently detected in tumors with submucosal involvement (32.7%) and lymph node (+) group (30.8%) than in the mucosal tumor (17.3%) and lymph node (-) group (24.5%), but the differences were not significant. Frequency of aneuploidy was not affected by either the histologic type or morphologic classification. On the other hand, high proliferative activities (SPF/PI) significantly correlated with the submucosal tumor invasion (66.7% vs. 45%; p < 0.05) and lymph node metastasis (28.6% vs. 7.5%; p < 0.05). CONCLUSION: Tumor aggressiveness is not directly related to DNA aneuploidy but proliferative activities are responsible for the aggressive nature of early gastric cancer. The results of this study show that DNA analysis by flow cytometry in considered to be one method of determining the biological activity of gastric cancer cells.

Adult↗
PubMed2002

Recovery from marked altered consciousness in a patient with adult-onset type II citrullinemia diagnosed by DNA analysis and treated with a living related partial liver transplantation.

A 21-year-old woman was admitted with altered consciousness and hyperammonemia. She was diagnosed as having adult-onset type II citrullinemia (CTLN2) by DNA analysis. The patient had mutations of the SLC25A13 gene, which were compound heterozygotes of 851 del 4 and IVS11+1G>A. CTLN2 has a poor prognosis, in spite of various intensive medications, and we performed a living related partial liver transplantation (LRLT). Over a 2-year follow-up, the patient has been well. CTLN2 can be diagnosed by the DNA analysis and can be treated by LRLT.

Adult↗
PubMed1986

Chemosensitivity of human small cell carcinoma of the lung detected by flow cytometric DNA analysis of drug-induced cell cycle perturbations in vitro.

A method based on detection of drug-induced cell cycle perturbation by flow cytometric DNA analysis has previously been described in Ehrlich ascites tumors as a way to estimate chemosensitivity. The method is extended to test human small-cell carcinoma of the lung. Three tumors with different sensitivities to melphalan in nude mice were used. Tumors were disaggregated by a combined mechanical and enzymatic method and thereafter have incubated with different doses of melphalan. After incubation the cells were plated in vitro on agar, and drug induced cell cycle changes were monitored by flow cytometric DNA analysis. Melphalan produced a dose-related S phase accumulation in the two sensitive tumors, whereas no changes in the cell cycle distribution were found in the resistant tumor. The size of S phase accumulation correlated to the chemosensitivity in vivo. For low concentrations of melphalan, the S phase accumulation was accompanied by G2 + M accumulation. The results indicate that the method may be extended to sensitivity testing of human solid tumors, including screening for new agents.

Animals↗
PubMed1995

Cytokine treatment of human bone marrow activates anti-leukaemia effector cells: monitoring of purging by polymerase chain reaction and DNA analysis.

The aims of this study were to investigate the role of cytokines (tumour necrosis factor alpha (TNF alpha), interferon gamma (IFN gamma) and interleukin-2 (IL-2) in augmenting graft-versus-leukaemia (GVL). We have investigated the effector cells involved in GVL, by studying the role of these cells in purging of the cell line K562 in short-term bone marrow cultures. The effect of the addition in vitro of rGCSF was also studied. Monitoring of purging was achieved by cytotoxicity assays, DNA analysis and the use of the polymerase chain reaction for the detection of bcr/abl transcripts in the Philadelphia positive (Ph+) K562 cell line. Supernatants from IL-2-treated and non-treated bone marrow were tested for cytokine production (TNF alpha and IFN gamma). The results have shown that the main cytotoxic effector cells in the bone marrow generated by IL-2 have the CD56+ CD8+ phenotype. Overnight incubation of bone marrow was sufficient to generate cytotoxic cells as measured by Chromium51 (Cr51) release assays. Measurable levels of TNF alpha but not IFN gamma were also detected in supernatants. Addition of TNF alpha and IFN gamma to the IL-2 in the bone marrow cultures augmented the cytotoxicity but tended to inhibit progenitor cell growth as measured by granulocyte-macrophage colony-forming unit (GM-CFU) and erythroid blast-forming unit (BFU-e) assays. An estimate of the purging of the marrow could also be achieved by DNA analysis of K562 DNA in bone marrow. The bcr/abl transcript could still be detected by PCR analysis in marrow containing 1% K562 and treated with IL-2 for 24 h, but by 6 days of incubation the bcr/abl transcript was weak or undectable. The results suggest that although reduction in the proportion of leukaemia in contaminated marrow can be detected after incubation with IL-2 for 24 h, complete elimination of minimal residual disease requires longer incubation times.

Biomarkers, Tumor↗
PubMed2004

The etiologic diagnosis of infectious discitis is improved by amplification-based DNA analysis.

OBJECTIVE: Blood cultures and cultures of disc material are required to identify and treat bacterial agents responsible for septic spondylodiscitis, but these methods have limited sensitivities. We undertook this study to compare nonculture amplification-based DNA analysis with conventional culture of disc aspirate. METHODS: Nineteen patients with spondylodiscitis, including 11 with a history of spinal surgery, presented with negative blood cultures and underwent percutaneous disc or epidural abscess puncture for bacterial diagnosis. Amplification by polymerase chain reaction was performed on 16S ribosomal DNA universal target genes and femA staphylococci-specific target genes in all patients, and on the upstream p34 mycobacterial gene in 1 patient. Species identification relied on amplicon sequencing and comparison with templates from GenBank. Amplification of the femA gene led to subsequent testing for methicillin resistance by amplification of the mecA gene. Further assessment using a staphylococci- and methicillin resistance-specific DNA array was performed on 3 samples. RESULTS: Microbiologic and molecular assays identified the causative organism in 14 of 19 patients (74%) and 19 of 19 patients (100%), respectively. In culture-positive patients, DNA-based and microbiologic results were highly correlated. Five agents (Staphylococcus simulans, Staphylococcus sciuri, Brucella species, Actinomyces israelii, and Mycobacterium tuberculosis complex) were identified only by DNA-based methods. In 1 sample, Corynebacterium jeikeium and coagulase-negative Staphylococcus were both cultured, whereas DNA analysis identified only Staphylococcus hominis. CONCLUSION: DNA-based methods are highly sensitive and specific. They can usefully complement standard microbiologic methods for identifying the cause of infectious spondylodiscitis and contribute to species-specific therapeutic orientation in patients with negative blood and disc aspirate cultures.

Adult↗
PubMed1996

[Flow cytometric DNA analysis of malignant potential in colorectal cancer].

Significance of flow cytometric DNA analysis for assessing malignant potential and survival of colorectal cancer was investigated using paraffin-embedded materials from 163 patients who underwent resection of curability A from 1971 to 1985, excluding intramucosal carcinoma. DNA diploid was confirmed in 46% (75 cases) of the patients and DNA aneuploid in 54% (88 cases). No significant correlation was seen between DNA ploidy and clinicopathological factors, such as tumor location, macroscopic type, histological type, depth of invasion, lymph node metastasis and stage. Cumulative survival rates after curable resection of colorectal cancer were significantly lower in patients with DNA aneuploid tumor than those with DNA diploid tumor. Furthermore, in patients in stage of II and III, survival rates were lower in DNA aneuploid patients than DNA diploid patients, respectively. A multivariate analysis of survival data using Cox's proportional hazard model showed that DNA ploidy was the significant discriminating factor on survival in stage II and III cancer. In conclusion, nuclear DNA ploidy in patients with stage II and III colorectal cancer undergoing curable resection may represent malignant potential and may be an independent prognostic factor.

Colorectal Neoplasms↗
PubMed1992

Identification of the skeletal remains of Josef Mengele by DNA analysis.

There has been considerable controversy over the identity of the skeletal remains exhumed in Brazil in 1985 and believed to be those of Dr Josef Mengele, the Auschwitz 'Angel of Death'. Bone DNA analysis was therefore conducted in an attempt to provide independent evidence of identity. Trace amounts of highly degraded human DNA were successfully extracted from the shaft of the femur. Despite the presence of a potent inhibitor of DNA amplification, microsatellite alleles could be reproducibly amplified from the femur DNA. Comparison of the femur DNA with DNA from Josef Mengele's son and wife revealed a bone genotype across 10 different loci fully compatible with paternity of Mengele's son. Less than 1 in 1800 Caucasian individuals unrelated to Mengele's son would by chance show full paternal inclusion. DNA analysis therefore provides very strong independent evidence that the remains exhumed from Brazil are indeed those of Josef Mengele.

Concentration Camps↗
PubMed1991

DNA analysis of Duchenne and Becker muscular dystrophy using pERT87 genomic probes and dystrophin cDNA probes--establishing the optimum strategy for carrier diagnosis in the Japanese population.

DNA analysis was performed on 19 unrelated Duchenne muscular dystrophy (DMD) families and one Becker muscular dystrophy (BMD) family in Japan to determine their carrier status. The intragenic genomic probe pERT87 with its subclones 87-1, 87-8, and 87-15 were used together with five cDNA probes from the 5' end of the dystrophin gene. The tests with both a high polymorphism information content (P.I.C.) and a high observed P.I.C. were most effective, i.e., pERT87-1/XmnI, pERT87-15/XmnI, pERT87-8/TaqI, and pERT87-8/BstXI. These test combinations were useful in the Japanese population but pERT87-15/TaqI was not, although it was effective in Caucasians. Two additional test combinations of pERT87-1/MspI and pERT87-15/BamHI were highly useful in detecting restriction fragment length polymorphisms (RFLPs) when other tests were not informative. Carrier status could be determined in 18 out of 20 clients who were at risk for DMD/BMD carrier status from 20 families, similar to the rate of detection in Caucasians. The total detection rate of deletions was 74% with the five cDNA probes. Deletions were concentrated on two hot spots where 92% of all deletions were detected by only two probes, 1-2a and 8. Deletions were detected in two males with DMD who had none of the eight RFLPs tested. Our results emphasize the usefulness of DNA analysis with pERT87 genomic probes and cDNA probes. In addition, an optimum strategy for carrier detection in Japanese DMD/BMD families was proposed.

Chromosome Deletion↗
PubMed1993

Prenatal monitoring of ornithine transcarbamoylase deficiency in two families by DNA analysis.

We examined the DNA in two families with ornithine transcarbamoylase (OTC) deficiency. Two point mutations of the OTC gene, a C-to-T (codon 141) and a G-to-A (codon 141), were identified. This allowed prenatal monitoring to be made for two fetuses in each family, using polymerase chain reaction (PCR), followed by allele-specific oligonucleotide hybridization or TaqI digestion of amplified sequence. The diagnoses showed heterozygotes of a wild type gene and the corresponding mutant gene in these fetuses; each was confirmed postnatally.

Amino Acid Sequence↗
PubMed1990

[Flow cytometric DNA analysis of pediatric solid tumor].

Ninety nine case of various solid tumors in children were clinically and histologically investigated and the findings were compared with the data obtained by flow-cytometric DNA analysis using paraffin-embedded tumor tissue. Most of the embryonal tumors such as neuroblastoma, nephroblastoma, or medulloblastoma tended to show a diploid DNA stemline (65.2%) in comparison with non-embryonal tumors (45.2%) (p less than 0.025). Aneuploid cases of embryonal tumors in children disclosed histologically rather differentiated appearances, and with a favorable clinical outcome. On the other hand, non-embryonal tumors in children revealed in general an aneuploid DNA stemline and higher rate in high grade malignancy, resembling that of the malignant neoplasms in adult. These prominent features of the flow-cytometric DNA analysis of the embryonal tumors in children suggest that there are some differences in the tumor cytogenetics or histogenesis between the embryonal tumors and the non-embryonal tumors.

Child, Preschool↗
PubMed1996

Psychosocial consequences of DNA analysis for MEN type 2.

Multiple endocrine neoplasia type 2 (MEN-2) is characterized by medullary thyroid carcinoma in combination with pheochromocytomas and, sometimes, parathyroid adenomas. Since 1993, the psychosocial implications of DNA analysis for MEN-2 have been studied in the Netherlands. This article summarizes the first results of that study. Individuals who applied for DNA analysis cited the need to reduce uncertainty as the major reason for wanting the test. An unfavorable test outcome resulted in anxiety and depression but also relief. Immediate preventive treatment was preferred to continued periodic screening. Carriers were preoccupied with disease-related complaints, and identified with other carriers and MEN-2 patients. A favorable test led, in most applicants and partners, to both relief and worry. Some noncarriers felt guilty and isolated from their families. One year after counseling, participants reported fewer psychosomatic complaints.

Adenoma↗
PubMed2006

DNA analysis of the SH3BP2 gene in patients with aggressive central giant cell granuloma.

A mutation of the SH3BP2 gene is known to cause cherubism. As there are clinical and histopathological similarities between central giant cell granuloma and cherubism, we made a constitutional DNA analysis of the SH3BP2 gene in four patients with aggressive giant cell granuloma (having one or more of the following features pain, paraesthesia, rapid growth, or root resorption). We found no mutations in the SH3BP2 gene, which indicates that cherubism is a separate entity. However, a somatic mutation in a specific group of cells could cause the focal lesions in giant cell granuloma. Further DNA analysis of the tissue of giant cell granulomas therefore seems indicated.

Adaptor Proteins, Signal Transducing↗
PubMed1977

Intracellular organization of bacteriophage T7 DNA: analysis of parenteral bacteriophage T7 DNA-membrane and DNA-protein complexes.

After infection of Escherichia coli with bacteriophage T7, the parenteral DNA forms a stable association with host cell membranes. The DNA-membrane complex isolated in cesium chloride gradients is free of host DNA and the bulk of T7 RNA. The complex purified through two cesium chloride gradients contains a reproducible set of proteins which are enriched in polypeptides having molecular weights of 54,000, 34,000, and 32,000. All proteins present in the complex are derived from host membranes. Treatment of the complex with Bruij-58 removes 95% of the membrane lipid and selectively releases certain protein components. The Brij-treated complex has an S value of about 1,000 and the sedimentation rate of this material is not altered by treatment with Pronase or RNase.

Bacterial Proteins↗