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At least 217 records · Page 12Linked to original sources
PubMed2002

SNPCEQer: detecting SNPs in sequences generated by the Beckman CEQ2000 DNA Analysis System.

SNPCEQer identifies and reports SNPs in sequences obtained from the Beckman CEQ2000 DNA Analysis System. SNPCEQer aligns sequences obtained using CEQ2000 heterozygote detection analysis and reports discrepancies between individual sequences and the consensus sequence it generates from this set as SNPs when the individual base calls have high-quality values. SNPCEQer reported comparable numbers of SNPs to the UNIX-based PolyPhred (148 vs. 165, respectively) in regions amplified from eight genes. A total of 21 different SNPs was discovered. Each gene region was analyzed in 96-306 samples. SNPCEQer was designed to operate from Windows NT, making SNP detection more accessible to users without UNIX systems. SNPCEQer is available free of charge at http://innovation.swmed.edu.

Base Sequence↗
PubMed1987

DNA clonal heterogeneity of hepatocellular carcinoma demonstrated by Feulgen-DNA analysis.

To demonstrate DNA clonal heterogeneity of hepatocellular carcinomas (HCC), the DNA histographic pattern of both primary HCCs and their recurrent or metastatic lesions were studied among 36 patients (33 men and 3 women). Thirty-six paired aspirations or imprints taken from primary, recurrent or metastatic lesions were stained, using the modified Feulgen method, and the DNA content was measured with a scanning microdensitometer at a wavelength of 550 nm. Paired aspirations or imprints taken from different parts of the same HCC were examined in 17 cases; the DNA distribution patterns were similar in 15 (88%) and differed in only two (12%). A similar DNA histogram was also shown among different tumors in 10 (71%) of 14 patients with multiple HCCs, with a DNA ploidy discrepancy in only four (29%). Two of two subcutaneous metastases and two of three recurrent tumors showed DNA distribution patterns similar to those in their primary HCCs. In summary, a DNA clonal heterogeneity of HCC was found in 19% (7/36). In contrast, the similar DNA histographic patterns found in most instances among different parts of the HCC and between the primary and recurrent or metastatic lesions suggest that HCC may derive from a single cell clone in the majority of cases.

Adult↗
PubMed1990

Survival of rectal carcinoma patients studied with flow cytometric DNA analysis.

The cellular DNA content was measured with flow cytometry from paraffin-embedded materials in 197 patients with primary rectal cancer who had had "curative" resection. All patients were followed clinically for from 2.5 to 7 years. There was a significant difference in recurrent rate between DNA diploid and aneuploid tumors. The cumulative survival rate (Kaplan-Meier) of curative operative rectal carcinomas was worse in DNA aneuploid than in DNA diploid tumors (p less than 0.05). These data suggest that tumor DNA content is an important prognostic indicator for both recurrence and overall survival in patients with primary rectal carcinoma.

DNA, Neoplasm↗
PubMed1982

Antenatal diagnosis of sickle cell disease: amniotic fluid cell DNA analysis.

Using recombinant DNA methods and amniocentesis, the antenatal diagnosis of sickle cell disorders can be accomplished. This article presents the authors' experiences with 21 pregnancies at risk using HpaI and Hind III restriction enzyme digestions of adult leukocytic and fetal amniotic fluid cell DNA. The authors were able to establish direct beta A- and beta S-globin gene linkages to the restricted fragments in 9 families. In 8 families no direct linkages could be determined and estimates of exclusion of fetal beta S homozygosity were used. These estimates were made on the basis of the frequencies of association of the HpaI fragments with the beta S and beta A genes in the Afro-American population. In 4 families, no estimates or linkages could be established, and the patients were counseled in reference to fetoscopy. The data also indicated the frequencies of association of the HpaI fragments with the beta A and beta S gene in the New Jersey-New York population. These studies did not seem to indicate any exclusive preferential segregation of the HpaI and Hind III polymorphisms.

Amniotic Fluid↗
PubMed1993

Detection of false DNA aneuploidy and false DNA multiploidy in flow cytometric DNA analysis.

Although false DNA aneuploid peaks have previously been described in normal tissue, criteria for distinguishing them from 'true' near-diploid peaks have not been established. Normal thyroid (n = 4) and kidney (n = 1) tissue were allowed to autolyze over a fixed period of time and DNA content was analyzed by flow cytometry (FCM). Autolysis was associated with the development of distinct separate G0/G1 peaks which had low DNA indices (1.09-1.18) and showed decreased forward light scatter (FSC) when compared to fresh tissue. Using DNA content and FSC measurements similar false DNA aneuploid peaks were identified in 29/94 surgical specimens. These cases included both benign and malignant lesions from thyroid (n = 63) with the remaining 31 neoplastic cases being from breast (16), lymphoma (8), sarcoma (4), lung (2) and uterine (1) tissue. In addition, false DNA multiploidy was identified. None of these cases showed histological evidence of necrosis. In a parallel comparison study using image cytometry (ICM) on the thyroid nodules, the presence of false DNA aneuploidy was supported. Investigators should routinely employ quality control criteria to identify possible cases of false DNA aneuploidy when measuring DNA content using FCM.

Adolescent↗
PubMed2003

Genetic identification and phylogeny of three species of the genus Trachurus based on mitochondrial DNA analysis.

The genetic identification and the phylogenetic relationships of 3 European species of the genus Trachurus (T. trachurus, T. mediterraneus, and T. picturatus) across their geographical distribution, have been investigated by mitochondrial DNA analysis. Both cytochrome b and 16S ribosomal DNA sequence analysis revealed the existence of several species-specific positions that distinguish the 3 studied species. Genetic distances between the species indicated that T. mediterraneus and T. picturatus are more closely related than T. trachurus. Similar topologies have been produced by neighbor-joining, maximum-likelihood, and maximum-parsimony trees, and they were in accordance with previous taxonomic classification. Internucleotide and intranucleotide diversity of T. picturatus was 2 times higher than that of T. mediterraneus and T. trachurus, possibly owing to the low levels of fishing pressure for T. picturatus. This is the first report of the phylogenetic relationships of the 3 Trachurus species and provides a possible scenario of the time of divergence related to the closure of the Gibraltar Straits. In addition, the present results can be used for genetic identification of the 3 species, even from the early stage of eggs, and for detection of commercial fraud.

Animals↗
PubMed1992

DNA analysis of malignant effusions. Comparison with cytologic diagnosis and carcinoembryonic antigen content.

Twenty-three consecutive malignant effusions from 19 patients submitted for cytologic examination were analyzed for carcinoembryonic antigen (CEA) content and for DNA analysis by flow cytometry. The study was undertaken to determine if the addition of DNA analysis would improve the sensitivity of cytologic diagnosis and CEA assay. CEA examination was performed on Papanicolaou-stained smears and hematoxylin-and-eosin-stained cell blocks. Final diagnoses were correlated with histologic examination (four patients), clinical and radiologic studies, and follow-up. The malignant effusions in 19 patients were secondary to carcinoma of the breast (5), lung (5), ovary (1), endometrium (1), mucinous carcinoma of the colon (1), unknown primary (1), extraovarian papillary carcinoma (1), mesothelioma (2) and large cell lymphoma (2). The sensitivity of cytologic diagnosis was 100% and specificity 100%. DNA aneuploidy, defined as the presence of two separate peaks in the histogram, was present in 7 of 23 fluids (sensitivity, 30%). Four fluids had insufficient cells for analysis, and one histogram showed debris (following chemotherapy). DNA aneuploidy was detected in effusions secondary to carcinoma of the breast (4), lung (1) and lymphoma (2). Using 5 ng/mL as the cutoff, the sensitivity of CEA was 68%. DNA analysis of cells in malignant effusions is less sensitive than cytologic diagnosis, and CEA assay and is not recommended for routine use in the diagnosis of malignant effusions.

Aged↗
PubMed1990

Static and flow cytometric DNA analysis compared to histologic prognostic factors in a cohort of stage T2 breast cancer.

DNA analysis with static and flow cytometry was performed on archival smears and tissue sections in 99 patients with T2 breast cancer (Stage II). Tumour size, histologic grade and axillary node metastases were significant prognostic predictors. Static cytometry revealed 63% aneuploid tumours, and ploidy was significantly correlated to histologic grade and survival. DNA measurements obtained by static and flow cytometry were strongly correlated. According to flow cytometry 53% of the tumours were aneuploid. Flow cytometric DNA analysis correlated to histologic grade and survival and gave prognostic information among the lymph-node negative patients. Ploidy seems to be a significant, although not an independent prognostic indicator for T2 breast cancer.

Adenocarcinoma↗
PubMed2002

Recent progress in DNA analysis by capillary electrophoresis.

A number of recent developments in DNA analysis by capillary electrophoresis are here reviewed. They include capillary arrays for fast, parallel DNA sequencing as well as microfabricated capillary arrays. Microfluidic chips for DNA sizing and quantitation are also covered, as well as microdevices containing arrays of regular obstacles acting as size-separators during DNA migration. Screening of DNA point mutations by two much improved techniques is also reported: in one case, such mutations are detected (but only on relative short, ca. 60-70 base-long fragments) by free electrophoresis in rather acidic (pH ca. 3) buffers; in the case of single-strand chain polymorphism, an improved technique is described based on near-neutral pH buffers with mixtures of Tris/MES cations/zwitterions. When studying the behavior of inorganic and organic cations in the Debye-Hückel layer of DNA, it was found that the latter (especially a large number of Good's buffers and other zwitterions, such as His) would bind to the DNA filament not only via charge interaction, but also via additional bonds, notably hydrogen bonds, thus altering the electrophoretic (and possibly the biological) behavior of DNA molecules. However, whether or not borate ions would bind to DNA remains still an unsettled question. Finally, capillary electrophoresis was found to be instrumental in measuring fine physicochemical parameters pertaining to DNA polyelectrolytes, such as their free mobility and their translational diffusion coefficients.

Animals↗
PubMed1989

Flow cytometric DNA analysis of 199 histologically favourable or unfavourable non-Hodgkin lymphomas.

We have studied the nuclear DNA content of histologically favourable (n = 82) or unfavourable (n = 117) non-Hodgkin lymphomas (NHLs) diagnosed between 1957 and 1978 in the Tampere University Central Hospital. The DNA analysis was done by applying a trypsin digestion method to archival tumour samples. DNA aneuploidy was seen in 40 per cent of the unfavourable cases and in 10 per cent of the favourable cases, but varied considerably between different histological subtypes. The unfavourable cases showed high proliferative activity (S-phase fraction, SPF), while considerable variation in the SPF among the favourable NHLs was noted. Among the unfavourable NHLs, cases with DNA-aneuploid tumours had significantly (P less than 0.01) worse prognosis than stage and treatment matched cases with DNA-diploid tumours. In general, survival of the patients who had high SPF tumours was significantly lower compared with patients with low SPF tumours (P less than 0.01). However, SPF was not related to the prognosis in the unfavourable NHLs. We conclude that the flow cytometric DNA analysis revealed characteristic features in the favourable and unfavourable NHLs and may be useful in predicting the clinical outcome of patients.

Adult↗
PubMed1999

Identification of victims of the 1998 Taoyuan Airbus crash accident using DNA analysis.

In February 1998 a civilian aeroplane carrying 196 individuals crashed in Taiwan and killed another 6 people on the ground. Although there were dental and medical records, fingerprints, photographic evidence and personal effects to identify some of the victims, DNA analysis was required to further identify severely damaged remains. From the 202 people known to have perished in the plane crash, a total of 685 fragments of human remains were subjected to DNA analysis. The analysis was carried out using nine microsatellite loci, plus amelogenin to cluster the 685 fragments into 202 groups, accounting for all the victims. To establish genetic relatedness of the victims to other victims and living relatives, additional DNA loci were used. In this case the paternity index was increased by using HLA DQA1 plus Polymarker. The same 16 DNA loci were used to test blood samples from 201 relatives to establish parent/child and sibling relationships. With the exception of 19 victims identified by non-genetic evidence, 183 victims were successfully identified by DNA typing with relatively high values of paternity index by the direct or indirect comparison of relatives. The 202 victims were from 37 different families, ranging in size from 2 to 13 members and 74 individuals known to be unrelated to any other victim. The DNA from living relatives was used to identify one member of a family group, from which other victims of the family could be identified. ABO blood group information was further used to confirm genetic relatedness within families. A comparison of the DNA profiling results to the ABO blood group of the victims showed no discrepancies with the exception of two mutations in the FGA locus. In cases of severely damaged victims from a plane crash, DNA analysis proved to be the best choice to identify victims.

Accidents, Aviation↗
PubMed1997

Flow cytometric DNA analysis of pediatric intracranial ependymomas.

OBJECTIVE: To examine the clinicopathologic features and perform flow cytometric DNA analysis of pediatric intracranial ependymomas to determine whether any of these parameters were predictors of clinical outcome. METHODS: Flow cytometric DNA analysis was performed on 17 paraffin-embedded tumors from patients aged 7 months to 16 years. RESULTS: Seven cases were aneuploid, while the remaining 10 were diploid. Proliferative fractions varied from 1% to 17%. CONCLUSIONS: No correlation between histologic features such as mitotic activity, cellularity, pleomorphism, vascular proliferation, and length of survival was observed. However, the presence of a diploid DNA stemline, elevated proliferative fraction, or young age were associated with a poor clinical outcome and shortened survival times (P < 0.05). Additional studies of larger patient groups with extended follow-up are necessary to confirm these findings.

Adolescent↗
PubMed1989

Prenatal diagnosis of sickle cell anemia. Hemoglobin electrophoresis versus DNA analysis.

The prenatal diagnosis of sickle cell anemia (hemoglobin SS) can be established by DNA analysis using two highly sensitive techniques (Southern blot and polymerase chain reaction [PCR]). Hemoglobin electrophoresis provides a third, simpler and more rapid, technique to analyze blood from a fetus at risk for sickle cell anemia. The authors present examples of prenatal diagnostic studies using both DNA analysis techniques and hemoglobin electrophoresis. Hemoglobin electrophoresis of fetal hemolysate can provide a simple and rapid alternative method to PCR analysis for the prenatal exclusion of sickle cell anemia, and it is especially useful in cases in which rapid results are needed because of advanced gestational age.

Adult↗
PubMed1989

[DNA analysis by flow cytometry in breast carcinoma].

Using deparaffinized tumor specimens, a flow cytometric DNA analysis was performed in 63 primary breast cancers from patients who were treated from 1976 through 1982. Fourty-three percent of the cases were found to be aneuploid, and 57% were diploid. No trend to increased aneuploid proportion with a more advanced disease was noted. There was no correlation between the level of ploidy and the clinicopathological factors. Aneuploid tumors seem to have a poorer survival, but no significant difference was found between the two patterns of ploidy. Patients with a low S-phase fraction (SPF) had a significantly longer survival than those with a high SPF. A DNA analysis of the tumor cells in breast cancer is felt to be use for a prognostic evaluation.

Aneuploidy↗
PubMed1988

A simple method for calculating risks before DNA analysis.

Calculation of carrier risk of an X linked disease may be performed on a small computer after DNA analysis, but a method for rapid hand estimation of the risk is still useful for a quick check of the results and weighing the relative importance of each element of information, such as the determination of a haplotype. Each risk estimation is a function of a prior risk and the product of likelihood ratios and these terms are derived themselves from parameters such as fitness or the relative mutation rate in male and female gametes. Even if it is often difficult to have strong experimental estimation of these variables, the existence of a normal father or grandfather must be considered whenever male fitness is not null. The likelihood ratio for a woman for not being a carrier, when her father is not affected and her mother has herself a likelihood R for not having the mutated gene, may be expressed as the ratio 2R/(CmR + 1), with Cm being a function of male fitness and relative mutation rate. Cm represents the odds ratio for the mother of a carrier not to be a carrier, given that the father of the known carrier is not affected. This formula can be used recurrently and reduces to 2R/(R + 1) in lethal X linked disease. When likelihood ratios are expressed as an algebraic function, maximum values are easily determined, hence fixing the limits of DNA analysis.

DNA↗
PubMed2006

A case of intramuscular cysticercosis diagnosed definitively by mitochondrial DNA analysis of extremely calcified cysts.

A case of obsolete intramuscular cysticercosis diagnosed definitively by mitochondrial DNA analysis of extremely calcified cysts was reported. X-ray and computed tomography findings highly suggested cysticercosis due to Taenia solium; however, no direct evidence of cysticercosis was obtained through serological or histopathological examinations. Mitochondrial DNA analysis of a histopathological specimen confirmed the causative agent to be the Asian genotype of T. solium.

Aged, 80 and over↗
PubMedDate not supplied

Single and multigland disease in primary hyperparathyroidism: clinical follow-up, histopathology, and flow cytometric DNA analysis.

Two-hundred seventy-four patients with primary hyperparathyroidism had selective removal of enlarged parathyroid glands. Biopsies were taken from all parathyroid glands. Normal-size glands were not resected irrespective of their histological appearance. After a mean follow-up of 13.5 years the rates of persistent and recurrent hyperparathyroidism were, respectively, 3.6% and 0.7%. Transient and permanent hypoparathyroidism occurred in 24% and 2.5% of the patients. The microscopic appearance of enlarged glands and of biopsies taken from normal-size glands were reviewed by two pathologists. Normal parathyroid glands were distinguished from abnormal glands fairly accurately (sensitivity 93%, specificity 80%). Microscopic classification of abnormal parathyroid glands as adenomas or hyperplastic glands correlated poorly with the gross classification as single or multigland disease. Flow cytometric DNA analysis of paraffin embedded parathyroid tissue showed significant differences for DNA index, % S-phase and % G2M (p less than 0.001). Differentiating single from multigland disease by means of DNA analysis was not possible. In conclusion, removal of only enlarged parathyroid glands results in acceptable rates of persistent and recurrent hyperparathyroidism. Biopsies should only be taken sparingly to prevent transient and permanent hypoparathyroidism. Microscopic examination and flow cytometric DNA analysis can differentiate normal from abnormal parathyroid glands but are unable to differentiate abnormal glands into single or multigland disease.

Adolescent↗
PubMedDate not supplied

Differentiated DNA analysis in relation to steroid receptor status, grading, and staging in human breast cancer.

Flow cytometric DNA analysis was performed in 100 cases of human breast cancer. Using a category system of six ploidy groups, ploidy status was distributed as follows: The majority of the neoplasias were either diploid (45%), hyperdiploid (21%), or tetraploid (15%), whereas the remaining marginal ploidy groups, i.e. hypodiploid (4%), hypertetraploid (9%), and multiploid (6%) were less frequent. In an attempt to evaluate the prognostic significance of DNA content, ploidy status was correlated with steroid hormone receptor status, histopathological grade, and TNM data. The higher incidence of negative estrogen and progestin receptor status and higher histopathological grade in hyperdiploid malignancies was significantly different from the prognostically more favorable positive receptor status and lower grade in diploid tumors. Tetraploid neoplasias statistically resembled the latter group with respect to both parameters. As far as TNM data are concerned, tendencies towards less favorable staging were observed in hyperdiploid as compared to diploid and tetraploid tumors. A definite statement of the prognostic significance of the marginal ploidy groups cannot be made at present. In order to characterize diploid malignancies more closely, proliferative activity expressed by %S-phase was analyzed. Steroid receptor status of diploid tumors exhibiting more than 6% S-phase did not differ statistically from that of hyperdiploid neoplasias. In contrast, diploid tumors expressing less than 6% S-phase closely resembled tetraploid ones. Our data emphasize the prognostic significance of differentiated DNA analysis.

Breast Neoplasms↗