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At least 379 records · Page 21Linked to original sources
PubMed2002

Microcysts and breast cancer: a study of biological markers in archival biopsy material.

Breast cysts are associated with an increased risk of breast cancer. Some biomarkers such as estrogen receptor alpha (ERa), progesterone receptor (PR), and cyclin D1, show similar patterns of expression in epithelial cells lining breast cysts as malignant epithelial cells in local and invasive ductal breast cancer. We have attempted to answer two questions: (1) Do epithelial cells lining breast microcysts (cysts which can only be seen with a microscope) express biomarkers in a similar pattern to breast ductal carcinoma in situ and invasive ductal carcinoma? (2) Are breast microcysts precursors of breast cancer or are they part of normal involution of the breast? Seventy two archival open breast biopsy specimens of ductal carcinoma in situ and invasive ductal carcinoma and 32 normal breast biopsies from Australian women who had breast reduction surgery were selected from hospital archives. All specimens were analysed by standard immunohistochemistry for ERa, PR, cyclin D1, bcl-2, p53 and erbB-2 expression. In the same specimens, the pattern of high biomarker expression was very similar for all the above biomarkers in epithelial cells lining microcysts and in both ductal carcinoma in situ and invasive ductal carcinoma c. ErbB-2 was not expressed in normal control specimens. ErbB-2 was expressed in the same specimens in an increasing proportion of normal breast acini, microcysts and cancer cells in 36% of specimens with breast cancer. An apparent progression was observed from normal breast acini, to proliferation of epithelial cells in microcysts, ductal carcinoma in situ and invasive ductal carcinoma in the same specimen. When these findings are considered with other reports we conclude: (1) that epithelial cells lining breast cysts highly express biomarkers in a similar pattern to ductal carcinoma in situ and invasive ductal carcinoma; (2) that some microcysts are not part of normal involution of the breast and in some women may be part of the transition from normal to cancer.

Biomarkers, Tumor↗
PubMed1998

Detection of mitochondrial DNA nucleotide 11778 point mutation of Leber hereditary optic neuropathy from archival stained histopathological preparations.

PURPOSE: We evaluated the availability of archival histopathological preparations for genetic diagnosis of Leber hereditary optic neuropathy (LHON). METHODS: Preparations of various tissues of an autopsied case of LHON, and of the optochiasmal arachnoidea of nine cases of bilateral optic neuropathy (BON) were studied to determine the presence of a point mutation of the mitochondrial DNA nucleotide (nt) 11778 using PCR method. RESULTS: An nt11778 point mutation was detected in all preparations of the autopsied case. Five preparations out of six BON cases who were diagnosed as LHON based on positive family history, revealed this point mutation. This mutation was also detected in two of three BON patients with no family history of the disease. CONCLUSION: The archival preparations were found to be available as materials of genetic diagnosis for LHON, which indicated that it would be capable to reevaluate retrospectively the pedigree of LHON and BON cases.

Adolescent↗
PubMed1985

Air pollution, weather, and violent crimes: concomitant time-series analysis of archival data.

Archival data covering a 2-year period were obtained from three sources in order to assess relations among ozone levels, nine measures of meteorological conditions, day of the week, holidays, seasonal trends, family disturbances, and assaults against persons. Confirming results obtained in laboratory studies, more family disturbances were recorded when ozone levels were high than when they were low. Two-stage regression analyses indicated that disturbances and assaults against persons were also positively correlated with daily temperatures and negatively correlated with wind speed and levels of humidity. Further, distributed lag (Box-Jenkins) analyses indicated that high temperatures and low winds preceded violent episodes, which occurred more often on dry than humid days. In addition to hypothesized relations, it was also found that assaults follow complaints about family disturbances, which suggests that the latter could be used to predict and lessen physical violence. It was concluded that atmospheric conditions and violent episodes are not only correlated but also appear to be linked in a causal fashion. This conclusion, however, was qualified by a discussion of the limitations of archival data and concomitant time-series analysis.

Air Pollution↗
PubMed1993

PCR-based microsatellite polymorphisms in the detection of loss of heterozygosity in fresh and archival tumour tissue.

PCR-based microsatellite polymorphisms have proved their power in genetic linkage analysis and other identification methods, due to their high information content and even distribution over the chromosomes. In the present study we applied microsatellite polymorphisms to detect loss of heterozygosity in fresh (snap-frozen) and in archival ovarian tumour tissue. Clear allele losses were found in fresh and paraffin embedded tumour samples. Conventional Southern analysis of flanking markers on the same tumour DNA samples confirmed the observed losses detected by microsatellite polymorphisms. Titration experiments suggest that loss of heterozygosity remains detectable in tumour samples despite 60% contamination with normal DNA. This technique provides a fast and reproducible alternative to conventional Southern blotting in the detection of loss of heterozygosity, with the crucial additional advantages of minimal sample requirements, making archival material available for genetic investigation.

Adenocarcinoma↗
PubMed1996

TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

The aim of this investigation was to examine the possibility of analysing TP53 mutations in archival paraffin-embedded material with the constant denaturant gel electrophoresis (CDGE) method. We extracted DNA from 193 archival primary breast carcinoma samples, diagnosed in 1981-83; further analysis was possible for 186 of these. TP53 mutations in exons 5-8 were detected with CDGE in 30 samples (16.1%) and 17 of these mutations were confirmed by sequencing. Immunohistochemistry demonstrated TP53 nuclear accumulation in 58 tumours (31%). A strong association between the presence of TP53 mutations and TP53 immunostaining was observed (P < 0.001). Our mutation and immunohistochemistry results are in agreement with other findings based on fresh tumour tissue. TP53 abnormalities were significantly related to high S-phase fraction, low oestrogen receptor (ER) content and high tumour grade. Survival of patients with TP53 abnormalities, in the group as a whole, did not differ from patients with normal TP53. Our study did, however, show that patients with abnormal TP53 had a significantly shorter post-recurrence survival (P = 0.005) than patients with normal TP53.

Amino Acid Sequence↗
PubMed1996

RET activation in adult and childhood papillary thyroid carcinoma using a reverse transcriptase-n-polymerase chain reaction approach on archival-nested material.

Activation of the RET tyrosine kinase domain occurs in a proportion of thyroid papillary carcinomas. Three chromosomal rearrangements have been described, of which PTC1 is the commonest. Wide differences (2.5-25%) in frequency of PTC1 in different populations have been reported; it is not clear whether these are due to environmental factors, racial differences or technical reasons. We have developed a simple and rapid reverse transcriptase nested polymerase chain reaction (RT-nPCR) method enabling the detection of gene expression from single 5 microns sections of formalin-fixed paraffin wax-embedded archival material. We have applied this approach to detect expression of the RET tyrosine kinase domain, allowing identification of RET activation resulting from any rearrangement, whether characterised or not, or from overexpression. A retrospective study was performed on 22 adult and 21 childhood papillary carcinomas. Thirteen of 22 (59%) adult and 10 of 21 (48%) childhood carcinomas showed evidence of RET activation, demonstrating a major role for the RET oncogene in UK thyroid papillary carcinogenesis. This study also shows a similar frequency of RET activation in both children and adults. The use of a technique that allows reliable amplification of RNA from archival material, using primers chosen in different exons so that amplified products are readily distinguished from genomic DNA, will allow correlation of translocations and chromosomal rearrangements with a variety of specific tumour types.

Actins↗
PubMed1996

Detection of microsatellite markers in leukaemia using DNA from archival bone marrow smears.

We describe a simple PCR method to detect highly polymorphic repetitive DNA markers (microsatellites) in leukaemia using DNA from fresh and archival bone marrow smears. Neither the period of storage nor staining of the slides affected microsatellite PCR. Comparison of slide DNA with constitutive DNA from buccal epithelium revealed loss of heterozygosity (LOH) with at least one marker in four of 11 leukaemias. Marrow smears offer an attractive archival source of DNA for the detection of microsatellite markers. Applications include detection of LOH or tracing the origin of cell populations, e.g. in bone marrow transplant recipients.

Bone Marrow↗
PubMed1998

DNA extraction from archival Giemsa-stained bone-marrow slides: comparison of six rapid methods.

The ability of six rapid DNA extraction procedures to provide DNA for the polymerase chain reaction from archival Giemsa-stained bone marrow slides was tested on 120 samples. Boiling in distilled water, freeze-thaw method, boiling in 10% Chelex-100 resin solution, proteinase K/Tween 20/NP-40 method coupled with simplified phenol/ chloroform/isoamyl alcohol protocol or salting-out procedure using saturated NaCl and modification of commercial QIAamp procedure (Qiagen. Chatsworth, Calif.) gave DNA extraction efficiencies of 50%, 70%, 85%, 95%, 100% and 100%, respectively. Our results demonstrate that rough DNA extraction methods have decreased efficiencies compared to complete DNA extraction protocols and that the latter are required to ensure highly reproducible results from archival Giemsa-stained bone marrow slides.

Azure Stains↗
PubMed1999

Use of a common computerized program for echocardiogram archiving and reporting over a regional territory: feasibility and clinical and research impact during a 5-year experience.

The aims of this study were to optimize interlaboratory standardization of echocardiographic reporting (qualitative terms and quantitative parameters) and to evaluate the feasibility and clinical and research impact of collecting echocardiographic data in a standard computerized format over a geographical territory. In April 1992, a computer program of echocardiogram archiving and reporting (ARCE) was distributed at no cost to the 23 hospital echocardiographic laboratories operating in our region (Liguria). In April 1993 (1-year survey), 16 (70%) of the 23 hospital echo laboratories operating in our region were routinely using ARCE. In April 1997 (4-year survey ), 21 (87%) of the 24 echo laboratories were routinely using the system and 128,642 echocardiograms had been databased. ARCE is a powerful tool both for education and training in cardiac ultrasound and for undertaking multicenter studies by 95% of the users. Regarding the quality improvement process, we achieved 3 main goals: (1) a unique report format from 87% of Ligurian echo laboratories, which improved the communication between echocardiographers and other physicians; (2) development of specific, Ligurian population-based reference limits for M-mode and 2-dimensional quantitative parameters; and (3) interlaboratory comparison and standardization of both quantitative and semiquantitative evaluation of heart valve disease, left ventricular systolic and diastolic function, valve prosthesis function, and left ventricular hypertrophy. Regarding the scientific activity in Liguria, 9 multicenter studies in which 15 Ligurian echo laboratories took part were organized and completed in 5 years. Our 5-year experience shows that it is possible to create a large database of echocardiographic data that uses a fast, easy-access, and easy-to-use program of echo archiving and reporting that contains standardized variables. The use of this program on a regional territory scale appeared feasible and useful both for educational and training purposes. In addition, it stimulated the quality improvement process in echocardiography as well as performance of epidemiologic and clinical multicenter studies.

Computer Communication Networks↗
PubMed1997

Design Specifications for a Radiation Oncology Picture Archival and Communication System.

The handling of various types of images is an important function in radiotherapy and can be aided significantly by the use of a picture archival and communication system (PACS). The conventional imaging PACS has been well-studies, but the radiotherapy picture archival and communication system (RT-PACS) is relatively unfamiliar to the medical community. While many of the massive data handling requirements of a conventional imaging PACS may not be necessary for an RT-PACS, the RT-PACS must support various image operations that are unique to radiotherapy. This report describes some of the desired functional capabilities of the RT-PACS and the design specifications required to support these capabilities.

Journal Article↗
PubMedDate not supplied

London Archive of Longitudinal Growth Data.

An Archive of longitudinal growth data, accessible to research workers under the usual safeguards, has been set up in the Department of Growth and Development. The present S.I.R. database contains seven British and one Indian study. The Archive is open to receive other contributions if researchers wish.

Adolescent↗
PubMedDate not supplied

Polymerase chain reaction amplification of archival material for parvovirus B19 in children with transient erythroblastopenia of childhood.

The relationship between transient erythroblastopenia of childhood (TEC) and parvovirus B19 infection remains uncertain. Large series using primarily serologic evaluation have not shown an association, whereas smaller series have reported parvovirus B19 infection in such patients. Further, parvovirus DNA or antigen has been detected in some patients seronegative for the virus at presentation. Polymerase chain reaction (PCR) amplification has never been used to evaluate patients with TEC for parvovirus B19. We used the PCR in an attempt to detect parvovirus B19 in DNA extracted from archived bone marrow coverslips of 16 patients diagnosed with TEC. The patients ranged in age from 3 to 23 months and presented with a mean hemoglobin value of 5.4 g/dL. Sixty-nine percent were neutropenic and none was thrombocytopenic. None of the patients had histologic evidence of parvovirus B19 infection in the bone marrow. DNA amplification for parvovirus B19 was negative in each case. In contrast, parvovirus B19DNA was amplified from DNA isolated from archived bone marrow coverslips of a patient with known parvovirus B19 infection, indicating that the PCR assay was sufficiently sensitive to detect virus from archieved bone marrow coverslips. Review of the literature indicates that the patients with parvovirus-associated TEC are generally older and often present with concomitant thrombocytopenia, whereas patients with parvovirus B19-negative TEC are younger and present without thrombocytopenia, similar to the patients in our study. Our results suggest that parvovirus B19 is not the cause of anemia in the young patient with typical features of TEC. Rather, parvovirus B19 infection of older, previously healthy children may occasionally cause a protracted anemia, often with thrombocytopenia, which may be diagnosed by some as TEC.

Child, Preschool↗
PubMed2001

PCR-based methylation testing for Prader-Willi or Angelman syndromes using archived fixed-cell suspensions.

All Prader-Willi syndrome (PWS) and 75% of Angelman syndrome (AS) patients have specific DNA methylation pattern alterations that can be used for diagnostic evaluation. The methylation testing identifies a significantly higher proportion of patients as compared to fluorescence in situ hybridization (FISH)-based microdeletion analysis and is thus a useful diagnostic evaluation for clinically suspect, but FISH-negative, patients. We used two independent PCR-based protocols for methylation testing on fixed cell specimens archived after FISH analyses. Changes in DNA methylation due to the procedure of cell fixation were ruled out by testing control specimens before and after fixation. Then methylation testing was carried out on 20 standard fixed-cell supsensions from people suspected for PWS or AS. These fixed specimens were stored after negative FISH analysis for up to 4 years at 4 degrees C in 3:1 methanol/acetic acid. Methylation patterns associated with AS (one specimen) and with PWS (one specimen) were identified for both protocols. The observed methylation patterns were concordant with the phenotypes of the positive individuals and for the two protocols used. We have, thus, shown that archived fixed-cell suspensions from individuals suspected as PWS or AS that were negative for cytogenetic/FISH microdeletions, can now be re-evaluated with PCR-based methylation testing without the need for additional blood samples from the previously studied individuals.

Angelman Syndrome↗
PubMed1993

Diagnosis of cytomegalovirus pneumonia by the polymerase chain reaction with archived frozen lung tissue and bronchoalveolar lavage fluid.

The authors developed a polymerase chain reaction (PCR) procedure to detect cytomegalovirus (CMV) in archived, frozen lung tissue and bronchoalveolar lavage (BAL) fluid preparations. The procedure incorporated an internal beta-globin control to assess the adequacy of the sample. Twenty-nine lung tissue and 96 archived BAL specimens from marrow transplant recipients were tested. One of the lung tissue specimens and 46 of the BAL specimens had insufficient tissue for PCR analysis because they did not show a beta-globin band. In lung tissue, the PCR had a sensitivity of 100% and specificity of 89% compared with conventional tube culture. In BAL specimens, the PCR had a sensitivity of 87% and specificity of 90% compared with conventional tube culture or centrifugation culture. Provided tissue was sufficient, the results suggest that the PCR can be used to diagnose CMV interstitial pneumonia effectively from frozen specimens of lung tissue or BAL fluid.

Base Sequence↗
PubMed2002

The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation.

UNLABELLED: Most of the current bioinformatics literature lacks an explicit and clear description of the data used in experiments when introducing or evaluating computational tools. Without the exact data set that was fed into computational tools in experiments, any mistaken preparation of the data for later experiments may lead to discrepancy in conclusion. The NCTU BioInfo Archive is a new web-based bioinformatic data archive. It serves as a test bed for evaluating computational tools, as a bridge to link other research communities with bioinformatics, and also as an environment full of motivations and possibilities to encourage more exploratory research in bioinformatics. AVAILABILITY: http://bioinfo.cis.nctu.edu.tw

Computational Biology↗
PubMed1994

H-ras 61st codon activation in archival proliferative hepatic lesions isolated from female B6C3F1 mice exposed to the leukotriene D4-antagonist, LY171883.

LY171883, a peroxisome proliferator and leukotriene D4-antagonist, induced a statistically significant increase in the number of hepatic lesions in B6C3F1 female mice in a 2 year oncogenicity study at dietary doses of 0.0225% and 0.075%. The mutation frequency and spectrum of the 61st codon of H-ras was determined for 64 independent, archived lesions from the LY171883 2 year oncogenicity study using the polymerase chain reaction (PCR), allele specific oligo hybridization (ASO) and DNA sequencing. Results showed 41 (64%) of these lesions had mutations at the 61st codon (16/21 hepatocellular carcinomas, 4/10 hepatocellular adenomas, 19/26 focal hepatocellular hyperplasias and 2/7 focal hepatocellular atypia). These mutations consisted of 18 C-A transversions, 16 A-G transitions and seven A-T transversions. Compared to the mutation frequency for spontaneously occurring archival B6C3F1 hepatic lesions (41%), the frequency of LY171883 lesions (64%) was significantly higher (P < 0.01). The frequencies of H-ras 61st codon mutations among the LY171883 lesion types (hepatocellular carcinomas 76%, hepatocellular adenomas 40%, focal hepatocellular hyperplasias 73% and hepatocellular atypia 29%) were also significantly different (P = 0.035). In contrast, spontaneous lesions showed no statistical difference in the frequencies of mutation among lesion types (P > 0.5). The mutation spectrum of the LY171883 lesions was not significantly different from the spontaneous spectra. It may be concluded that based on the similarity in mutation spectrum and the increase in mutation frequency, LY171883 may selectively promote spontaneous hepatic lesions containing H-ras 61st codon mutations. In addition, the difference in mutation frequency among lesion types does not support a linear progression of all LY171883 lesions through focal atypia, focal hepatocellular hyperplasias, hepatocellular adenomas and hepatocellular carcinomas.

Acetophenones↗
PubMedDate not supplied

Archive of mass spectral data files on recordable CD-ROMs and creation and maintenance of a searchable computerized database.

A database containing names of mass spectral data files generated in a forensic toxicology laboratory and two Microsoft Visual Basic programs to maintain and search this database is described. The data files (approximately 0.5 KB/each) were collected from six mass spectrometers during routine casework. Data files were archived on 650 MB (74 min) recordable CD-ROMs. Each recordable CD-ROM was given a unique name, and its list of data file names was placed into the database. The present manuscript describes the use of search and maintenance programs for searching and routine upkeep of the database and creation of CD-ROMs for archiving of data files.

CD-ROM↗
PubMed1997

Archival fixed and analysed preimplantation human embryonic cells: a DNA resource for retrospective PCR analysis at the cellular level.

Biopsies of human embryonic cell preparations previously analysed by cytogenetic and/or fluorescent in-situ hybridization (FISH) chromosome probes provide a unique reference DNA resource for the archival preimplantation genetic diagnosis (PGD) of the transferred embryo. DNA polymerase chain reaction (PCR) may be utilized on these fixed cell preparations to verify equivocal FISH/PGD results. Retrospective PCR screens of the genotype of biopsied embryonic cell(s) may be of benefit in the case of a suspected genetic mutation. Currently, carrier detection or linkage analysis is often not possible because of early death of the fetus, or of patients with a lethal disease. Alternatively, fixed/stained 'failed fertilized' oocytes provide a resource to extend genetic analysis to infertile patients. A successful research is described which minimizes loss of individual analysed fixed/stained oocytes, metaphase chromosomes, and embryonic cell samples. Initial DNA amplification takes place in situ using a modified PCR protocol. Comparative cellular studies using primer sets previously used for PGD analyses show that 65% of the preparations amplified unequivocally using the modified protocol and primers for a CA repeat motif gene sequence, in comparison with 81% using the original PCR protocol. With further refinement and optimization, the methods outlined have the potential to retrospectively screen archival fixed chromosomes, gametes, and embryonic cells for clinical application, and enable the further study of the fixed human preimplantation embryo at the morphological, cell and molecular level.

Biopsy↗