Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Molecular Classification”

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 1,477 records · Page 82Linked to original sources
PubMed2007

Hodgkin's and non-Hodgkin's lymphomas.

The diagnosis and management of lymphoma have undergone significant changes in the past 20 years. For example, new immunophenotypic and molecular methods have replaced traditional histology-based classification schemes for lymphoma. Fluorine-18-deoxyglucose (FDG) positron emission tomography (PET) has evolved into a potent staging tool and prognostic indicator in many kinds of lymphoma. The role of radiation therapy, especially in patients who have early-stage Hodgkin's disease, has changed substantially. The introduction of anti-CD 20 antibody therapy (Rituximab) has improved the treatment of B-cell lymphoma. These changes are linked with higher expectations for imaging, such as detection of more subtle lymphoma manifestations, evaluation of residual changes, and better assessment of early response. This article reviews clinical and radiologic features of both Hodgkin's disease and non-Hodgkin's lymphoma. It also describes the radiologic staging of lymphoma and the emerging role of FDG-PET for assessing lymphoma.

Age Factors↗
PubMed2001

Allelic loss is often the first hit in the biallelic inactivation of the p53 and DPC4 genes during pancreatic carcinogenesis.

The presumed precursor lesions of pancreatic ductal adenocarcinoma were recently classified according to their increasing grade of dysplasia and were designated as pancreatic intraepithelial neoplasia (PanIN) 1 through 3. In this study, we tested whether molecular genetic alterations can be correlated with this classification and may help to further categorize the various PanIN grades. We determined the frequencies of allelic loss at chromosomal arms 9p, 17p, and 18q in 81 microdissected duct lesions of various PanIN grades, using a combination of whole genome amplification and microsatellite analysis. In addition we examined the p53 and Dpc4 protein expression patterns by immunohistochemical analysis. In PanIN-1, we did not detect allelic losses. In PanIN-2, allelic losses were found in increasing frequency, and were particularly high in those lesions with moderate-grade dysplasia (low grade, 20, 33, and 17%, loss at 9p, 17p, and 18q, respectively; moderate grade, 46, 77, and 58%). PanIN-3 and invasive carcinomas exhibited abundant losses. Abnormal p53 and Dpc4 protein expression was only rarely identified in PanIN-2 lesions, but occurred frequently in PanIN-3 lesions and invasive carcinomas. The combined genetic and protein expression data support a model in which allelic loss is the first hit in the biallelic inactivation of the p53 and DPC4 tumor suppressor genes. In addition, our data indicate that allelic loss analysis may be useful in separating PanIN-2 lesions with low-grade dysplasia from those PanIN-2 lesions with moderate-grade dysplasia, each potentially representing a distinct progression step toward invasive carcinoma.

Alleles↗
PubMed1998

Long-term follow-up of Stargardt's disease and fundus flavimaculatus.

OBJECTIVE: To understand better the shared characteristics of Stargardt's macular dystrophy (SMD) and fundus flavimaculatus (FF) by reviewing the clinical morphologic and retinal function changes in a large group of affected patients. DESIGN: The study design was a retrospective case review. PARTICIPANTS: Fifty-two patients with SMD and 48 patients with FF were observed from 1 to 22 years. INTERVENTION: Visual acuity (VA), visual fields (VFs), fundus photographs (FPs), fluorescein angiography (FA), electro-oculography (EOG), and electroretinography (ERG) were studied at various intervals. MAIN OUTCOME MEASURES: Changes of VA, VF, FP, FA, EOG ratio, and ERG amplitudes and implicit time at different periods in patients with SMD and patients with FF were measured. RESULTS: Visual acuity decreased gradually in both the SMD and FF groups, and once the 20/200 level was reached, little further change occurred. The yellowish flecks associated with these entities faded with time, and areas of retinal pigment epithelial (RPE) and choriocapillary atrophy developed. In advanced longstanding disease, retinal vessel attenuation and peripheral pigmentary changes were noted. Ninety-four percent of patients with FF were noted to have macular dystrophy at their last visit. Patients who had only central lesions did not have peripheral lesions develop. Intrafamilial variation in the funduscopic pattern was shown in four families. The EOG ratio was abnormal in 2.6% of the patients with SMD and in 48.6% of the patients with FF. An abnormal scotopic ERG was noted in 21.1% of the patients with FF and in none of the patients with SMD. The photopic ERG was abnormal in 32.4% of the patients with FF and in 5.4% of the patients with SMD. In patients with FF, a statistical dependence was noted between the duration of the disease and the ERG results, but no such correlation was seen in the SMD group. CONCLUSIONS: Morphologic changes and retinal function deterioration are more severe in patients with FF than in patients with SMD. The duration of the disease has a greater effect on patients with FF than on patients with SMD. These clinical morphologic and physiologic data may be used to supplement laboratory molecular biologic studies and aid in the further classification of these entities.

Adolescent↗
PubMed1998

The myelodysplastic syndromes: towards a functional classification.

The French-American-British classification of myelodysplastic syndromes (MDS) has contributed greatly to better communication and conduct of clinical trials. However, the advent of novel cytogenetic, immunological and molecular techniques in recent years warrant some alterations to this purely morphological classification. This review aims at highlighting the advances which reflect more closely the unique biological and clinical features of various subtypes of MDS. We propose a comprehensive classification of MDS, to include the newly defined categories, as well as those not included in previous classifications, such as the therapy-induced and hereditary MDS. We hope that this classification will help in focusing attention on the biological features of MDS, the understanding of which will be crucial to combat this disease.

Adult↗
PubMed1996

Histopathology of the enteric neuropathies. From silver staining to immunohistochemistry.

The gut is abundantly supplied with neurons, extrinsic and intrinsic nerve fibers. Knowledge regarding the structure of the enteric nervous system derives principally from the classic silver-staining methods. Because silver stains do not provide information on the molecular constituents of neurons, these data only facilitate classification and may have diagnostic significance. Studies using histochemistry and immunohistochemistry are now completing the morphologic picture and laying the groundwork for the formulation of therapeutic strategies based upon demonstrable chemical defects in enteric disease.

Coloring Agents↗
PubMed2000

Pathologic diagnosis of acute lymphocytic leukemia.

With present knowledge, the optimal management of individual patients with acute leukemia requires that every case be studied by morphology, cytochemistry, cytogenetic, immunologic and molecular techniques. An algorithm for diagnostic evaluation and classification of ALL is provided in Fig. 11. Other techniques, such as DNA or cDNA [figure: see text] microarray, are at present important research tools but have not yet had a major effect on patient care. More detailed studies of individual patients need to be conducted at specialized cancer centers, where preservation of cells, DNA, RNA, or protein is possible. Such investigations will yield important information on the clinical importance of the expression of various markers, the prevalence and relevance of bilineage and biphenotypic leukemias, and above all will reveal the mechanisms of leukemogenesis and of disease evolution. Such insights will further aid clinicians in treating ALL and in preventing refractory disease.

Adult↗
PubMed2004

Phylogeny of the Mexican coastal leopard frogs of the Rana berlandieri group based on mtDNA sequences.

Phylogenetic relationships among specimens from 25 different locations for the six Mexican coastal leopard frog species of the Rana berlandieri species group were investigated using 797 bp of the mitochondrial 12S rDNA gene. Relationships among the haplotypes obtained were recovered using maximum parsimony and Bayesian analyses. Most of the clades recovered by both tree building methods are strongly supported, but conflicting clades recovered by each analysis are generally poorly supported. Both analyses reject the previously proposed subgroupings of the R. berlandieri species group. Based on the strongly supported relationships, genetic differentiation, and geographic distribution of the haplotypes examined, nine independent lineages appear to comprise the group of study. However, confirmation of the new proposed lineages will require further analyses based on other genetic markers and additional samples that cover their entire geographic distribution. Concordance was noted between Miocene-Pliocene geological and climatic events in Mexico and the relationships recovered among the lineages proposed and their geographic distribution.

Animals↗
PubMed2004

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences.

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.

Algeria↗
PubMed2002

Optimal gene expression analysis by microarrays.

DNA microarrays make possible the rapid and comprehensive assessment of the transcriptional activity of a cell, and as such have proven valuable in assessing the molecular contributors to biological processes and in the classification of human cancers. The major challenge in using this technology is the analysis of its massive data output, which requires computational means for interpretation and a heightened need for quality data. The optimal analysis requires an accounting and control of the many sources of variance within the system, an understanding of the limitations of the statistical approaches, and the ability to make sense of the results through intelligent database interrogation.

Algorithms↗
PubMed2002

Neuroticism, major depression and gender: a population-based twin study.

BACKGROUND: A portion of the genetic risk factors for the personality trait neuroticism (N) may also increase risk for major depression (MD). Females have both higher levels of N and higher rates of MD than males, suggesting that these traits may be more genetically correlated in females. METHODS: Structured interviews, including a lifetime assessment for MD by DSM-III-R criteria, were administered to 863 male-male MZ (monozygotic), 649 male-male DZ (dizygotic), 506 female-female MZ, 345 female-female DZ, and 1,408 opposite-sex twin pairs. N was assessed using the short-form of the Eysenck Personality Questionnaire. A sex-limited Cholesky model was fitted which allowed us to decompose into additive genetic, common environmental, and individual-specific environmental components two main classes of correlations: within-sex between-variable and between-sex within-variable. RESULTS: Our best-fitting model contained only additive genetic and individual-specific environmental factors for both N and MD. The within-sex genetic correlations between N and MD were estimated at +0.68 in men and +0.49 in women. This model fitted only slightly better than one in which the N-MD within-sex genetic correlation was constrained to be equal across the sexes, and estimated at +0.55. There may be sex-specific genes influencing both N and MD. CONCLUSION: Our best-fitting model failed to establish a significant sex difference in the genetic correlation between N and MD. These results, as well as evidence for sex-specific genetic factors for both traits, have implications for the diagnosis, classification, and treatment of the affective disorders, and molecular genetic approaches to the study of these traits.

Adult↗
PubMed2003

Genetic differentiation of the Aspergillus section Flavi complex using AFLP fingerprints.

Twenty-four isolates of Aspergillus sojae, A. parasiticus, A. oryzae and A. flavus, including a number that have the capacity to produce aflatoxin, have been compared using amplified fragment length polymorphisms (AFLPs). Based on analysis of 12 different primer combinations, 500 potentially polymorphic fragments have been identified. Analysis of the AFLP data consistently and clearly separates the A. sojae/A. parasiticus isolates from the A. oryzae/A. flavus isolates. Furthermore. there are markers that can be used to distinguish the A. sojae isolates from those of A. parasiticus, which form the basis for species-specific markers. However, whilst there were many polymorphisms between isolates within the A. oryzae/A. flavus subgroup, no markers could be identified that distinguish between the two species. Sequencing of the ribosomal DNA ITS (internal transcribed spacers) from selected isolates also separated the A. sojae/A. parasiticus subgroup from the A. oryzae/A. flavus subgroup, but was unable to distinguish between the A. sojae and A. parasiticus isolates. Some ITS variation was found between isolates within the A. oryzae/A. flavus subgroup, but did not correlate with the species classification, indicating that it is difficult to use molecular data to separate the two species. In addition, sequencing of ribosomal ITS regions and AFLP analysis suggested that some species annotations in public culture collections may be inaccurate.

Aflatoxins↗
PubMedDate not supplied

A multivariate analysis of HIV-1 protease inhibitors and resistance induced by mutation.

This paper describes the use of the multivariate statistical procedure principal component analysis as a tool to explore the inhibitory activity of classes of protease inhibitors (PIs) against HIV-1 viruses (wild type and more-frequent single mutants, V82A, V82F, and I84V) and against protease enzymes. The analysis of correlations between biological activity and molecular descriptors or similarity indexes allowed a reliable classification of the 51 derivatives considered in this study. The best results were obtained in the case of the I84V mutant for which a high number of predictions was achieved. On this basis, this statistical approach is proposed as a reliable method for the prediction of the activity of PIs, for which the data against mutant strains have not been reported.

Drug Resistance, Viral↗
PubMed2005

Clinicopathological features of the tauopathies.

Developments in molecular neuropathology have led to protein-based classification systems for neurodegenerative disorders. Key proteins include alpha-synuclein, amyloid and tau. Alternative mRNA splicing and post-translational change, induced by a bewildering variety of protein modifying processes such as phosphorylation and ubiquitination, have generated insights into new mechanisms of selective neuronal degeneration. The task now is to bring these developments in protein chemistry to the clinic, to try to determine whether this biochemical diversity can help in explaining the phenotypic variability that is so typical of neurodegeneration in general. In this review, we will explore the clinicopathological diversity of the tau-related disorders with specific reference to three of the most common tauopathies, frontotemporal dementia (familial and sporadic), progressive supranuclear palsy and corticobasal degeneration.

Brain↗
PubMed2000

The Diagnosis and Treatment of Ductal Carcinoma In Situ of the Breast.

Ductal carcinoma in situ of the breast is the most favorable presentation of breast cancer; therefore appropriate local treatment is imperative. Intraductal carcinoma is being diagnosed more frequently with the increasing use of screening mammography. A number of pathologic features have been identified which are useful for classification and for prognostic information. In addition, the molecular pathology and its relationship to tumor behavior and prognosis is becoming more well understood. The role of axillary dissection has been examined in a number of series and is generally agreed to be unnecessary for this presentation of breast cancer, allowing many women to avoid the sequela of axillary surgery. This review discusses the use of breast conservation treatment and the evolving indications for excision alone in the treatment of ductal carcinoma in situ. The outcomes for breast conservation therapy from both randomized trials and institutional series have confirmed excellent survival rates. Salvage therapy for local recurrence is frequently successful, resulting in nearly equivalent survivals in women undergoing breast conservation therapy compared to mastectomy. In addition, intriguing but preliminary results from both breast cancer prevention studies and trials looking at the use of tamoxifen for intraductal cancer suggest a local control benefit in women using the drug.

Journal Article↗
PubMedDate not supplied

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences.

Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1,000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.

Animals↗
PubMed2004

Congenital myasthenic syndromes.

Congenital myasthenic syndromes are genetic disorders of neuromuscular transmission that should be considered in the differential diagnosis of seronegative myasthenia gravis and other neuromuscular disorders. They are present at birth but may not manifest until childhood or adult life. A classification system of congenital myasthenic syndromes based on molecular genetics is under evolution. Clinical and neurophysiological correlations with molecular studies have defined diagnostic criteria that assist the clinician in identifying specific clinical myasthenic syndromes. Some types of congenital myasthenia (e.g., slow-channel and fast-channel syndrome, acetylcholinesterase deficiency, and choline acetyltransferase deficiency) can be identified by clinical features, response to cholinesterase inhibitors, and standard electrodiagnostic studies. The molecular genetics, pathogenesis, clinical features, differential diagnosis, natural history, and treatment of well-characterized congenital myasthenic syndromes are discussed.

Acetylcholinesterase↗