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 1,063 records · Page 59Linked to original sources
PubMed2002

The value of molecular analysis by PCR in the diagnosis of cutaneous lymphocytic infiltrates.

The diagnosis and classification of cutaneous lymphomas remain a challenge for the clinician and dermatopathologist. This diagnostic dilemma is mainly encountered in the distinction between an early malignant lymphoma and a benign reactive lymphocytic infiltrate (pseudolymphoma). Until the beginning of the 1980s, our diagnostic tools were limited to the clinical presentation, course, and histopathology in diagnosis and classification of lymphocytic infiltrates. Advances in immunology and, in particular, in molecular genetics with the introduction of the Southern blot technique and the polymerase chain reaction (PCR) have revolutionized the diagnosis of lymphocytic infiltrates by determination of clonality. In some series, more than 90% of cutaneous T-cell lymphomas have a clonal rearrangement of the T-cell receptor gamma-chain gene, as opposed to very low percentages of rearrangement in T-cell pseudolymphomas. However, the presence of clonality does not necessarily imply malignancy. Cases of pseudolymphomas, lichen planus and pityriasis lichenoides et varioliformis acuta were reported with clonal lymphocytic proliferations. Therefore, care should be exercised in the evaluation of the results of molecular analysis, and these should always be correlated with the clinical, histological and immunophenotypic picture to arrive at the correct diagnosis. It may be expected that the molecular methods for diagnosis of lymphocytic infiltrates will be improved and refined in future, and that sensitivity and specificity will increase.

Clone Cells↗
PubMedDate not supplied

Molecular imaging: state of the art.

Molecular imaging includes all imaging methods applied in the identification, characterization and assessment "in vivo" of biological processes which occur at the cellular and molecular level. Molecular imaging parallels the remarkable advances achieved in the medical field, culminated in the sequencing of human DNA, the genome project. The understanding of the genetic basis of diseases and of human biology in general, together with the development of new drugs, led to a growing need for novel, sensitive and safe imaging technology to be rapidly translated from animal models into patients. The present evaluation of presence/absence of disease is based on anatomic and morphologic changes, the result of underlying molecular alterations. Direct "in vivo" visualization of these alterations allows early diagnosis before the onset of typical pathologic manifestations. Similarly, short-term effects of therapy can be directly visualized. In a near future, "evidence-based" medicine will become "presymptomatic" medicine. Histopathology will be replaced by "molecular pathology" with genomic implications in disease classification. In the near future the conventional morphologic methods should be supported and then replaced by the new functional and molecular methods with additional information proved useful for the diagnostic approach. In this article, the potentialities and applications of Nuclear Medicine, Magnetic Resonance Imaging, Optical Imaging and Contrast-enhanced Ultrasound are reviewed.

Diagnostic Imaging↗
PubMed2006

Molecular genetics of autosomal-dominant axonal Charcot-Marie-Tooth disease.

The autosomal-dominant axonal peripheral neuropathies comprise a genetically heterogeneous group of disorders that are clinically subsumed under Charcot-Marie-Tooth disease type 2 (CMT2). A significant increase in the number of genes underlying major forms of CMT2 has improved the classification of specific CMT phenotypes. The molecular dissection of cellular functions of the related gene products has only begun and detailed pathophysiological models are still missing, but already the biological scope of genes linked to CMT2 is more diversified than CMT1. The known CMT2 genes present key players in these pathways and will likely prove as powerful tools in identifying eventual future targets for therapeutic intervention.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Molecular markers derived from RAPD, SCAR, and the conserved 18S rDNA sequences for classification and identification in Pyrus pyrifolia and P. communis.

We generated RAPD, SCAR, and conserved 18S rDNA markers for classifying and identifying cultivars of Pyrus pyrifolia (Japanese pear) and P. communis (European pear). PCR amplification with selected specific primers-LCH327UP and LCH327DOWN-was performed using DNA extracted from 25 P. pyrifolia and P. communis cultivars. The 1,380-bp fragment was amplified from P. communis cvs. Beurre Giffard, Cascade, Conference, Clapp's Favorite, Packhams Triumph, and Winter Nelis. RAPD has only a dominant single band of 1,380-bp, however, SCAR has one or more band of the same size. Amplification involving sequence-specific primer pairs LCH346UP and LCH346DOWN resulted in a loss of polymorphism. The 1,190-bp fragment was amplified from all P. pyrifolia cultivars. The conserved sequences of the 18S rDNA fragment of 25 pear cultivars were amplified and analyzed with 42 restriction enzymes. Compared with P. pyrifolia cultivars, they lacked the restriction enzyme site of KpnI and had one less RsaI site. Cultivar Gamcheonbae had a specific PstI restriction site, while cvs. Mansoo and Conference pear digested with AluI showed a different presentation than other cultivars. For the Okusankichi and Shinil pears TaqI was best marker for identification in P. pyrifolia. These results can be adopted for identifying pear cultivars; to date there is no standard marker for identifying the cultivars of fruit trees in Korean fruit tree breeding programs.

Conserved Sequence↗
PubMed2005

Multilineage involvement of light microscopic myeloperoxidase-negative acute leukemia.

The classification of acute leukemia has traditionally been based on a combination of morphology and cytochemical staining data, including myeloperoxidase (MPO) reaction; however, a recent World Health Organization (WHO) classification entails use of cytogenetic and molecular findings in addition to the classic morphological and immunophenotypic analyses. Nevertheless, there have been rare cases in which blastic cells show multilineage phenotypes. These cases may be classified as acute leukemia of ambiguous lineage in the recent WHO classification. We report the case of a 49-year-old man with acute leukemia with multilineage phenotypes. Morphological findings led to a diagnosis of acute myeloid leukemia M2 by the French-American-British classification, but at light microscopy the results of MPO staining were negative for blast cells. In contrast, results of reverse transcription polymerase chain reaction and fluorescence-activated cell sorter analyses were positive for expression of MPO messenger RNA and protein. The blast cells expressed CD4, CD19, CD22, CD33, CD38, CD79a, and HLA-DR and showed rearrangement of the immunoglobulin heavy chain and TCR-3 genes. Results of immunoelectron microscopic analysis of the blast cells were positive for MPO, CD19, CD33, CD34, CD38 and glycophorin A but not for platelet peroxidase. According to these results, the blast cells had at least 4 lineage phenotypes. We concluded that the multiparameter analyses conducted in this case, including immunological and ultrastructural assays, were important in arriving at the appropriate diagnosis of acute leukemia of ambiguous lineage in the new WHO classification.

Acute Disease↗
PubMed1997

[What is a virus?].

Viruses are simple biological particles, consisting of a genome, a protein capsid and, in the case of enveloped viruses, an external lipidic envelope. Owing to the presence of envelope, most enveloped viruses are fragile although some exceptions may be observed. Viruses behave as complete intracellular parasites. Their multiplication results from the replication and self-assembly of viral components, this process being directed by the viral genome after it has been released within an infected cell. Virus classification is now essentially based on molecular properties, concerning both the structure and replication strategy of viruses. In virus taxonomy, serial hierarchical levels are family, subfamily, genus and species. Within species, lower hierarchical levels are type, subtype, variant and strain. Knowledge of virus structure and classification is essential for considering the physiopathology, diagnosis and therapy of viral infections.

Humans↗
PubMed2026

Molecular profiling of pancreatic acinar cell carcinoma and amphicrine-like carcinoma: high frequency of homologous recombination deficiency and molecular heterogeneity.

BACKGROUND: The 6th edition of the WHO Classification of Digestive System Tumours distinguishes amphicrine-like carcinomas (ALCs) from mixed neuroendocrine-non-neuroendocrine neoplasms (MiNENs). Acinar cell carcinomas (ACCs) with an intimately admixed and not separated neuroendocrine component comprising >30% of the tumour are classified as amphicrine-like ACCs (AL-ACCs). We characterised the genomic landscape of pancreatic ACCs and AL-ACCs to validate current classification and identify therapeutic targets. METHODS: Among 2,151 pancreatic biopsy and resection cases that underwent targeted next-generation sequencing using the OncoPanel AMC v4.3 or v4.5 (DNA-based hybrid capture, targeting 323 genes (v4.3) or 343 genes (v4.5)), eight ACCs, seven AL-ACCs originally diagnosed as MiNENs under the 5th edition of the WHO classification scheme, and four neuroendocrine tumours (NETs) were identified, diagnosed between 2020 and 2026. RESULTS: Homologous recombination deficiency (HRD)-associated alterations, involving BRCA1/2, ATM and FANCD2, were identified in 87.5% (7/8) of ACCs and 29% of AL-ACCs. One ACC had an ATRX nonsense mutation. Genomic heterogeneity was observed in molecular profiling of AL-ACCs; two demonstrated a 'true hybrid' signature with co-occurrence of lineage-specific drivers: MEN1 deletion and splice site mutation (neuroendocrine-associated), APC, SMAD4 and CTNNB1 alterations (exocrine-associated). Two others exhibited 'ACC-like' signatures, including missense BRCA1 and nonsense TP53 mutations and MDM4 and AKT3 amplifications, located on chromosome 1q, despite their neuroendocrine differentiation. CONCLUSIONS: Pancreatic ACCs frequently harbour HRD-related alterations, suggesting potential for PARP-inhibitor therapy. AL-ACCs comprise molecularly heterogeneous groups, including true hybrid and ACC-like patterns. Larger studies are required to elucidate the molecular distinction between true hybrid AL-ACCs and those with single-lineage alterations to refine their classification.

acinar↗
PubMed2005

Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity.

The TOpological MOlecular COMputer Design (TOMOCOMD-CARDD) approach has been introduced for the classification and design of antimicrobial agents using computer-aided molecular design. For this propose, atom, atom-type, and total quadratic indices have been generalized to codify chemical structure information. In this sense, stochastic quadratic indices have been introduced for the description of the molecular structure. These stochastic fingerprints are based on a simple model for the intramolecular movement of all valence-bond electrons. In this work, a complete data set containing 1006 antimicrobial agents is collected and presented. Two structure-based antibacterial activity classification models have been generated. The models (including nonstochastic and stochastic indices) classify correctly more than 90% of 1525 compounds in training sets. These models permit the correct classification of 92.28% and 89.31% of 505 compounds in an external test sets. The TOMOCOMD-CARDD approach, also, satisfactorily compares with respect to nine of the most useful models for antimicrobial selection reported to date. Finally, a virtual screening of 87 new compounds reported in the antiinfective field with antibacterial activities is developed showing the ability of the TOMOCOMD-CARDD models to identify new leads as antibacterial.

Anti-Bacterial Agents↗
PubMed2003

[Molecular imaging in rheumatoid arthritis].

Advances in molecular biology and technical developments in the field of imaging are increasingly allowing for non-invasive visualization and quantitation of biological processes at the molecular level. Such technologies, defined as molecular imaging, promise early diagnosis and improved classification of the stage and severity of disease, objective assessment of treatment efficacy, and reliable prognosis based on so-called molecular markers. Furthermore, molecular imaging is an important tool for the evaluation of physiological and pathophysiological processes and for drug development. Various different imaging modalities are available, such as conventional radiography (CR), computed tomography (CT), nuclear imaging, magnetic resonance imaging (MRI), ultrasound (US), as well as other methods including fluorescence-based optical imaging. These methods differ with respect to resolution and their potential to gather information at the anatomical, physiological, cellular and molecular level. Therefore, the choice of the imaging modality for molecular imaging depends on the questions that need to be answered. This review discusses the potential of imaging modalities for molecular imaging in rheumatoid arthritis (RA).

Animals↗
PubMed1998

Reliability of a Crohn's disease clinical classification scheme based on disease behavior.

Classification of Crohn's disease (CD) by disease behavior--either inflammatory (INF), fibrostenotic (FS), or fistulizing/perforating (FP)--has been proposed as a means of assisting management decisions and predicting outcomes for subgroup analysis in clinical trials and for making phenotype/genotype associations in molecular genetic studies. Accurate and reproducible classification of CD patient subgroups is of paramount importance in such studies but to be useful, the classification scheme must have good interrater agreement. We sought to assess the interrater agreement associated with the disease-behavior classification scheme of CD. Twelve patients with CD were randomly selected from a database of 964 patients with CD undergoing medical or surgical treatment or both. Clinical details of the 12 cases, along with their radiographs and surgical and pathological reports, were presented to a panel of 20 experts who were asked to classify each case based on the patient's overall disease course (scenario A) and as if the patient were being entered into a clinical trial on that day (scenario B). Calculations of strength of interrater agreement were made and were expressed as the kappa statistic (kappa), with kappa < 0.2 = poor strength of agreement; kappa 0.21 - 0.4 = fair; kappa 0.41 - 0.6 = moderate; kappa 0.61 - 0.8 = good; and kappa 0.81 - 1.0 = very good. Five panel participants did not complete the study, and three clinical vignettes were excluded because of incomplete scoring, leaving a total of 15 panel experts assessing nine cases. Overall interrater agreement was only fair with kappa = 0.353 for scenario A and kappa = 0.291 for scenario B. Interrater agreement was less when only the most straightforward case in each disease category was evaluated. Classification of CD by pattern of disease behavior yields only fair interrater agreement. This raises concerns regarding its applicability, particularly in ongoing studies of genotype/phenotype associations. Further refinement of disease subtypes and clear operational definitions are required.

Adult↗
PubMedDate not supplied

Quantification of the influence of single-point mutations on haloalkane dehalogenase activity: a molecular quantum similarity study.

Controlled modifications in certain protein amino acid residues can lead to changes in their function and stability. Amino acid structural features and their relation to these changes were examined by using quantum molecular similarity techniques. The effect of deliberate mutations in position 172 of the haloalkane dehalogenase enzyme, yielding to variations on the dehalogenation of 1,2-dibromoethane, was studied qualitatively and quantitatively using molecular quantum similarity techniques. A valuable classification of the residues according to their effect on activity was obtained by representing the optimal two-dimensional classical scaling solution. In addition, satisfactory quantitative relationships were found, comparable to those attained by previous studies on this same data set using other techniques. Molecular quantum similarity analysis provides a consistent, unbiased, and homogeneous set of molecular descriptors and is a feasible alternative to the use of physicochemical properties.

Hydrolases↗
PubMed2006

Combined mitochondrial and nuclear sequences support the monophyly of forcipulatacean sea stars.

Previous molecular phylogenetic analyses of forcipulatacean sea stars (Echinodermata: Asteroidea) have reconstructed a non-monophyletic order Forcipulatida, provided that two or more forcipulate families are included. This result could mean that one or more assumptions of the reconstruction method was violated, or else the traditional classification could be erroneous. The present molecular phylogenetic analysis included 12 non-forcipulatacean and 39 forcipulatacean sea stars, with multiple representatives of all but one of the forcipulate families and/or subfamilies. Bayesian analysis of approximately 4.2kb of sequence data representing seven partitions (nuclear 18S rRNA and 28S rRNA, mitochondrial 12S rRNA, 16S rRNA, 5 tRNAs and cytochrome oxidase I with first and second codon positions analyzed separately from third codon positions) recovered a consensus tree with three well-supported clades (78%-100% bootstrap support) that corresponded at least approximately to traditional taxonomic ranks: the superorder Forcipulatacea (Forcipulatida + Brisingida) + Pteraster, the Brisingida/Brisingidae and Asteriidae + Rathbunaster + Pycnopodia. When a molecular clock was enforced, the partitioned Bayesian analysis recovered the traditional Forcipulatacea. Five of six genera represented by two or more species were monophyletic with 100% bootstrap support. Most of the traditional subfamilial and familial groupings within the Forcipulatida were either unresolved or non-monophyletic. The separate partitions differed considerably in estimates of model parameters, mainly between nuclear sequences (with high GC content, low rates of sequence substitution and high transition/transversion rate ratios) and mitochondrial sequences.

Animals↗
PubMed2003

DNA arrays in clinical oncology: promises and challenges.

Cancer is a complex genetic disease characterized by the accumulation of multiple molecular alterations. Current diagnostic and prognostic classifications, based on clinical and pathologic factors, are insufficient to reflect the whole clinical heterogeneity of tumors. Most current anticancer agents do not differentiate between cancerous and normal cells, leading sometimes to disastrous adverse effects. Recent advances in human genome research and high-throughput molecular technologies make it possible finally to tackle the molecular complexity of malignant tumors. With DNA array technology, mRNA expression levels of thousands of genes can be measured simultaneously in a single assay. Oncology is benefiting on multiple fronts. Gene expression profiles are revealing new biologically and clinically relevant tumor subclasses previously indistinguishable and are identifying new diagnostic and prognostic biomarkers as well as new potential therapeutic targets. Here, we review the technology and present clinical applications for which promising results have been obtained. Finally, we discuss issues that must be resolved in the near future to allow DNA arrays to translate into benefits for cancer patients.

Gene Expression Profiling↗
PubMed1997

Achondroplasia: recent advances in diagnosis and treatment.

Achondroplasia (ACH) is the most common form of chondrodysplasia in humans. This disorder is inherited as an autosomal dominant trait, though most cases are sporadic. Recent advances in molecular biology have revealed its genetic defect in fibroblast growth factor-3 gene. This may introduce a new diagnostic tool and the classification of ACH and related disorders. Recent molecular engineering techniques have made it possible to provide large amounts of the various kinds of biofactors, such as erythropoietin, granulocyte colony stimulating factor and human growth hormone (GH), for clinical use. In fact, GH has been widely used to treat non-GH-deficient forms of short stature, such as Turner's syndrome, skeletal dysplasia, intrauterine growth retardation, chronic illness and idiopathic short stature, with beneficial effects. This may also be introduced into the medical management of ACH.

Achondroplasia↗
PubMed2001

Posttransplantation lymphoproliferative disorders in pediatric patients undergoing liver transplantation.

OBJECTIVES: To study the clinicopathologic and molecular genetic findings in posttransplantation lymphoproliferative disorders (PTLDs) following pediatric liver transplantation and to determine the applicability of a recently proposed consensus classification system. DESIGN: The clinical, pathologic, and molecular genetic findings of 11 PTLDs that occurred in 10 patients are presented. These 10 patients were derived from a group of 121 pediatric patients who underwent liver transplantation at the University of California, San Francisco. The PTLDs were classified using the proposed Society for Hematopathology scheme. Clonality was determined by immunohistochemical detection of monotypic immunoglobulin or by using polymerase chain reaction-based methods to detect monoclonal immunoglobulin heavy-chain gene rearrangements. Epstein-Barr virus (EBV) was detected by immunohistochemistry, in situ hybridization, or polymerase chain reaction. Epstein-Barr virus typing and the presence of LMP1 gene deletions were also analyzed by polymerase chain reaction. RESULTS: There were 3 early lesions, 4 polymorphic PTLDs, and 4 monomorphic PTLDs. Monoclonality was demonstrated in 8 of 9 cases assessed. Epstein-Barr virus was present in all cases; of 9 cases assessed by polymerase chain reaction, the virus was type A in 8 and type B in 1. No EBV LMP1 gene deletions were identified. The corresponding liver explants were negative for EBV in 8 cases and positive in 1 case. Greater than 3 foci of disease and monomorphic PTLD were associated with decreased actuarial survival (P <.05). CONCLUSIONS: The prognosis of pediatric patients with PTLD is favorable for early lesions and polymorphous PTLD, particularly in patients with localized disease. Multifocal disease and monomorphic PTLD are associated with an unfavorable prognosis.

Child↗
PubMed2003

Oligodendroglioma: toward molecular definitions in diagnostic neuro-oncology.

Oligodendroglial tumors have attracted great interest in both basic and clinical neuro-oncology over the past decade. This interest is mainly due to the clinical observation that anaplastic oligodendrogliomas and anaplastic oligoastrocytomas, in contrast to the vast majority of anaplastic astrocytomas and glioblastomas, frequently respond favorably to chemotherapy. In addition, oligodendroglial tumors are associated with longer survival times than the diffuse astrocytic gliomas. These differences in response to therapy and in prognosis have been associated with distinct genetic aberrations, in particular the frequent loss of alleles on chromosome arms 1p and 19q in oligodendroglial tumors. In addition, other genetic changes have been reported as indicators of poor response to therapy and short survival, including homozygous deletion of the CDKN2A gene at 9p21, mutation of the PTEN gene at 10q23, and amplification of the EGFR gene at 7p12. In this review we summarize the current state of the art concerning the molecular genetics of oligodendroglial tumors. A particular focus is placed on the role of molecular genetic findings in the diagnostic and prognostic assessment of these neoplasms. As a result of the recent advances in the field, we propose that clinical decisions in the management of patients with oligodendroglial tumors should be based on the combined assessment of clinical and neuroimaging features, histological classification and grading, as well as molecular genetic characteristics.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1997

Phylogeny of North American Cicindela tiger beetles inferred from multiple mitochondrial DNA sequences.

Tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae) have been used as a model system for studies in ecology and conservation biology. Work on this group will greatly benefit from the availability of a phylogenetic hypothesis. We selected a representative sample of 23 North American Cicindela and 6 outgroups to reconstruct a phylogeny based on 1896 nucleotide positions from three mitochondrial genes (Cytochrome b, Cytochrome oxidase III, and 16S rRNA). Cladistic analysis of these three data sets yielded widely different tree topologies, but character conflict between them appears to be relatively low. The combined analysis of all data resulted in three similar shortest trees of 3453 steps. One of these was also recovered after successive weighting and was considered the best estimate of relationships. The most basal taxa of North American Cicindela (s.l.) were in the cosmopolitan subgenus Cylindera. The derived taxa were in the subgenus Cicindela (s. str.), a group dominating at higher latitudes in the Nearctic and Palearctic Region. The molecular analysis was essentially in agreement with the traditional classification which has been worked out based on male genitalic structures by E. Rivalier (1954, Rev. Entomol. Française 21:249-268). In the molecular analysis, Rivalier's species groups and subgenera were mostly found to be composed of closely related taxa but several of them were not monophyletic. Implicit in the traditional classification is a sequence from basal to derived groups which we found to be essentially reversed in the molecular analysis. We also discuss the conceptual differences in the establishment of the traditional classification by Rivalier (1954) and the cladistic analysis presented in this study.

Animals↗