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 1,405 records · Page 78Linked to original sources
PubMed2026

Gastric carcinoma classification in the WHO 6th edition (2026): Updated framework and emerging entities.

The sixth edition of the WHO Classification of Digestive System Tumours (2026) represents an important step in the continuing evolution of gastric carcinoma classification. While preserving morphology as the foundation of diagnosis, it incorporates advances in molecular pathology, genotype-phenotype correlations, tumour evolution, and predictive biomarker assessment. This review summarizes the development of the WHO classification from the third edition (2000) to the sixth edition (2026) and highlights its relationship with other major classification systems, including those of Laurén, Nakamura, and the Japanese Gastric Carcinoma Association (JGCA). Major histological categories remain largely unchanged; however, several important conceptual and diagnostic refinements have been introduced. These include recognition of crawling-type adenocarcinoma as a distinctive variant of tubular adenocarcinoma, subclassification of poorly cohesive carcinoma into signet-ring cell and non-signet-ring cell subtypes, introduction of the concept of pure signet-ring cell carcinoma, and increased emphasis on tumour evolution. The sixth edition also expands and refines the spectrum of uncommon gastric carcinoma subtypes, including gastric carcinoma with lymphoid stroma, AFP-producing carcinoma, micropapillary adenocarcinoma, gastric adenocarcinoma of fundic-gland type, and gastric sarcomatoid carcinoma. Crucially, molecular subgroups originally proposed by The Cancer Genome Atlas (TCGA) and actionable biomarkers-including HER2 (ERBB2), Claudin 18.2, mismatch repair deficiency/microsatellite instability (dMMR/MSI), and programmed death-ligand 1 (PD-L1)-have transitioned from research-based categories into essential tools for precision oncology. Rather than providing exhaustive diagnostic criteria, this review offers a conceptual framework and encourages consultation of the original WHO text for full details. These advances illustrate the transition of gastric carcinoma classification from a predominantly morphology-based system toward an integrated histomolecular framework that more closely links pathological diagnosis with tumour biology, prognostication, and therapeutic stratification.

Crawling-type adenocarcinoma↗
PubMed2002

[Surgical therapy for patients with thymoma or thymic carcinoma; based on WHO classification].

The treatment strategy for patients with thymoma or thymic carcinoma still has not been confirmed, and the molecular biologic characteristics of these tumors have not been defined also. We have emphasized the clinical significance of this classification so far by the research cooperation with professor Müller-Hermelink, the institute of pathology, Würzburg University. This time, We introduced clinico-pathological findings based on the new WHO classification in 59 Case of thymic epithelial tumor and reffered the treatment strategy for patients with thymic cancer.

Adult↗
PubMed1980

Evolution and gene transfer in purple photosynthetic bacteria.

A concern voiced in connection with recent sequencing of cytochrome c from the Rhodospirillaceae or purple non-sulphur photosynthetic bacteria is that molecular information might be of little use in deciphering bacterial phylogeny because of the possibility of lateral transfer of genes and the consequent scrambling of the genetic record. This could be true for many proteins, of course, but the immediate question is, is it true for cytochroms available for comparison? The evidence suggests that this is probably not so. The disagreement between cytochrome c sequences and the standard taxonomy of the Rhodospirillaceae in Bergey's Manual is not a problem. That reference, as its title indicates, is a manual of determinative rather than evolutionary bacteriology. Its goal is a reproducible system for identification of bacteria. If one claims that these determinative categories also have phylogenetic or evolutionary meaning, this is an assertion that must be proven. The argument outlined below suggests that molecular traits may eventually become more a dependable basis for classification of the Rhodospirillaceae than is gross morphology.

Base Sequence↗
PubMed2003

The influence of central review on outcome associations in childhood malignant gliomas: results from the CCG-945 experience.

To examine the influence of the pathology review mechanism on the results of analyses of therapeutic efficacy and biological prognostic correlates for pediatric high-grade gliomas, we evaluated the effects of using single-expert review or consensus review, as alternatives to institutional classification, in determining outcome results of a large randomized trial. The study group was the randomized cohort of Children's Cancer Group study 945, which compared efficacy of 2 chemotherapy regimens adjuvant to surgery and radiation. Trial eligibility required institutional histopathologic diagnosis of high-grade glioma. Sections of study tumors also were centrally reviewed, initially by a study review neuropathologist and subsequently by 5 neuropathologists, including the review pathologist. Reviews were independent, and reviewers were masked to clinical factors and outcomes, and consensus diagnoses of the panel were then established. Among 172 eligible patients, 42 tumors were classified as discordant on single-expert review and 51 on consensus review. Progression-free survival probabilities calculated for patients with tumors classified as high-grade gliomas by either single-expert or consensus review were inferior to those for the overall, institutionally diagnosed cohort. However, conclusions of the study regarding relative efficacy of treatment and clinical and molecular outcome correlates were unaffected by diagnosis method. Resection extent, proliferation index, and p53 expression were associated strongly with outcome, regardless of diagnosis method. However, comparisons between arms in which inclusion was determined by different review criteria for each arm caused spurious conclusions about efficacy differences between treatments. We conclude that the pathology review mechanism had little effect on within-trial comparisons of therapeutic effects or prognostic correlates in this randomized study, but strongly influenced survival distributions that were calculated for each treatment arm. These results support the implementation of expedited central review in therapeutic studies involving childhood malignant gliomas as a way to prospectively identify and exclude cases with discordant diagnoses and indicate the need for additional measures, such as molecular assessments, to increase the reproducibility of neuropathologic classification for these tumors.

Antineoplastic Protocols↗
PubMedDate not supplied

[Diffuse large cell lymphoma: new molecular approaches].

The term lymphoma comprises a group of neoplasias that develop within the lymphatic system and represent one of the most frequent types of cancer worldwide. During the last decade, significant advances on the molecular biology of lymphoma have been achieved, which have been important not only to understand the etiology of this disease, but also in the development of fast and accurate diagnostic and prognostic methods, which in turn, will allow us to develop appropriate treatments for individual patients. Current systems for the classification of lymphomas have also been influenced by new molecular tools, recently developed. The main goal of this article is to present a general view on the latest advances in the molecular biology of lymphoma. In order to do so, we have focused on Diffuse Large B-Cell Lymphoma (DLBCL), one of the most common, and most studied, types of lymphoma. It is noteworthly that most of what we know about DLBCL arises from studies on lymph nodes, and this is reflected in the present review; however, here we have also included recent information regarding cellular and molecular findings in bone marrow from DLBCL patients. These latter observations may be relevant in opening new lines of research in the near future.

Hematopoiesis↗
PubMed2000

Molecular phylogeny: pitfalls and progress.

Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects.

Artifacts↗
PubMed1996

Diagnosis and classification of the acute leukemias: recent advances and controversial issues.

Although morphology and cytochemistry continue to be the mainstay of the diagnosis of acute leukemia (AL), new developments in immunophenotyping, cytogenetics, molecular biology, and in vitro assays have dramatically improved our understanding of this disease and enabled the identification of entities with distinct clinico-biologic features. Immunophenotyping is essential for diagnosing and subclassifying acute lymphoblastic leukemia (ALL) and is also very helpful in certain types of acute myeloid leukemias (AML), such as AML with minimal differentiation or acute megakaryoblastic leukemia. Cytogenetic findings are clinically relevant for diagnosis and prognosis. Nonrandom chromosomal abnormalities such as t(15;17)(q22;q12) or t(1;19)(q23;p13) have been so closely associated with distinct types of acute leukemias that their recognition can allow diagnosis independent of the other criteria. Molecular analysis is a powerful method in the assessment of the malignant potential, clonality, and classification of the ALs. It has become clear that in some leukemias a proportion of patients exhibit the biologically relevant molecular defect in the absence of a karyotypic equivalent. On the other hand apparently uniform chromosomal abnormalities such as the t(1;19), t(9;22), t(8;14), or t(15;17) may differ at the molecular level. In vitro assays can evaluate the growth pattern and cell-cycle kinetics of leukemic cells, as well as their sensitivity to therapeutic agents. All these data are relevant to the management of AL. Because the French-American-British (FAB) classification does not fully correlate with much of this new information, alternative classifications have been proposed. In this review we concentrate on recent diagnostic contributions resulting from advances in biotechnology and discuss some of the points that arouse controversy in the single classifications.

Acute Disease↗
PubMed1999

Molecular evaluation of acute myeloid leukemias.

Traditionally, acute myeloid leukemia (AML) has been diagnosed and classified based on the morphologic and cytochemical criteria of the French-American-British (FAB) classification system. However, more recent studies have demonstrated that the cytogenetic and molecular genetic abnormalities consistently associated with distinct forms of AML confer the most important prognostic information. Each broad category of de novo AML that arises in infants and children, young adults, and the elderly, or, AML arising secondary to antecedent myelodysplasia (MDS) or prior exposure to chemotherapy, radiotherapy, or environmental agents is characterized by distinct cytogenetic and molecular genetic abnormalities. Over the past 15 years, a number of these recurrent cytogenetic abnormalities have been cloned and characterized, yielding valuable insights into the mechanisms of leukemogenesis and providing powerful molecular tools for precise diagnosis and monitoring of minimal residual disease. As cytogenetic and molecular genetic characterization of AML cells is now considered crucial for both diagnostic and therapeutic decision-making, it is essential to have a working knowledge of the molecular basis of AML. This chapter reviews the molecular genetic features of different forms of AML and the new automated molecular technologies for residual disease assessment; the emerging molecular paradigms in this disease that are being exploited for therapeutic decision-making are presented.

Acute Disease↗
PubMed1997

[Current lymphoma classification: a step forward for pathologists and clinicians].

Non-Hodgkin lymphomas encompass a heterogeneous group of lymphoid malignancies from the clinical as well as from the pathological point of view. Consequently, one condition of optimal communication among pathologists, clinicians and scientific researchers is an adequate classification system. A new classification of lymphomas was proposed in September 1994, the Revised European-American Lymphoma Classification (REAL classification). The REAL classification is aiming at integration of pathological and clinical data, making it possible to distinguish clinical-pathological entities each of which has its characteristic pathological spectrum, clinical evolution and clinical presentation. The REAL classification is based not only on morphological and immunohistochemical but also on molecular and cytogenetic data. Such a system may make it possible to develop specific therapies for specific pathological entities. The REAL classification constitutes an important step forward in haemato-oncology.

Hodgkin Disease↗
PubMedDate not supplied

[Diagnosis of myeloid hematologic malignancies: contributions of the 2001 World Health Organization (WHO) classification].

Although the French-American-British (FAB) morphologic classification of myeloid malignancies has been accepted for many years, the important advances in cytogenetic, immunophenotype and genetic fields needed to be integrated in an updated approach using all the available informations. Thus, the World Health Organization (WHO) Classification of haematopoietic malignancies not only incorporates morphology, immunophenotype, cytogenetic and molecular features, but also ensures to be clinically useful. This collaborative project has begun in 1995 and has been published in 2001. The proposed WHO classification is less a disruption with regard to the FAB classification than an updated revision where morphology is always important. These review emphasises the modifications proposed in the new WHO classification concerning the myeloid disorders.

Acute Disease↗
PubMed2005

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.

Animals↗
PubMed2002

Classifying the medulloblastoma: insights from morphology and molecular genetics.

Significant advances in the treatment of the medulloblastoma (MB) have been made in the last 30 years, reducing mortality by 2-fold. Further improvements in the cure rate require an increased understanding of the biology of MBs, and this will translate into refinements in their classification. Scrutiny of the cytological variation found among MBs has recently led to the concept of the anaplastic MB, which overlaps the large-cell variant and appears to share its poor prognosis. In contrast, the MB with extensive nodularity, a distinctive nodular/desmoplastic variant occurring in infants, has a better outcome than most MBs in these young patients. Building on cytogenetic studies that have drawn attention to abnormalities on chromosome 17 in over a third of MBs, research shows non-random losses on chromosomes 8, 9, 10, 11 and 16, and gains on chromosomes 1, 7 and 9. Overexpression of ErbB2 receptors and losses on chromosome 17p have been proposed as independent indicators of aggressive behaviour, while high TrkC receptor expression indicates a favourable outcome. There is a strong association between anaplastic/large-cell tumours and MYC amplification, which has previously been linked with aggressive disease, but associations between abnormalities on chromosome 17 and anaplastic/large-cell MBs and between abnormalities in the shh/PTCH pathway and the desmoplastic variant are more controversial. Classification of the MB histopathologically and according to profiles of molecular abnormalities will help both to rationalize approaches to therapy, increasing the cure rate and reducing long-term side-effects, and to suggest novel treatments.

Cerebellar Neoplasms↗
PubMed1995

DNA profiling of banana and plantain cultivars using random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers.

Polymerase chain reaction (PCR) amplification of genomic DNA from 57 Musa cultivars with 60 random 10-mer primers generated 605 polymorphic amplification products which were useful in unambiguous cultivar identifications. Unweighted pair-group method analysis of this data grouped the cultivars into specific clusters depending on their genomic similarities. The diploid ancestral species of cultivated banana and plantains, namely Musa acuminata sp malaccensis, an A genome donor and M. balbisiana, a B genome donor, were farthest apart from each other in the phenogram. The edible fruit yielding cultivars with the genomic constitutions AA, AAA, AB, AAB, ABB, and ABBB grouped in different clusters according to overall genetic homologies. The restriction fragment length polymorphisms (RFLPs) prevalent among the cultivars were studied by hybridization of 19 random genomic clones to blots of HindIII, EcoRI and MspI digests. Cluster analysis of these data on 107 polymorphic alleles resulted in a phenogram comparable to the one obtained with random amplified polymorphic DNA (RAPD) analysis. Two multilocus probes useful in distinguishing all the 57 cultivars analyzed were also identified. The A and B types of cytoplasms in the cultivars were further distinguished by hybridization of heterologous chloroplast DNA probes. Results showed that use of different kinds of molecular markers in gene banks is essential for characterization and classification of germplasm collections.

Base Sequence↗
PubMed2006

Dystonia: genetics and treatment update.

BACKGROUND: Dystonia refers to a syndrome of sustained muscle contractions, frequently causing twisting and repetitive movements or abnormal postures. Although age at onset, anatomic distribution, and family history are essential elements in the evaluation of dystonia, new classification increasingly relies on etiologic and genetic data. In recent years, much progress has been made on the genetics of various forms of dystonia and its pathophysiology underlying the clinical signs. The treatment of dystonia has continued to evolve to include newer medications, different forms of botulinum toxin, and various surgical procedures. REVIEW SUMMARY: In this article, the author reviewed and summarized the history of dystonia, its evolving classification, and recent genetic data, as well as its clinical investigation and treatment. CONCLUSIONS: Recent advances in molecular biology have led to the discovery of novel dystonia genes and loci, updating classification schemes, and better understanding of underlying pathophysiology. Treatment strategies for dystonia have significantly been updated with the introduction of different forms of botulinum toxin therapy, new pharmacologic agents, and most recently pallidal deep brain stimulation. A systematic approach to the diagnosis and treatment evaluation of dystonic patients provides optimal care for long-term management.

Baclofen↗
PubMed2004

Validation of molecular and immunological factors with predictive importance in lung cancer.

Histological classification and staging are cornerstones of diagnosis in lung cancer. Treatment options have been enriched in the last few years by the development of a number of new drugs, and therapy is now increasingly being carried out within multimodal concepts and at earlier stages. Still, outcome of the disease is far from satisfactory and progress in clinical and preclinical research is time-consuming. With the whole variety of potent new therapeutic compounds including classical cytostatics and biological factors at hand, many now believe that a clear improvement of treatment results will be derived from a better understanding of the biology of these tumours and a resulting improvement of diagnosis. Biological factors reflecting the underlying tumour biology and aspects of clinically important pathomechanisms may not only better predict outcome of the disease but also of its treatment, serving as surrogate markers for a more appropriate general intensification of therapy and ideally for specific "targeted" interventions. This article describes the different insights in the biology of these tumours in relation with the representing surrogate markers, and opens routes to possible diagnostic and therapeutic consequences.

Biomarkers, Tumor↗
PubMed2005

Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases.

Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, phiA1122, T3, phiYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used to scan the corresponding genomes, a significant gap in the individual information distribution was observed between functional promoter sites and other sequences, suggesting that the models can be used to identify new T7-like promoters. When a combined 76-site model was used to scan the eight phages, 108 of the total 109 promoters were found, while none were found for other T7-like phages, phiKMV, P60, VpV262, SIO1, PaP3, Xp10, P-SSP7 and Ppu40, indicating that these phages do not belong to the T7 group. We propose that the T7-like transcription system, which consists of a phage-specific RNA polymerase and a set of conserved T7-like promoters, is a hallmark feature of the T7 group and can be used to classify T7-like phages. Phylogenetic trees of the T7-like promoter models and their corresponding RNA polymerases are similar, suggesting that the eight phages of the T7 group can be classified into five subgroups. However the SP6-like polymerases have apparently diverged from other polymerases more than their promoters have diverged from other promoters.

DNA-Directed RNA Polymerases↗
PubMed1997

A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa.

In an attempt to characterize an unusual mycobacterial strain isolated from a 2-year-old Somali patient with lymphadenitis, we applied various molecular methods not previously used for the taxonomic classification of mycobacteria. This isolate, designated So93, did not differ from Mycobacterium tuberculosis in the biochemical tests and in its 16S rRNA sequence, but produced smooth and glossy colonies, which is highly exceptional for this species. This smooth phenotype was unstable and switched nonreversibly to a rough colony morphology with a low frequency. The two colony types were equally virulent for the guinea pig, exhibiting characteristic tuberculous disease. Both morphotypes had shorter generation times than the M. tuberculosis reference laboratory strain H37Rv and clinical isolates of M. tuberculosis and Mycobacterium bovis. Furthermore, the So93 isolate differed from all M. tuberculosis complex strains described thus far by having only a single copy of insertion sequence IS1081, an unusual composition of the direct repeat cluster, and a characteristic phenolic glycolipid and lipooligosaccharide. This glycolipid had previously been observed only in a smooth isolate of M. tuberculosis obtained in 1969 by Canetti in France. Analysis of the Canetti strain showed that it shared virtually all genetic properties characteristic of So93, distinguishing these two strains from the known M. tuberculosis complex taxa, M. tuberculosis, Mycobacterium africanum, M. bovis, and Mycobacterium microti. The natural reservoir, host range, and mode of transmission of the group of bacteria described in this paper are presently unknown. This study, partly based on not previously used molecular criteria, supports the idea that the established members within the M. tuberculosis complex and the newly described Canetti grouping should be regarded as a single species, which likely will be designated "M. tuberculosis".

Animals↗