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At least 577 records · Page 32Linked to original sources
PubMed2000

Comparative genetic patterns of glioblastoma multiforme: potential diagnostic tool for tumor classification.

Cytogenetic and molecular genetic studies of glioblastoma multiforme (GBM) have shown that the most frequent alterations are gains of chromosome 7, losses of 9p loci and chromosome 10, and gene amplification, primarily of the epidermal growth factor receptor (EGFR) gene. Although this profile is potentially useful in distinguishing GBM from other tumor types, the techniques used tend to be labor intensive, and some can detect only gains or losses of genetic loci. Comparative genomic hybridization (CGH) is a powerful technique capable of identifying both gains and losses of DNA sequences. The present study compares the CGH evaluation of 22 GBM with classic cytogenetics, loss of heterozygosity by allelotyping, and gene amplification by Southern blot analysis to determine the reliability of CGH in the genetic characterization of GBM. The CGH and karyotypic data were consistent in showing gain of chromosome 7 accompanied by a loss of chromosome 10 as the most frequent abnormality, followed by a loss of 9p in 17 of 22 GBM cases. Loss of heterozygosity of chromosomes 10 (19/22) and 9p (9/22) loci confirmed the underrepresentation by CGH. Genomic amplifications were observed by CGH in 5 of the 10 cases where gene amplification was detected by Southern blot analysis. The data show that CGH is equally reliable, compared with the more established genetic methods, for recognizing the prominent genetic alterations associated with GBM and support its use as a plausible adjunct to glioma classification.

Adult↗
PubMed2005

[Urinary bladder tumours. The new 2004 WHO classification].

Increasing knowledge in molecular genetic research on urinary bladder carcinoma has allowed us to classify the morphological picture on the basis of a better understanding. But this new knowledge will only be ground-breaking if it can be correlated with the clinical outcome of urinary bladder tumours and with histopathological findings. The use of the new 2004 WHO classification results in a standardized diagnosis of urothelial tumours by means of an exact definition of the subgroups. In the future, trials can thus be compared worldwide and risk profiles can be stratified. Further research in molecular genetics and correlation with the current classification together with molecular biological techniques may allow refinement of this scheme, e.g. by immunohistochemical subclassifications, enabling identification of potentially genetically unstable tumours. In this paper we present the new 2004 WHO classification of urinary bladder tumours emphasizing the changes in relation to the former classifications focusing on histological typing, grading and molecular characterization. Until the new classification is finally validated, and those working in the field have become familiar with it, the WHO classification of 1973 should be mentioned additionally in the histopathological report.

Humans↗
PubMed2004

Grouping of tropical mid-altitude maize inbred lines on the basis of yield data and molecular markers.

The classification of maize inbred lines into heterotic groups is an important undertaking in hybrid breeding. The objectives of our research were to: (1) separate selected tropical mid-altitude maize inbred lines into heterotic groups based on grain yield data; (2) assess the genetic relationships among these inbred lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers; (3) examine the consistency between yield-based and marker-based groupings of the inbred lines. Thirty-eight tropical mid-altitude maize inbred lines were crossed to two inbred line testers representing the flint and dent heterotic pattern, respectively. The resulting testcrosses were evaluated in a trial at three locations for 2 years. Significant general combining ability (GCA) and specific combining ability (SCA) effects for grain yield were detected among the inbred lines. The tester inbred lines classified 23 of the 38 tested inbred lines into two heterotic groups based on SCA effects and testcross mean grain yields. This grouping was not related to endosperm type of the inbred lines. The outstanding performance of testcrosses of the remaining 15 inbred lines indicates the presence of significant genetic diversity that may allow the assignment of the lines into more than two heterotic groups. Diversity analysis of the 40 maize inbred lines using AFLP and SSR markers found high levels of genetic diversity among these lines and subdivided them into two main groups with subdivision into sub-groups consistent with breeding history, origin and parentage of the lines. However, heterotic groups formed using yield-based combining ability were different from the groups established on the basis of molecular markers. Considering the diversity of the genetic backgrounds of the mid-altitude inbred lines, the marker-based grouping may serve as the basis to design and carry out combining ability studies in the field to establish clearly defined heterotic groups with a greater genetic similarity within groups.

Altitude↗
PubMed2006

Molecular markers for discrimination of benign and malignant follicular thyroid tumors.

OBJECTIVE: To identify molecular markers useful for the diagnostic discrimination of benign and malignant follicular thyroid tumors. METHODS: A panel of thyroid tumors was characterized with expression profiling using cDNA microarrays. A robust algorithm for gene selection was developed to identify molecular markers useful for the classification of heterogeneous tumor classes. The study included tumor tissue specimens from 10 patients with benign follicular adenomas and from 10 with malignant tumors. The malignant tumors mainly consisted of clinically relevant minimally invasive follicular carcinomas. The mRNA expression level of a candidate gene, FHL1, was evaluated in an independent series of 61 tumors. RESULTS: 22 gene expression markers were identified as differentially expressed. Several of the identified genes, for example DIO1, CITED1, CA12 and FN1, have previously been observed as differentially expressed in various thyroid tumors. FHL1 was significantly underexpressed in carcinomas compared to adenomas in the independent panel of tumors. The results indicate that a small number of genes can be useful to distinguish follicular adenomas from follicular carcinomas. CONCLUSIONS: Our findings clearly corroborate previous studies and identify novel candidate molecular markers. These genes have the potential for molecular classification of follicular thyroid tumors and for providing improved understanding of the molecular mechanisms involved in thyroid malignancies.

Adenocarcinoma, Follicular↗
PubMed2001

Pathologic classification of rhabdomyosarcomas and correlations with molecular studies.

Rhabdomyosarcoma, the most common soft-tissue malignancy of childhood and adolescence, comprises a group of differing pathobiologic entities linked by their common propensity for formation of neoplastic skeletal muscle, a feature that results from biological forces related to aberrant transcription signals and the resultant production of myogenic proteins. At a molecular level, however, rhabdomyosarcomas form a heterogeneous group that can be subdivided into distinct clinicopathologic entities based on morphologic appearance and genetic makeup. These differing morphologic features were recognized in the mid-1900s by Horn and Enterline with their division of rhabdomyosarcomas into embryonal, alveolar, botryoid, and pleomorphic subtypes. More recent histologic and biologic studies have resulted in description of additional entities, such as spindle cell and anaplastic rhabdomyosarcoma, and refinements in recognition of the original entities, such as solid-alveolar rhabdomyosarcoma. Familiarity with newer classifications and their relationship to molecular aberrations is key to stratifying patients on current therapeutic protocols and proposed innovative genetic therapies.

Adolescent↗
PubMed1997

Heteroduplex analysis in medical entomology: A rapid and sensitive sequence-based tool for population and phylogenetic studies.

Classical studies on the insect vectors of parasitic diseases have relied on morphological, biochemical and cytological characters to classify vector species. These are often inadequate for a detailed dissection of the dynamics of the parasite-vector relationship. Molecular techniques have the potential to provide more reliable data on various aspects of vector biology, including population genetics, molecular phylogenetics, and molecular differentiation and classification of closely related species. However, most molecular techniques are expensive, cumbersome or difficult to apply to the analysis of a large number of samples. Here, Jianming Tang and Tom Unnasch discuss the practical advantages of heteroduplex analysis for the study of medically important vectors, using the black flies that serve as vectors for the filarial parasite Onchocerca volvulus as an example. This technique is simple, rapid, inexpensive and capable of detecting minor differences among DNA sequences.

Journal Article↗
PubMed2002

Molecular validation of the modified Vienna classification of colorectal tumors.

Although the Vienna classification has been introduced to resolve discrepancies in histological diagnoses of colorectal tumors between Western and Japanese pathologists, practical applications of this classification scheme have been problematic because invasion of the lamina propria of tumor cells is often difficult to recognize. Therefore, the following refinements of the classification criteria are needed: category 3, low-grade adenoma/dysplasia; category 4, intramucosal borderline neoplasia; 4-a, high-grade adenoma/dysplasia; 4-b, well-differentiated adenocarcinoma; category 5, definite carcinoma; 5-a, intramucosal moderately-differentiated adenocarcinoma; and 5-b, submucosal carcinoma. We attempted to test whether molecular genetic alterations are related to the modified classification scheme and whether they may help to further categorize the various intramucosal neoplasia grades of colorectal tumors. Two-hundred-thirty-two colorectal tumors were examined using flow cytometric analysis of DNA content, polymerase chain reaction microsatellite assays, and single-strand conformational polymorphism assays to detect abnormalities of DNA content, chromosomal allelic loss, and Ki-ras and p53 gene mutations. Microsatellite instability (MSI) was also examined. Frequencies of genetic alterations and DNA aneuploid states increased with an increase in the grade assigned according to the modified Vienna classification. MSI was a rare event in colorectal adenomas and their frequency of MSI did not correlate with tumor grade. The combined genetic and DNA ploidy data support the conclusion that analysis of genetic alterations and DNA aneuploid states may help in appropriate categorization of colorectal tumors according to the modified Vienna scheme. In addition, MSI-positive tumors may represent a specific subtype of colorectal adenomas.

Adenocarcinoma↗
PubMed2001

Large scale molecular analysis of traditional European maize populations. Relationships with morphological variation.

A representative sample of 130 European traditional maize populations was analysed for both their morphological and molecular variation. The morphological analysis of 19 variables revealed a significant variability. Correlation analysis allowed us to distinguish between traits affected by earliness (plant and ear height) and structural traits (plant architecture, grain structure). Two main morphological types could be distinguished. Molecular analyses were performed for 29 RFLP loci on DNA bulks. The number of alleles detected was high when compared to previous studies (9.59 alleles per locus). Genetic diversity was also high (0.55), with a strong differentiation between populations (GST value of 35.6%). A clear relationship between the genetic diversity of the populations and their agronomic performances was highlighted. Morphological and molecular distances showed a tendency towards a triangular relationship. We therefore considered a two-phase process to be the most efficient approach for the classification of genetic resources: firstly, a molecular study to define groups of genetically close populations, and secondly a morphological description of populations from each group. In our European collection, this approach allowed us to separate the populations from Northern and Southern Europe and to define six groups of genetically close populations, comparable to European races. This study opens new prospects concerning the molecular analysis of very large collections of genetic resources, hitherto limited by the necessity of individual analyses, and proposes a first molecular classification of European maize germplasm.

Alleles↗
PubMed2006

Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas.

The classification of peripheral T-cell lymphomas (PTCL) is still a matter of debate. To establish a molecular classification of PTCL, we analysed 59 primary nodal T-cell lymphomas using cDNA microarrays, including 56 PTCL and three T-lymphoblastic lymphoma (T-LBL). The expression profiles could discriminate angioimmunoblastic lymphoma, anaplastic large-cell lymphoma and T-LBL. In contrast, cases belonging to the broad category of 'PTCL, unspecified' (PTCL-U) did not share a single molecular profile. Using a multiclass predictor, we could separate PTCL-U into three molecular subgroups called U1, U2 and U3. The U1 gene expression signature included genes known to be associated with poor outcome in other tumors, such as CCND2. The U2 subgroup was associated with overexpression of genes involved in T-cell activation and apoptosis, including NFKB1 and BCL-2. The U3 subgroup was mainly defined by overexpression of genes involved in the IFN/JAK/STAT pathway. It comprised a majority of histiocyte-rich PTCL samples. Gene Ontology annotations revealed different functional profile for each subgroup. These results suggest the existence of distinct subtypes of PTCL-U with specific molecular profiles, and thus provide a basis to improve their classification and to develop new therapeutic targets.

Gene Expression Profiling↗
PubMed2005

[The new classification of renal tumors--what is relevant for the practice?].

During recent years, the understanding of the histogenesis of renal tumors has been expanded by novel molecular findings. The classification of renal tumors is now based on specific molecular alterations. Further, novel tumor entities have been identified. The knowledge of these novel tumor entities has a dramatic influence on the selection of therapeutic strategies. Here, cases showing the relevance of molecular diagnostic methods for the classification of renal tumors are demonstrated. The current WHO classification of renal tumors is discussed on the basis of case reports.

Adult↗
PubMedDate not supplied

Classification of potential endocrine disrupters on the basis of molecular structure using a nonlinear modeling method.

A methodology for the classification of endocrine disruption chemicals is proposed. It is based on a data set of 106 substances extracted from the list of 553 chemicals that were inspected by the European Union Commission for the scientific evidence of their endocrine disruption activity. The substances belong to different categories defined in the EU Commission report: (i) literature evidence for certainly active as endocrine disrupters, (ii) for potentially active, (iii) for less probable active--lacking evidence, and (iv) for certainty nonactive. 3D molecular coordinates were calculated using the AM1or the PM3 optimization method. From 3D coordinates an extensive set of molecular descriptors was calculated. The classification model based on the counterpropagation neural network was constructed and evaluated. This is the first time that the counterpropagation neural network is applied for the classification of compounds regarding their literature evidence for the endocrine disruption activity. The developed classification model is proposed as a tool for a preliminary assessment of potential endocrine disrupters, which would help the assessors to make the priority list for a large amount of chemicals that have to be tested with more expensive in vitro and in vivo methods.

Journal Article↗
PubMed2004

Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution.

An analysis of the phylogenetic relationships of the 13 orders of Demospongiae, based on 18S and C1, D1 and C2 domains of 28S rRNA (for, respectively, 26 and 32 taxa) has been performed. The class Demospongiae as traditionally defined is not found to be monophyletic. Instead, a clade comprising all demosponges except Homoscleromorpha is well-supported, and we define phylogenetically the name Demospongiae in this more restricted sense to preclude the possibility of drastic alterations of the meaning of Demospongiae in the future, depending on the position of Homoscleromorpha. Within this clade Demospongiae s.s., ceractinomorphs and tetractinomorphs are polyphyletic, implying homoplastic evolution of characters such as reproductive strategies (viviparity vs. oviparity) and skeleton architecture (reticulate vs. radiate). The topology derived from our molecular data provides a basis for proposing a new classification of Demospongiae s.s., and suggests a reverse polarity of some characters, with respect to traditional conceptions: viviparity, presence of monaxon spicules and of spongin appear to be ancestral, whereas oviparity, and presence of tetraxon spicules appear as derived characters.

Animals↗
PubMed2003

Alterations in molecular pathways of diffusely infiltrating glial neoplasms: application to tumor classification and anti-tumor therapy (Review).

Recent advances in our understanding of the molecular genetic mechanisms underlying diffusely infiltrating brain neoplasms have important implications for the classification and therapy of these tumors. Traditionally, primary brain tumors have been classified histologically; however, it is now clear that tumors within a single histologically defined category are heterogeneous from a molecular genetic perspective. Furthermore, many new experimental therapeutic strategies directed against these almost invariably fatal tumors are aimed at molecular rather than histologic abnormalities. Consequently, the classification of these tumors is in the process of being re-evaluated as underlying molecular genetic mechanisms continue to be elucidated. This review covers traditional histologic based classification of infiltrating glial neoplasms together with molecular abnormalities of these tumors involving p53, epidermal growth factor receptor, the retinoblastoma pathway, platelet derived growth factor receptor, genetic losses on chromosome 10, and loss of heterozygosity on chromosomes 1p and 19q. The contribution of these molecular genetic abnormalities to the classification and therapy of these tumors is discussed. Although at the present no molecular system for the classification of brain tumors has been generally accepted, microarray technologies offer the exciting prospect of practical molecular classification in the future.

Antineoplastic Agents↗
PubMed1994

Application of QSARs in risk management of existing chemicals.

QSAR-estimates of aquatic toxicity of relatively unreactive (narcosis-type) organic chemicals for 19 species were used to predict "no-effect-levels" (NELs) at the ecosystem level by means of several extrapolation models which were recently discussed by the Organisation for Economic Cooperation and Development (OECD). It appeared that the differences between the numerical results of these extrapolation methods, despite their different statistical assumptions, were small. Equilibrium-partitioning theory for sediment and water as well as biota and water was used to derive NELs for aquatic sediments and whole-body residues. Simple equations are given, from which NELs for water, and subsequently for sediments and whole-body residues, can be predicted on the basis of only the octanol-water partition coefficient. Actual application of the models presented absolutely requires the availability of methods to recognize chemicals that act by the unspecific mechanism of narcosis. To this end, a classification scheme, based on molecular structure, was developed. This classification scheme was applied to the approximately 2000 so-called High Production Volume Chemicals (HPVCs) listed in Annex 1 of the Council Regulation on the Evaluation and the Control of the Environmental Risks of Existing Chemicals of the European Communities. From the classification of these 2000 HPVCs it is concluded that, for a large portion of all existing chemicals, reliable QSAR estimates of aquatic toxicity can be made; this considerably speeds up the process of priority setting and risk assessment of existing chemicals. The validity of this (dual) approach was tested by a comparison of estimated NELs with actual FCC values for all compounds from the US-EPA Water Quality Guidelines list that classify as narcosis-type compounds. This comparison shows that for many existing chemicals QSARs may be used to derive quality guidelines for water, aquatic sediments and residues in aquatic biota.

Amphibians↗
PubMed2005

Modern classification of neoplasms: reconciling differences between morphologic and molecular approaches.

BACKGROUND: For over 150 years, pathologists have relied on histomorphology to classify and diagnose neoplasms. Their success has been stunning, permitting the accurate diagnosis of thousands of different types of neoplasms using only a microscope and a trained eye. In the past two decades, cancer genomics has challenged the supremacy of histomorphology by identifying genetic alterations shared by morphologically diverse tumors and by finding genetic features that distinguish subgroups of morphologically homogeneous tumors. DISCUSSION: The Developmental Lineage Classification and Taxonomy of Neoplasms groups neoplasms by their embryologic origin. The putative value of this classification is based on the expectation that tumors of a common developmental lineage will share common metabolic pathways and common responses to drugs that target these pathways. The purpose of this manuscript is to show that grouping tumors according to their developmental lineage can reconcile certain fundamental discrepancies resulting from morphologic and molecular approaches to neoplasm classification. In this study, six issues in tumor classification are described that exemplify the growing rift between morphologic and molecular approaches to tumor classification: 1) the morphologic separation between epithelial and non-epithelial tumors; 2) the grouping of tumors based on shared cellular functions; 3) the distinction between germ cell tumors and pluripotent tumors of non-germ cell origin; 4) the distinction between tumors that have lost their differentiation and tumors that arise from uncommitted stem cells; 5) the molecular properties shared by morphologically disparate tumors that have a common developmental lineage, and 6) the problem of re-classifying morphologically identical but clinically distinct subsets of tumors. The discussion of these issues in the context of describing different methods of tumor classification is intended to underscore the clinical value of a robust tumor classification. SUMMARY: A classification of neoplasms should guide the rational design and selection of a new generation of cancer medications targeted to metabolic pathways. Without a scientifically sound neoplasm classification, biological measurements on individual tumor samples cannot be generalized to class-related tumors, and constitutive properties common to a class of tumors cannot be distinguished from uninformative data in complex and chaotic biological systems. This paper discusses the importance of biological classification and examines several different approaches to the specific problem of tumor classification.

Cell Differentiation↗
PubMed2002

Hürthle cell tumors: using molecular techniques to define a novel classification system.

BACKGROUND: Since ret/PTC gene rearrangements are specific to papillary thyroid carcinoma (PTC), the diagnosis of Hürthle cell PTC (HCPTC) has recently been expanded to include a subset of Hürthle cell tumors (HCTs) that may lack both papillary architecture and/or classic nuclear features but that harbor a ret/PTC gene rearrangement. We hypothesize that such HCPTCs behave in a fashion analogous to other papillary carcinomas, while Hürthle cell carcinomas (HCCs) behave similarly to follicular carcinomas. EDUCATIONAL OBJECTIVES: At the conclusion of this article, participants should be able to discuss HCTs and to identify HCPTCS using molecular techniques. METHODS: A retrospective chart review was carried out on 56 patients with HCTs. All pathological specimens were analyzed for ret/PTC gene rearrangements. Hürthle cell adenoma (HCA) was defined as an HCT that did not exhibit capsular and/or vascular invasion and that lacked a ret/PTC gene rearrangement when evaluated by immunohistochemical and reverse transcription polymerase chain reaction analysis. An HCC was defined as an HCT with capsular and/or vascular invasion that lacked a ret/PTC gene rearrangement, and an HCPTC was defined as any HCT that harbored a ret/PTC gene rearrangement. RESULTS: The subclassification of the 56 HCTs was as follows: 21 HCAs, 15 HCCs, and 20 HCPTCs. No patients with HCA or HCC were ret/PTC positive. Five of the 6 patients with definite lymph node metastasis were in the HCPTC group, demonstrating that molecular analysis helps to explain biological behavior. CONCLUSIONS: Hürthle cell neoplasms can now be classified using histopathological as well as molecular criteria. It appears that the new subclassification of malignant HCTs into follicular (HCC) and papillary (HCPTC) variants identifies 2 distinct biological groups.

Adenoma, Oxyphilic↗
PubMed2004

Derivation and applications of molecular descriptors based on approximate surface area.

Three sets of molecular descriptors that can be computed from a molecular connection table are defined. The descriptors are based on the subdivision and classification of the molecular surface area according to atomic properties (such as contribution to logP, molar refractivity, and partial charge). The resulting 32 descriptors are shown (a) to be weakly correlated with each other; (b) to encode many traditional molecular descriptors; and (c) to be useful for QSAR, QSPAR, and compound classification.

Quantitative Structure-Activity Relationship↗
PubMed1977

Historical outline of attempts to classify skin diseases.

Over the years physicians have attempted to classify skin diseases. Plenck and Willan were the first to outline clearly the basic components of skin diseases and to devise classifications based on living gross pathologic features. With the development of molecular biology, etiologic classification--a system unrelated to that of clinical appearance--was begun. Most current textbooks present combinations of these two systems and those based on location or on other concepts.

Austria↗