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Cytogenetic Data (cytogenetic + data)
Selected AbstractsA prime inference on genetic diversity (RAPDs) in the marine fish Atherinella brasiliensis (Teleostei, Atherinopsidae) from Southern BrazilACTA ZOOLOGICA, Issue 2 2010Maria Cristina Da Silva Cortinhas Abstract Da Silva Cortinhas, M. C., Glienke, C., Prioli, A. J., Noleto, R. B., Matoso, D. A. and Cestari, M. M. 2010. A prime inference on genetic diversity (RAPDs) in the marine fish Atherinella brasiliensis (Teleostei, Atherinopsidae) from Southern Brazil. ,Acta Zoologica (Stockholm) 91: 242,248 As a result of the importance of Atherinella brasiliensis in estuarine environments, random amplified polymorphic DNA (RAPD) markers were used to verify the genetic diversity in A. brasiliensis from two different places in Paranaguá Bay (Paraná State) and one from the Conceição Lagoon (Santa Catarina State). Cytogenetic data have shown a high karyotypic diversity in some populations, although in others this peculiarity demonstrates rearrangements such as heterochromatinization. In the present study, a low level of genetic structuring between the samples from Conceição Lagoon compared with the others was observed through principal coordinate analysis (PCO), analysis of molecular variance and Mantel test according to 79 RAPD markers. As this specie does not perform horizontal migration and the individuals of Conceição Lagoon are isolated, three hypotheses are proposed to explain the results: (i) similar environments may show homogeneous populations not depending on the geographical distance, (ii) because vicariant events that formed the bays occurred in a recent period, the fragmentation effects over the structuring of the genetic diversity may still be low and not totally detectable by the RAPD technique and (iii) the isolation time or the number of generations may not be enough to promote a possible differentiation and genetic structuring between the specimens of these three places. The specimens of these places present a low level of differentiation and genetic structuring so we can consider them as a unique homogeneous population. [source] Statistical behavior of complex cancer karyotypesGENES, CHROMOSOMES AND CANCER, Issue 4 2005Mattias Höglund Epithelial tumors commonly show complex and variable karyotypes that obscure the identification of general patterns of the karyotypic evolution. To overcome some of these problems, we previously systematically analyzed the accumulated cytogenetic data from individual tumor types by using various statistical means. In the present study, we compare previous results obtained for nine tumor types and perform several meta-analyses of data obtained from a number of epithelial tumors, including head and neck, kidney, bladder, breast, colorectal, ovarian, and lung cancer, as well as from malignant melanoma and Wilms tumor, with the specific aim of discovering common patterns of karyotypic evolution. We show that these tumors frequently develop through a hypo- or a hyperdiploid pathway and progress by an increasing number of alternative imbalances through at least two karyotypic phases, Phases I and II, and possibly through a third, Phase III. During Phase I, the karyotypes exhibited a power law distribution of both the number of changes per tumor and the frequency distribution at which bands were involved in breaks. At the transition from Phase I to Phase II/III, the observed power law distributions were lost, indicating a transition from an ordered and highly structured process to a disordered and chaotic pattern. The change in karyotypic orderliness at the transition from Phase I to Phase II/III was also shown by a drastic difference in karyotypic entropy. © 2005 Wiley-Liss, Inc. [source] Comparative analysis of MLL partial tandem duplication and FLT3 internal tandem duplication mutations in 956 adult patients with acute myeloid leukemiaGENES, CHROMOSOMES AND CANCER, Issue 3 2003Christine Steudel Partial tandem duplication (PTD) of the MLL gene and internal tandem duplication (ITD) of the juxtamembrane region of the FLT3 receptor tyrosine kinase gene have been described in acute myeloid leukemia (AML) patients, preferentially in those with normal cytogenetics. These alterations have been associated with a poor prognosis. In our study, we analyzed the prevalence and the potential prognostic impact of these aberrations in a large unselected and well-defined cohort of 956 patients with AML. Results were correlated with cytogenetic data and clinical outcome. MLL PTD was detected by RT-PCR, subsequent nucleotide sequencing, and Southern blotting. The overall incidence was found to be 5.0% (48/956), whereas FLT3 ITD was detected in 19.2% (184/956). Sixteen cases were positive for both alterations. The rate of MLL PTD in FLT3 ITD positive patients was significantly higher than that in FLT3 ITD negative patients [16/184 (8.7%); 32/772 (4.1%); P = 0.025]. However, both aberrations were highly increased in patients with normal karyotype (MLL PTD 35/431, P = 0.004; FLT3 ITD 132/334, P < 0.001). When restricted to this subgroup, the rate of MLL PTD in patients with FLT3 mutations was not significantly increased. No statistically significant differences were detected between patients positive for MLL PTD and patients negative for MLL PTD in the rate of complete remissions or the overall survival, although we did see a significantly shorter disease-free survival in patients age 60 or younger. In conclusion, although there is an overlap in the mutational spectrum in AML with FLT3 ITD and MLL PTD mutations, our data do not support a common mechanistic basis. Although associated with inferior disease-free survival, the results of this study do not unequivocally support the notion that MLL PTD mutations represent an independent prognostic factor. © 2003 Wiley-Liss, Inc. [source] Cytogenetic analysis of 101 skull base tumorsHEAD & NECK: JOURNAL FOR THE SCIENCES & SPECIALTIES OF THE HEAD AND NECK, Issue 5 2008Ziv Gil MD Abstract Background. Skull base tumors are rare neoplasms and the cytogenetic data on these tumors are limited. The authors cytogenetically analyzed a large series of tumors and compared the findings with patients' pathologic data. Methods. The karyotypes of pathologically confirmed samples of 101 patients, who were operated for oncological extirpation of tumors, were analyzed using G-banding and spectral-karyotyping techniques. Results. Of the 67 malignant tumors, 32 (48%) had chromosomal aberrations, some with complex numerical and structural chromosomal anomalies. Recurrent chromosomal breakpoints were identified in squamous cell carcinomas, adenoid cystic carcinomas (ACCs), sinonasal undifferentiated carcinomas, chordomas, and sarcomas. Specific breakpoints established the diagnosis of various soft tissue sarcomas. Novel chromosomal aberrations were found in various other malignant and benign tumors. Conclusion. This study highlights the value of cytogenetic analysis for diagnosis of skull base tumors. The data add further information on the biological behavior of these rare neoplasms. © 2007 Wiley Periodicals, Inc. Head Neck, 2008 [source] DNA Index in childhood acute lymphoblastic leukaemia: a karyotypic method to validate the flow cytometric measurementINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 3 2010P. RACHIERU-SOURISSEAU Summary The DNA index (DI) is a prognostic factor in childhood acute lymphoblastic leukemia (ALL). The accuracy of DI measurement is important for treatment stratification: hyperdiploidy with DI , 1.16 is predictive of favorable prognosis whereas hypodiploidy is associated with poor prognosis. The aim of this study was to validate the accuracy of the DI measured by flow cytometry (FCM) by comparison with the karyotype. From samples of 112 childhood ALL, we created a formula to calculate a theoretical DNA index (tDI) based on the blast cell karyotype, taking into account the additional or missing chromosome material of the major clone. FCM DI correlated with tDI calculated from karyotype (R = 0.987) and with modal chromosome number (DI = 0.0202 × Modal NB + 0.0675 and R = 0.984). In three cases a hypodiploid blast cell population was detected by FCM, while only the duplicated clone was identified by the karyotype. The strong correlation between tDI and DI validates the accuracy of FCM quantification, which is technically fast on fresh or frozen samples. If the karyotype is essential to analyze chromosomal abnormalities, FCM provides complementary information in aneuploid ALLs, either by confirming the cytogenetic data or by detecting additional clones not identified when only using cytogenetic data. [source] Coexistence of light chain disease and chronic lymphocytic leukaemia, a complex karyotype with a rapid fatal outcomeINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 2 2006H. CASTRYCK Summary We report on a 48-year-old man with concomitantly diagnosed kappa expressing chronic lymphocytic leukaemia (CLL) and lambda light chain disease with highly complex chromosomal aberrations. The clinical course of the disease was very aggressive with survival of only 1 month. We demonstrate the distinct clonal origin by cytogenetic data and immunoglobulin rearrangement studies. To our knowledge this is the first report of a light chain disease associated with CLL. [source] Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequenceBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010ANNA A. BANNIKOVA To examine phylogenetic relationships within the Asian lineage of voles (Microtus) belonging to subgenus Alexandromys, the mitochondrial cytochrome b gene (cytb) was sequenced for its representatives, and the results were compared with the cytogenetic, morphological, and paleontological data. In all the trees inferred from maximum likelihood, parsimony, and Bayesian phylogenetic analyses, the Asian clade is subdivided into highly supported Alexandromys s.s. and moderately supported Pallasiinus lineages. Four subclades are recovered within Alexandromys: (1) Microtus maximowiczii and Microtus sachalinensis; (2) Microtus miiddendorffii s.l., Microtus mongolicus and Microtus gromovi; (3) Microtus fortis; and (4) Microtus limnophilus. Thus, M. limnophilus demonstrates clear affinities to Alexandromys s.s. but not to Microtus oeconomus (subgenus Pallasiinus), which was always regarded as its sibling species. The results obtained indicate M. mongolicus as a member of Alexandromys but not of the Microtus arvalis group, thus being concordant with the cytogenetic data. The mitochondrial data support the species status of M. gromovi; moreover, its placement as a part of a trichotomy with M. miiddendorffii s.l. and M. mongolicus contradicts the traditional affiliation of M. gromovi with M. maximowiczii. The divergence rate of cytb third position transversions in Microtus is estimated at approximately 8% per Myr, which corresponds to approximately 30% per Myr for all substitution types at all codon positions. The maximum likelihood distance based on complete sequence showed a tendency for a progressive underestimation of divergence and time for older splits. According to our molecular clock analysis employing nonlinear estimation methods, the split between Alexandromys and Pallasiinus and basal radiation within Alexandromys date back to approximately 1.2 Mya and 800 Kya, respectively. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 595,613. [source] Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae): patterns, mechanisms, and evolutionary implicationsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2008MARTIN VÖLKER Chromaphyosemion killifishes are a karyotypically highly diverse group of small, sexually dimorphic fishes living in rainforest rivulets in tropical West and Central Africa. In the present study, we used various chromosome banding and staining techniques to analyse the karyotypes of 13 populations representing seven described species (Chromaphyosemion loennbergii, Chromaphyosemion punctulatum, Chromaphyosemion splendopleure, Chromaphyosemion volcanum, Chromaphyosemion malumbresi, Chromaphyosemion melanogaster, Chromaphyosemion bitaeniatum) and two undescribed forms (Chromaphyosemion cf. lugens, Chromaphyosemion sp. Rio Muni GEMHS00/41). Diploid chromosome numbers (2 n) and the number of chromosome arms (NF) ranged from 2 n = 24 in C. malumbresi to 2 n = 40 in C. bitaeniatum and from NF = 40 in C. volcanum and C. cf. lugens to NF = 54 in one population of C. loennbergii. A tentative XX/XY sex chromosome system was revealed in C. loennbergii, C. melanogaster, C. malumbresi, and Chromaphyosemion sp. Rio Muni GEMHS00/41. Mapping cytogenetic data for all described Chromaphyosemion species onto a recently published mitochondrial DNA phylogeny revealed a complex pattern of chromosomal evolution with several independent reductions of 2 n and independent modifications of NF and nucleolus organizer region phenotypes. Together with the results of preliminary crossing and mate choice experiments, the cytogenetic and molecular phylogenetic data suggest that, contrary to previous hypotheses, chromosomal rearrangements are probably not the most important and certainly not the only factor driving speciation in Chromaphyosemion killifishes. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 143,153. [source] Neural networks compared with Cox regressionACTA OPHTHALMOLOGICA, Issue 2008B DAMATO Purpose Survival prediction is useful in patient care and research. Most studies rely on Cox analysis and Kaplan-Meier curves whereas we have preferred neural networks. The aim of this presentation is to compare these methods and to discuss the advantages and limitations of each. Methods This presentation will be based on our experience with uveal melanoma. A neural network was trained with data from 1780 patients and evaluated with data from another 874 patients. Clinical, histopathological and cytogenetic data were included in the model. All cause mortality was reported, both for patients and for the matched general population. Results Cox analysis assumes linear correlations between variables and proportional hazards throughout the follow-up period. Kaplan-Meier analysis requires large patient categories, so that the precision of any prognostication is reduced. Neural networks overcome these limitations. Our model does censor non-metastatic deaths so that melanoma-related mortality is not exaggerated in groups of patients with significant competing risks. Conclusion Neural networks allow large numbers of variables to be included in predictive models with relatively small numbers of patients, thereby improving prognostication. Nevertheless, care must be taken when interpreting survival results to avoid serious misconceptions about the natural history of a disease and the impact of treatment. [source] | |||||||||||||