Search

Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.

Plasma cell myeloma (PCM) is disease with heterogeneous clinical outcomes. It is increasingly evident that the genetic features of the tumor cells largely dictate the clinical heterogeneity of PCM. Primary chromosomal alterations in myeloma can be divided into hyperdiploid and non-hyperdiploid subtypes. Secondary chromosomal changes occur during progression of disease. Cytogenetic abnormalities are important prognostic markers in PCM and some of them were incorporated into the current prognostic staging system of PCM. The presence of t(4;14), t(14;16), t(14;20), gain of 1q or TP53 deletion is considered to be high-risk myeloma. Detection of these alterations can be performed by interphase fluorescence in situ hybridization (FISH) after separation or identification of the plasma cells. The proper FISH examination in myeloma has to meet further requirements regarding aspirating and timing of samples, probe selection and their cut-off levels, the criteria of accurate analysis and reporting. Based on the literature, we here present technical recommendations regarding FISH in PCM. Furthermore, we share our own experience in FISH diagnostics acquired over 12 years. In this period, we have performed nearly 2,050 FISH tests in 603 myeloma patients and used two different methods of myeloma FISH: FISH on immunolabeled plasma cells, and target FISH with the BioView system.

Purpose: Homologous recombination (HR) deficiency (HRD) is one of the key determinants of PARP inhibitor response in ovarian cancer, and its accurate detection in tumor biopsies is expected to improve the efficacy of this therapy. Because HRD induces a wide array of genomic aberrations, mutational signatures may serve as a companion diagnostic to identify PARP inhibitor–responsive cases. Experimental Design: From the The Cancer Genome Atlas (TCGA) whole-exome sequencing (WES) data, we extracted different types of mutational signature–based HRD measures, such as the HRD score, genome-wide LOH, and HRDetect trained on ovarian and breast cancer–specific sequencing data. We compared their performance to identify BRCA1/2-deficient cases in the TCGA ovarian cancer cohort and predict survival benefit in platinum-treated, BRCA1/2 wild-type ovarian cancer. Results: We found that the HRD score, which is based on large chromosomal alterations alone, performed similarly well to an ovarian cancer–specific HRDetect, which incorporates mutations on a finer scale as well (AUC = 0.823 vs. AUC = 0.837). In an independent cohort these two methods were equally accurate predicting long-term survival after platinum treatment (AUC = 0.787 vs. AUC = 0.823). We also found that HRDetect trained on ovarian cancer was more accurate than HRDetect trained on breast cancer data (AUC = 0.837 vs. AUC = 0.795; P = 0.0072). Conclusions: When WES data are available, methods that quantify only large chromosomal alterations such as the HRD score and HRDetect that captures a wider array of HRD-induced genomic aberrations are equally efficient identifying HRD ovarian cancer cases.

Graphical abstract, Myocardial infarction knowledge base (MIKB; http://www.sysbio.org.cn/mikb/; latest update: December 31, 2020) is an open-access and manually curated database dedicated to integrating knowledge about MI to improve the efficiency of translational MI research. MIKB is an updated and expanded version of our previous MI Risk Knowledge Base (MIRKB), which integrated MI-related risk factors and risk models for providing help in risk assessment or diagnostic prediction of MI. The updated MIRKB includes 9701 records with 2054 single factors, 209 combined factors, 243 risk models, 37 MI subtypes and 3406 interactions between single factors and MIs collected from 4817 research articles. The expanded functional module, i.e. MIGD, is a database including not only MI associated genetic variants, but also the other multi-omics factors and the annotations for their functional alterations. The goal of MIGD is to provide a multi-omics level understanding of the molecular pathogenesis of MI. MIGD includes 1782 omics factors, 28 MI subtypes and 2347 omics factor-MI interactions as well as 1253 genes and 6 chromosomal alterations collected from 2647 research articles. The functions of MI associated genes and their interaction with drugs were analyzed. MIKB will be continuously updated and optimized to provide precision and comprehensive knowledge for the study of heterogeneous and personalized MI.

Background: Comparative genomic hybridization (CGH) microarrays are used forgenome-wide evaluation of copy number variations (CNV) of known prognostic significance;however, unannotated variants of uncertain significance (VUS) are frequently present. Toidentify potentially actionable targets, we retrospectively analyzed VUS loci using CGH datafrom 192 cases of cancer or genetic disorders treated at TTUHSC.Methods: DNA was hybridized onto CytoSure Constitution V3 arrays, scanned with theAgilent microarray D scanner, and analyzed by CytoSure Interpret Software.Results: We found 794 distinct CNVs, the most frequent being 14q32.22 (112rearrangements), 14q11.2 (100), 8p11.2 (98), 15q11.1-q11.2 (83), and 8p23.1 (77). In particular,8p11.22 alterations were found in many pediatric tumors, with gain/loss ratio of 4.7. Linkage ofTACC1, TM2D2, KAT6A and ADAM32 was indicated by a similar 5-year survival rate of 75.3%(n = 253), which was greater than in unaltered cases (62.2%, n = 15,809 cases) in The CancerGenome Atlas database.Conclusion: Knockdown of genes occurring at variants of uncertain significance (VUS)loci may help identify new therapy targets.

Soybean represents a valuable source of food for humans and animals and the quality of the seeds has great importance for the establishment and high productivity of this crop. Soybean seeds require continuous improvement, which is dependent on a better understanding of the regulatory mechanisms that coordinate seed germination. To investigate whether the method of water absorption into soybean seeds could lead to abnormal seedlings, and if this could be associated with cytogenetical consequences, we premoistened the seeds of three cultivars; M 6410 IPRO, M6210 IPRO, and BMX Potência RR by direct immersion (fast method), use of a wet substrate (intermediate method), and by moist atmosphere (slow method) with distilled water at 25ºC for 24 hours. We investigated the normal and abnormal seedlings, electrical conductivity, mitosis, cell death, and the chromosomal abnormalities index. The comet assay was applied to investigate DNA fragmentation. Direct immersion in water induced seedling growth inhibition and caused cytological alterations associated with genotoxicity effects in the studied soybean genotypes. Slow premoistening of the seeds increased seedling performance as a result of higher final germination percentage (above 85%), reduced abnormal seedlings (below 5%, on average), and reduced the electrical conductivity of seeds. All three genotypes of soybean seeds lost their ability to withstand the imbibitional damage induced by direct immersion as abnormal seedlings increased. We concluded that the fast water absorption by seeds poses a threat to genomic integrity owing to its potential for genotoxicity to DNA, manifesting as breaks or loss of whole chromosomes. Slow premoistening of the seeds resulted in a longer time period to deal with damage. Stabilized seedling growth was provided by altering cytogenetic responses during uptake of water by soybean seeds through the maintenance of cell viability. Soybean represents a valuable source of food for humans and animals and the quality of the seeds has great importance for the establishment and high productivity of this crop. Soybean seeds require continuous improvement, which is dependent on a better understanding of the regulatory mechanisms that coordinate seed germination. To investigate whether the method of water absorption into soybean seeds could lead to abnormal seedlings, and if this could be associated with cytogenetical consequences, we premoistened the seeds of three cultivars; M 6410 IPRO, M6210 IPRO, and BMX Potência RR by direct immersion (fast method), use of a wet substrate (intermediate method), and by moist atmosphere (slow method) with distilled water at 25ºC for 24 hours. We investigated the normal and abnormal seedlings, electrical conductivity, mitosis, cell death, and the chromosomal abnormalities index. The comet assay was applied to investigate DNA fragmentation. Direct immersion in water induced seedling growth inhibition and caused cytological alterations associated with genotoxicity effects in the studied soybean genotypes. Slow premoistening of the seeds increased seedling performance as a result of higher final germination percentage (above 85%), reduced abnormal seedlings (below 5%, on average), and reduced the electrical conductivity of seeds. All three genotypes of soybean seeds lost their ability to withstand the imbibitional damage induced by direct immersion as abnormal seedlings increased. We concluded that the fast water absorption by seeds poses a threat to genomic integrity owing to its potential for genotoxicity to DNA, manifesting as breaks or loss of whole chromosomes. Slow premoistening of the seeds resulted in a longer time period to deal with damage. Stabilized seedling growth was provided by altering cytogenetic responses during uptake of water by soybean seeds through the maintenance of cell viability.

The use of eco-friendly engineered nanomaterials represents a recent solution for an effective and safe treatment of contaminated dredging sludge. In this study, an eco-designed engineered material based on cross-linked nanocellulose (CNS) was applied for the first time to decontaminate a real matrix from heavy metals (namely Zn, Ni, Cu, and Fe) and other undesired elements (mainly Ba and As) in a lab-scale study, with the aim to design a safe solution for the remediation of contaminated matrices. Contaminated freshwater sludge was treated with CNS coupled with a filtering fine-mesh net, and the obtained waters were tested for acute and sublethal toxicity. In order to check the safety of the proposed treatment system, toxicity tests were conducted by exposing the bacterium Aliivibrio fischeri and the crustacean Heterocypris incongruens, while subtoxicity biomarkers such as lysosomal membrane stability, genetic, and chromosomal damage assessment were performed on the freshwater bivalve Dreissena polymorpha. Dredging sludge was found to be genotoxic, and such genotoxicity was mitigated by the combined use of CNS and a filtering fine-mesh net. Chemical analyses confirmed the results by highlighting the abetment of target contaminants, indicating the present model as a promising tool in freshwater sludge nanoremediation.

Piperine and capsaicin are important molecules with biological and pharmacological activities. This study aimed to evaluate the cytogenotoxic and protective effect of piperine and capsaicin on Allium cepa cells. A. cepa roots were exposed to negative (2% Dimethylsulfoxide) and positive (Methylmethanesulfonate, MMS, 10 µg/mL) controls, and four concentrations (25-200 µM) of piperine or capsaicin (alone) or associated before, simultaneously or after with the MMS. Only the lowest concentration of piperine (25 µM) showed a protective effect because it was not genotoxic. Piperine and capsaicin were cytotoxic (50, 100 and 200 µM). Piperine (50 to 200 µM) caused a significant increase in the total average of chromosomal alterations of in A. cepa cells. For capsaicin, the genotoxic effect was dose-dependent with a significant increase for all concentrations, highlighting the significant presence of micronuclei and nuclear buds for the two isolates. In general, bioactive compounds reduced the total average of chromosomal alterations against damage caused by MMS, mainly micronuclei and/or nuclear buds. Therefore, the two molecules were cytotoxic and genotoxic at the highest concentrations, and did not have cytoprotective action, and the lowest concentration of piperine demonstrated important chemopreventive activity.

Este estudio se basa en la relevancia de la citogenética como una importante herramienta que tiene muchas aplicaciones clínicas en el diagnóstico de enfermedades, como el cáncer. Y el objetivo principal es realizar una revisión crítica de la literatura sobre la citogenética y biología del cáncer, a fin de identificar alteraciones cromosómicas que se relacionan con mayor frecuencia con neoplasias linfoproliferativas, para usarlas como herramienta en el diagnóstico oportuno, pronóstico y monitoreo al tratamiento de pacientes. En la introducción se trata la contextualización y el problema del cáncer, y la descripción de las neoplasias malignas. En los primeros capítulos se analizan las aplicaciones clínicas de estudios citogenéticos de anormalidades malignas y se exponen aquellas neoplasias que se relacionan con alteraciones cromosómicas primarias y secundarias, clasificadas en tres grupos de riesgo. Dichas alteraciones se resumen en una tabla, para beneficio del lector. En los últimos capítulos, se demuestra la importancia del aporte de las alteraciones citogenéticas como uso de biomarcadores útiles para el control de estas enfermedades, apoyándose en las nuevas tecnologías desarrolladas en esta área como son el FISH y la técnica del PCR; y se hacen recomendaciones para avanzar en el uso de la citogenética en esta problemática.

The prognosis for patients diagnosed with ependymoma is relatively poor, with a 5-year overall survival rate of 24–75%. Currently, tumors are treated by surgical resection followed by radiotherapy, as resection is the most consistent prognostic marker (up to 80%). Therefore, there is a pressing need to improve our understanding of the biology of these tumors and to develop new therapeutic targets. The present work was a systematic review of the current molecular knowledge of pediatric ependymomas. From January 2000 to December 2017, we carried out a search using “MeSH” (Medical Subject Heading), and “free-text” protocols in the databases Medline/PubMed, SCOPUS, Web of Science, and EMBASE (OVID platform), combining the terms chromosomal alterations, genetic changes, epigenetic changes, and protein expression changes. We selected articles with samples from pediatric patients and chose publications with complete clinical features. Only 33 articles met the criteria for a meta-analysis, suggested by the state of methylation and expression of a characteristic marker of pediatric ependymomas. We found a chromosomal alteration and one gene associated with survival; these are candidates for bad prognosis biomarkers.

Background Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata using sequential fluorescence (5S rDNA, 18S rDNA and pSc119.2 probes) and genomic in situ hybridisation (four genomic probes of diploid taxa, i.e., Aegilops, Dasypyrum, Hordeum and Pseudoroegneria). Results The concurrent presence of Hordeum (descended from E. repens) and Dasypyrum + Aegilops (descended from E. intermedia) chromosome sets in all cytotypes of E. ×mucronata confirmed the assumed hybrid origin of the analysed plants. The following different genomic constitutions were observed for E. ×mucronata. Hexaploid plants exhibited three chromosome sets from Pseudoroegneria and one chromosome set each from Aegilops, Hordeum and Dasypyrum. Heptaploid plants harboured the six chromosome sets of the hexaploid plants and an additional Pseudoroegneria chromosome set. Nonaploid cytotypes differed in their genomic constitutions, reflecting different origins through the fusion of reduced and unreduced gametes. The hybridisation patterns of repetitive sequences (5S rDNA, 18S rDNA, and pSc119.2) in E. ×mucronata varied between and within cytotypes. Chromosome alterations that were not identified in the parental species were found in both heptaploid and some nonaploid plants. Conclusions The results confirmed that both homoploid hybridisation and heteroploid hybridisation that lead to the coexistence of four different haplomes within single hybrid genomes occur in Elytrigia allopolyploids. The chromosomal alterations observed in both heptaploid and some nonaploid plants indicated that genome restructuring occurs during and/or after the hybrids arose. Moreover, a specific chromosomal translocation detected in one of the nonaploids indicated that it was not a primary hybrid. Therefore, at least some of the hybrids are fertile. Hybridisation in Triticeae allopolyploids clearly and significantly contributes to genomic diversity. Different combinations of parental haplomes coupled with chromosomal alterations may result in the establishment of unique lineages, thus providing raw material for selection. Electronic supplementary material The online version of this article (10.1186/s12870-019-1806-y) contains supplementary material, which is available to authorized users.

Chromosomal alterations have recurrently been identified in Wilms tumors (WTs) and some are associated with poor prognosis. Gain of 1q (1q+) is of special interest given its high prevalence and is currently actively studied for its prognostic value. However, the underlying mutational mechanisms and functional effects remain unknown. In a national unbiased cohort of 30 primary WTs, we integrated somatic SNVs, CNs and SVs with expression data and distinguished four clusters characterized by affected biological processes: muscle differentiation, immune system, kidney development and proliferation. Combined genome-wide CN and SV profiles showed that tumors profoundly differ in both their types of 1q+ and genomic stability and can be grouped into WTs with co-occurring 1p−/1q+, multiple chromosomal gains or CN neutral tumors. We identified 1q+ in eight tumors that differ in mutational mechanisms, subsequent rearrangements and genomic contexts. Moreover, 1q+ tumors were present in all four expression clusters reflecting activation of various biological processes, and individual tumors overexpress different genes on 1q. In conclusion, by integrating CNs, SVs and gene expression, we identified subgroups of 1q+ tumors reflecting differences in the functional effect of 1q gain, indicating that expression data is likely needed for further risk stratification of 1q+ WTs.

Clonal hematopoiesis (CH) results from somatic genomic alterations that drive clonal expansion of blood cells. Somatic gene mutations associated with hematologic malignancies detected in hematopoietic cells of healthy individuals, referred to as CH of indeterminate potential (CHIP), have been associated with myeloid malignancies, while mosaic chromosomal alterations (mCAs) have been associated with lymphoid malignancies. Here, we analyzed CHIP in 55,383 individuals and autosomal mCAs in 420,969 individuals with no history of hematologic malignancies in the UK Biobank and Mass General Brigham Biobank. We distinguished myeloid and lymphoid somatic gene mutations, as well as myeloid and lymphoid mCAs, and found both to be associated with risk of lineage-specific hematologic malignancies. Further, we performed an integrated analysis of somatic alterations with peripheral blood count parameters to stratify the risk of incident myeloid and lymphoid malignancies. These genetic alterations can be readily detected in clinical sequencing panels and used with blood count parameters to identify individuals at high risk of developing hematologic malignancies. Genomic analyses in the UK Biobank show that clonal hematopoiesis of indeterminate potential in the lymphoid lineage is associated with a higher risk of developing lymphoid malignancies

One of the most curious findings emerged from genome-wide studies over the last decade was that genetic mosaicism is a dominant feature of human ageing genomes. The clonal dominance of genetic mosaicism occurs preceding the physiological and physical ageing and associates with propensity for diseases including cancer, Alzheimer's disease, cardiovascular disease and diabetes. These findings are revolutionizing the ways biologists thinking about health and disease pathogenesis. Among all mosaic mutations in ageing genomes, mosaic chromosomal alterations (mCAs) have the most significant functional consequences because they can produce intercellular genomic variations simultaneously involving dozens to hundreds or even thousands genes, and therefore have most profound effects in human ageing and disease etiology. Here, we provide a comprehensive picture of the landscapes, causes, consequences and rejuvenation of mCAs at multiple scales, from cell to human population, by reviewing data from cytogenetic, genetic and genomic studies in cells, animal models (fly and mouse) and, more frequently, large-cohort populations. A detailed decoding of ageing genomes with a focus on mCAs may yield important insights into the genomic architecture of human ageing, accelerate the risk stratification of age-related diseases (particularly cancers) and development of novel targets and strategies for delaying or rejuvenating human (genome) ageing.

Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities (“B allele” frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the “B allele” frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.

Terminalia actinophylla (Mart), commonly known as "chapada", is used in folk medicine for the treatment of diarrhea, diabetes and anti-inflammatory. However, studies on its toxicity are still incipient. The present work was carried out with the objective of evaluating the phytochemical profile and the cytogenotoxic effect of the ethanolic extract of the T. actinophylla bark using the Allium cepa L. seed. Seeds of A. cepa were subjected to different extract concentrations (1.25, 2.5, 5 and 10 mg/mL), a negative control (NC - distilled water) as well as trifluralin (PC - positive control), during 24 h of exposure. The phytochemical profile of the extract was obtained to identify the main secondary metabolites. The cytotoxicity (mitotic index) and the genotoxicity (chromosomal alterations) were analyzed by means of the collection of 5,000 meristematic cells. The statistical analysis was carried out using the Kruskal-Wallis test (p

Neuroblastoma (NB) is a heterogeneous tumor with extremely diverse prognosis according to clinical and genetic factors such as specific combinations of chromosomal imbalances. Molecular karyotyping data from a national neuroblastic tumor database of 155 NB samples were analyzed and related to clinical data. Segmental chromosomal alterations (SCA) were detected in 102 NB, whereas 45 only displayed numerical alterations. Incidence of SCA was higher in stage M (92%) and MYCN amplified (MNA) NB (96%). Presence of SCA was associated with older age, especially 1q gain and 3p deletion. 96% of the deaths were observed in the SCA group and 85% of the relapsed NB contained SCA. The alteration most commonly associated with a higher number of other segmental rearrangements was 11q deletion, followed by 4p deletion. Whole-chromosome 19 gain was associated with lower stages, absence of SCA and better outcome. SCA are not randomly distributed and are concentrated on recurrent chromosomes. The most frequently affected chromosomes identify prognostic factors in specific risk groups. SCA are associated with older age and MNA. We have identified a small subset of patients with better outcome that share whole-chromosome 19 numeric gain, suggesting its use as a prognostic biomarker in NB.

A key goal of cancer systems biology is to use big data to elucidate the molecular networks by which cancer develops. However, to date there has been no systematic evaluation of how far these efforts have progressed. In this Analysis, we survey six major systems biology approaches for mapping and modelling cancer pathways with attention to how well their resulting network maps cover and enhance current knowledge. Our sample of 2,070 systems biology maps captures all literature-curated cancer pathways with significant enrichment, although the strong tendency is for these maps to recover isolated mechanisms rather than entire integrated processes. Systems biology maps also identify previously underappreciated functions, such as a potential role for human papillomavirus-induced chromosomal alterations in ovarian tumorigenesis, and they add new genes to known cancer pathways, such as those related to metabolism, Hippo signalling and immunity. Notably, we find that many cancer networks have been provided only in journal figures and not for programmatic access, underscoring the need to deposit network maps in community databases to ensure they can be readily accessed. Finally, few of these findings have yet been clinically translated, leaving ample opportunity for future translational studies. Periodic surveys of cancer pathway maps, such as the one reported here, are critical to assess progress in the field and identify underserved areas of methodology and cancer biology.

A retrospective descriptive study is conducted at the San Juan de Dios Hospital, San Jose, Costa Rica, during the period from February 2016 to March 2017, with a total of 37 patients from which a combined screening during the first trimester of pregnancy was conducted, evaluating maternal age, biochemical and sonographic methods that together can predict the risk of fetal chromosomal alterations during pregnancy. The purpose of using combined screening as a noninvasive method is to identify high risk gestations and to minimize the number of invasive procedures to detect the highest number of cases. Four patients with higher risk of aneuploidy during pregnancy were identified through this screening.

We present an integrative genome-wide analysis that can be used to predict the risk of progression from leukoplakia to oral squamous cell carcinoma (OSCC) arising in the gingivobuccal complex (GBC). We find that the genomic and transcriptomic profiles of leukoplakia resemble those observed in later stages of OSCC and that several changes are associated with this progression, including amplification of 8q24.3, deletion of 8p23.2, and dysregulation of DERL3, EIF5A2, ECT2, HOXC9, HOXC13, MAL, MFAP5 and NELL2. Comparing copy number profiles of primary tumors with and without lymph-node metastasis, we identify alterations associated with metastasis, including amplifications of 3p26.3, 8q24.21, 11q22.1, 11q22.3 and deletion of 8p23.2. Integrative analysis reveals several biomarkers that have never or rarely been reported in previous OSCC studies, including amplifications of 1p36.33 (attributable to MXRA8), 3q26.31 (EIF5A2), 9p24.1 (CD274), and 12q13.2 (HOXC9 and HOXC13). Additionally, we find that amplifications of 1p36.33 and 11q22.1 are strongly correlated with poor clinical outcome. Overall, our findings delineate genomic changes that can be used in treatment management for patients with potentially malignant leukoplakia and OSCC patients with higher risk of lymph-node metastasis., TRANSLATIONAL ONCOLOGY, 10 (3)

Purpose of investigation The aim of this study was to assess the efficacy of the quantitative fluorescent-polymerase chain reaction (QF-PCR) and multiplex ligation-dependent probe amplification (MLPA) combined system to detect chromosome alterations in miscarriage products, as an alternative to conventional cytogenetic testing. Material and methods This study was conducted between 2011 and 2015 on 264 samples, analyzed using the combined system: QF-PCR/MLPA. This approach first analyzed miscarriage products for chromosomes 13, 18, 21, X and Y, using QF-PCR analysis; in case of ovular fragments, an analysis of maternal DNA was carried out in order to establish the origin of material. Whenever fetal origin was determined, MLPA analysis on the subtelomeric regions was car- ried out. Results On 264 miscarriages analyzed, 229 were of fetal origin and produced the following results: 53.7% normal and 46.3% pathological. Of the latter, 74.4% were autosomal aneuploidies, 10.4% triploidies, 8.5% sex chromosomal aneuploidies, 3.7% structural alterations, and 2.7% multiple aneuploidies. Results from QF-PCR were obtained from all samples, whereas unambiguous MLPA re- sults were obtained in about 90% of all cases. Conclusion This approach results being highly effective for examining all chromosome aneuploidies, triploidies, as well as structural unbalanced alterations in the subtelomeric regions.

Background Stably acquired mutations in hematopoietic cells represent substrates of selection that may lead to clonal hematopoiesis (CH), a common state in cancer patients that is associated with a heightened risk of leukemia development. Owing to technical and sample size limitations most CH studies have characterized gene mutations or mosaic chromosomal alterations (mCAs) individually. The relationship between acquired gene mutations and mCAs in CH and their joint roles in leukemia development have not been systematically investigated. Methods We developed a method to reliably map mCAs at low cell fractions from deep targeted sequencing data. We applied this method in a cohort of 32,442 solid tumor patients who have undergone prospective clinical sequencing (MSK-IMPACT). We characterized gene mutations in our patient cohort using an established variant calling procedure from our previous studies. Results We jointly characterized 383 mCA events (median aberrant cell fraction 32%, range 10%-90%) and 14,789 mutations across 457 genes. mCA was significantly associated with age (OR=1.8, P20% VAF, compared to 1% of the general cohort. We identify co-mutational patterns characteristic of diverse mechanisms of clonal selection. We observe that mutations in DNMT3A, TET2, JAK2, MPL, EZH2, TP53 and ATM form recurrent double-hits with deletions or CNLOHs, resulting in either oncogene mutant dosage adjustment or inactivation of tumor suppressors. Notably, certain mCA events were highly directed events acting on previously acquired gene mutations in the corresponding loci. Of six events of 7qCNLOH, all six co-localized with an EZH2 (7q36.1) mutation (q During patient follow-up, the 3-year cumulative incidence of leukemias was significantly higher in patients with composite CH genotypes (14.6%, CI: 7-22%) as compared to patients with either mCA, gene mutation alone or no CH, of which all had a 3-year cumulative incidence of Conclusions Our joint characterization of gene mutations and mCAs in a large prospective sequencing cohort reveals a previously unrecognized layer of complexity in the evolutionary dynamics of clonal hematopoiesis that converges towards characteristic genotypes associated with distinct leukemia subtypes. This puts mCAs in the context of the continuous evolutionary process of oncogenesis that can often span years and sheds new lights on its patterns of acquisition and progression. We demonstrate that the integration of chromosomal aberrations provides additional resolution to risk stratification as well as interpretation of clinical phenotypes and that mCAs should be screened in conjunction with gene mutations to improve existing CH surveillance programs in cancer patients. Disclosures Bolton: GRAIL: Research Funding. Medina:Isabl: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. Mantha:MJH Associates: Honoraria; Physicians Education Resource: Honoraria. Solit:Pfizer: Honoraria; Loxo Oncology: Honoraria; Lilly Oncology: Honoraria; Illumina: Honoraria; Vivideon Therapeutics: Honoraria. Diaz:Neophore: Consultancy, Current equity holder in private company; Merck: Consultancy; Johns Hopkins University: Patents & Royalties; Jounce Therapeutics: Current equity holder in private company; Thrive Earlier Detection: Current equity holder in private company; Personal Genome Diagnostics: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. Berger:Illumina: Research Funding; Roche: Consultancy; Grail: Research Funding. Levine:Lilly: Consultancy, Honoraria; Janssen: Consultancy; Roche: Consultancy, Honoraria, Research Funding; Loxo: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Imago: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Isoplexis: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Research Funding; Prelude Therapeutics: Research Funding; Gilead: Honoraria; Amgen: Honoraria; Morphosys: Consultancy; Novartis: Consultancy; Astellas: Consultancy; Qiagen: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees. Zehir:Memorial Sloan Kettering Cancer Center: Current Employment; Illumina: Honoraria. Papaemmanuil:Celgene: Consultancy, Honoraria, Research Funding; Prime Oncology: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Illumina: Consultancy, Honoraria; Kyowa Hakko Kirin: Consultancy, Honoraria; Isabl: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; MSKCC: Patents & Royalties.

Alzheimer's disease (AD) has as its main characteristic the deterioration of cerebral functions. Its etiology is still complex and undefined despite the progress made in understanding its neurological, infectious, biochemical, genetic and cytogenetic mechanisms. Considering this, the aim of this study was to investigate the presence of chromosomal alterations in the peripheral blood lymphocytes, and to verify if there was a high frequency of these alterations in patients diagnosed with AD at the University Hospital GetúLio Vargas Outpatient Clinic Araújo Lima in Manaus, Amazonas, Brazil. Among the nine patients in the AD group, only one patient did not have metaphases with chromosomal alterations (2n = 46,XX), while eight patients with AD showed numerical chromosomal alterations, classified as X chromosome aneupLoidy (2n = 45,X) and double aneupLoidy (2n = 44,X,-X,-10; 2n = 44,X,-X,-13 and 2n = 44,X,-X,-21). In the control group, no chromosomal changes were found in the karyotypes of these individuals. Therefore, the karyotypes of patients with AD undergo chromosomal alterations at different levels. These findings are being described for the first time in the population of Amazonas, and they highlight the importance of the inclusion of cytogenetic investigations in the routine management of patients with AD. RESUMO Doença de Alzheimer (DA) tem como principal característica a deterioração das funções cerebrais. Quanto a sua etiologia ainda é complexa e indefinida, apesar do progresso alcançado na compreensão de seus mecanismos neurológicos, infecciosos, bioquímicos, genéticos e citogenéticos. Considerando isto, nós investigamos a presença de alterações cromossômicas nos Linfócitos de sangue periférico e verificamos se há uma alta frequência dessas alterações em pacientes já diagnosticados com doença de Alzheimer no Hospital Universitário Getulio Vargas / Ambulatório Araújo Lima, Manaus / Amazonas / Brasil. Assim, dos 09 pacientes do grupo DA, somente 01 paciente não apresentou metáfases com alterações cromossômicas (2n = 46,XX) enquanto que 08 pacientes com DA apresentaram alterações cromossômicas numéricas, sendo classificadas como aneupLoidia do cromossomo X (2n = 45,X) e aneupLoidia dupLa (2n = 44,X,-X,-10; 2n = 44,X,-X,-13 e 2n = 44,X,-X,-21). No grupo controle, não foram encontradas aLterações cromossômicas nos cariótipos desses indivíduos. Estes achados para a popuLação do Amazonas/ BrasiL estão sendo descritos pela primeira vez. Os cariótipos de pacientes com DA sofrem aLterações cromossômicas em diferentes níveis e demonstraram a importância das investigações citogenéticas no manejo rotineiro de pacientes com DA.

© 2020 by the authors., The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis–relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse. In addition, there was a significant increase in the frequency of chromosomal lesions at the time of relapse (p = 0.019). MLPA and aCGH techniques showed that IKZF1 was the most frequently deleted gene. TP53 was the most frequently mutated gene at relapse. Two TP53 mutations were detected only at relapse, whereas the three others showed an increase in their mutational burden at relapse. Clonal evolution patterns were heterogeneous, involving the acquisition, loss and maintenance of lesions at relapse. Therefore, this study provides additional evidence that BCP-ALL is a genetically dynamic disease with distinct genetic profiles at diagnosis and relapse. Integrative NGS, aCGH and MLPA analysis enables better molecular characterization of the genetic profile in BCP-ALL patients during the evolution from diagnosis to relapse., This work was supported in part by a grant from the Consejería de Educación, Junta de Castilla y León, Fondos FEDER (SA085U16, SA271P18), Proyectos de Investigación de la Gerencia Regional de Sanidad, SACYL, (GRS 1847/A/18; GRS 2062/A/19), SYNtherapy. Synthetic Lethality for Personalized Therapy-based Stratification In Acute Leukemia (ERAPERMED2018-275); ISCIII (AC18/00093), co-funded by ERDF/ESF, “Investing in your future”, Fundación Castellano Leonesa de Hematología y Hemoterapia (FUCALHH 2017), and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC CB16/12/00233). A grant to AM from the Junta Provincial de Salamanca of the Asociación Española Contra el Cáncer (AECC), a grant to MFC from the Universidad Pedagógica y Tecnológica de Colombia—Vicerrectoría de Investigación y Extensión (Grupo de Investigación en Ciencias Biomédicas UPTC—GICBUPTC, Escuela de Ciencias Biológicas). M. Hernández-Sánchez holds a Sara Borrell post-doctoral contract (CD19/00222) from the Instituto de Salud Carlos III (ISCIII). co-founded by Fondo Social Europeo (FSE) “El Fondo Social Europeo invierte en tu futuro”, MM is currently supported by an “Ayuda predoctoral de la Junta de Castilla y León” by the Fondo Social Europeo (JCYL- EDU/556/2019 PhD scholarship) and a grant to JR and JMR from Instituto Carlos III (PI14/01971).

Resumen Introducción: Poincianella bracteosa (Tul.) L.P. Queiroz. (Fabaceae), conocida como catingueira, es tradicionalmente utilizada en la medicina para tratar diarrea, hepatitis y anemia. Sin embargo, no hay estudios sobre los efectos tóxico genéticos de la P. bracteosa. Objetivo: En el presente estudio se tuvo como objetivo investigar el perfil fitoquímico y el potencial mutagénico y antimutagénico del extracto acuoso de la cáscara de P. bracteosa en Allium cepa y Mus musculus. Métodos: El extracto de la cáscara fue diluido en agua destilada para fornecer las cuatro concentraciones (2, 4, 8 y 16 mg/ml) utilizadas en el bioensayo A. cepa y las tres dosis (10, 20 y 40 mg / Kg) fueron administradas a los ratones (5 animales por grupo). El perfil fito-químico fue realizado por el test colorimétrico para identificar los principales metabólitos secundarios en el extracto de la cáscara. Tras el tratamiento, 5 000 células meristemáticas fueron analizadas para determinar el índice mitótico, el promedio de alteraciones cromosómicas y el porcentaje de reducción de daños. Para ratones, tras 24, 48 y 72 h, la sangre de la cola de cada animal fue recolectado para la preparación de dos láminas por animal. Para cada animal, 2 000 eritrocitos normocromáticos por ratón fueron evaluados para establecer el número de micronúcleos y el efecto protector. Se analizaron los dados por el test de Kruskal-Wallis (P < 0.05). El estudio fito-químico del extracto detectó azúcares reductores y taninos. Resultados: Ninguna de las concentraciones del extracto fue citotóxica y en todos los tratamientos (pre, simultáneo y después) fue observado el efecto citoprotetor en A. cepa. El promedio total de las alteraciones cromosómicas en todas las concentraciones apuntó actividad no mutagénica de la cáscara. El porcentaje de reducción del daño fue observada en los tratamientos pre (de 77.6 al 90.5 %), simultáneo (del 95.6 al 114.7 %) y tras (de 84.8 al 117.7 %). En los ratones, ninguna de las dosis del extracto presentó efecto mutagénico y el porcentaje de reducción del daño osciló de -21.2 al 78.6 % (pre); de 27.5 al 101.3 % (simultánea) y de 85.5 al 120.6 % (tras-tratamiento). Probablemente, los fito-químicos presentes en el extracto no interfirieron en el ciclo celular (A. cepa), tampoco causaron daños al DNA (A. cepa y ratones) y presentaron efecto protector en las dos especies estudiadas. Los datos observados apuntan la importancia del extracto de la cáscara de P. bracteosa para inhibición del daño y quimio prevención. Sin embargo, más estudios deben ser realizados para garantizar su efecto protector sobre el material genético. ABSTRACT Introduction: Poincianella bracteosa (Tul.) L.P. Queiroz. (Fabaceae), known as catingueira, is traditionally used in medicine to treat diarrhea, hepatitis and anemia. However, there are no studies on their toxicogenetic effects. Objective: The present study aimed to investigate the phytochemical profile as well as the mutagenic and antimutagenic potential of P. bracteosa aqueous bark extract in Allium cepa and Mus musculus. Methods: The extract from barks was diluted in distilled water to yield the four concentrations (2, 4, 8 and 16 mg/ml) used in the A. cepa bioassay and the three doses (10, 20 and 40 mg/Kg) administered to the mice (five animals per group). The phytochemical profile was performed by the colorimetric test to identify the main secondary metabolites in the bark extract. After treatment, five-thousand meristematic cells were analyzed to determine the mitotic index, the mean number of chromosome alterations and the percentage of damage reduction. For mice, after 24, 48 and 72 h, tail blood was collected from each animal for the preparation of two slides per animal. For each animal, 2 000 normochromatic erythrocytes per mice were evaluated to establish the number of micronuclei and the protective effect. Data were analyzed by Kruskal-Wallis test (P < 0.05). Results: The phytochemical analysis of the extract detected reducing sugars and tannins. None of the concentrations of extract was cytotoxic and the cytoprotective effect was observed in A. cepa for all treatments (pre-, simultaneous and post-). The total mean of chromosome alterations in all concentrations indicated a non-mutagenic activity of the bark. The percentage of damage reduction was observed in the pre- (77.6 to 90.5 %), simultaneous (95.6 to 114.7 %) and post- (84.8 to 117.7 %) treatments. In mice, none of the dosages of extract presented mutagenic effect and the percentage of damage reduction varied from -21.16 to 78.63 % (pre-); from 27.51 to 101.28 % (simultaneous) and from 85.47 to 120.63 % (post-treatment). Conclusions: Probably, the phytochemicals in the extract did not interfere with the cell cycle (A. cepa) nor caused damage to the DNA (A. cepa and mice), and exhibited protective effect in both studied species. The observed data indicate the importance of P. bracteosa bark extract for the inhibition of damage and chemoprevention. However, more studies should be carried out to ensure its protective effect on the genetic material.

Poincianella bracteosa (Tul.) L.P. Queiroz. (Fabaceae), known as catingueira, is traditionally used in medicine to treat catarrhal infections, diarrhea, hepatitis and anemia. However, there are no studies on toxicogenetics effects of P. bracteosa. The present study aimed to investigate the phytochemical profile as well as the mutagenic and antimutagenic potential of P. bracteosa aqueous barks extract in Allium cepa and Mus musculus. Barks from P. bracteosa were collected in Teresina (PI, Brazil) and male Swiss mice (Mus musculus) were provided by the vivarium from the Faculty of Medical Sciences (FACIME) (PI, Brazil). All procedures using animals were approved by the Ethics Committee on the Use of Animals (Protocol No. 07557/15) with five groups (five animals per group). The extract from barks was diluted in distilled water to yield the four concentrations (2, 4, 8 and 16 mg/mL) used in the A. cepa bioassay and the three doses (10, 20 and 40 mg/Kg) administered to the mice. The phytochemical profile was performed by the colorimetric test to identify the main secondary metabolites in the barks extract. After treatment, the roots of A. cepa were washed in distilled water and hydrolyzed (60°C) for 10 min. After hydrolysis, the roots were washed in distilled water and stained with Schiff's reagent (2 h) in the dark. Five thousand meristematic cells (ten slides) were analyzed to determine the mitotic index, the mean number of chromosome alterations and the percentage of damage reduction. For mice, after 24, 48 and 72 h, the blood of tail of each animal was collected for the preparation of two slides per animal. Slides were dried (24 h), fixed in methanol (5 min.), stained with Giemsa (15 min.) and washed with distilled water. For each animal assay, 2,000 normochromatic erythrocytes per mice were evaluated to establish the number of micronuclei and the protective effect. The data were analyzed by Kruskal-Wallis test (p < 0.05). Phytochemical study of the extract detected reducing sugars and tannins. Probably, the phytochemicals in the extract did not interfere with the cell cycle (A. cepa) nor caused damage to the DNA (A. cepa and mice), and exhibited protective effect in both studied species. The observed data indicate the importance of P. bracteosa bark extract for the inhibition of damage and chemoprevention. However, more studies should be carried out to ensure its protective effect on the genetic material. Poincianella bracteosa (Tul.) L.P. Queiroz. (Fabaceae), known as catingueira, is traditionally used in medicine to treat catarrhal infections, diarrhea, hepatitis and anemia. However, there are no studies on toxicogenetics effects of P. bracteosa. The present study aimed to investigate the phytochemical profile as well as the mutagenic and antimutagenic potential of P. bracteosa aqueous barks extract in Allium cepa and Mus musculus. Barks from P. bracteosa were collected in Teresina (PI, Brazil) and male Swiss mice (Mus musculus) were provided by the vivarium from the Faculty of Medical Sciences (FACIME) (PI, Brazil). All procedures using animals were approved by the Ethics Committee on the Use of Animals (Protocol No. 07557/15) with five groups (five animals per group). The extract from barks was diluted in distilled water to yield the four concentrations (2, 4, 8 and 16 mg/mL) used in the A. cepa bioassay and the three doses (10, 20 and 40 mg/Kg) administered to the mice. The phytochemical profile was performed by the colorimetric test to identify the main secondary metabolites in the barks extract. After treatment, the roots of A. cepa were washed in distilled water and hydrolyzed (60°C) for 10 min. After hydrolysis, the roots were washed in distilled water and stained with Schiff's reagent (2 h) in the dark. Five thousand meristematic cells (ten slides) were analyzed to determine the mitotic index, the mean number of chromosome alterations and the percentage of damage reduction. For mice, after 24, 48 and 72 h, the blood of tail of each animal was collected for the preparation of two slides per animal. Slides were dried (24 h), fixed in methanol (5 min.), stained with Giemsa (15 min.) and washed with distilled water. For each animal assay, 2,000 normochromatic erythrocytes per mice were evaluated to establish the number of micronuclei and the protective effect. The data were analyzed by Kruskal-Wallis test (p < 0.05). Phytochemical study of the extract detected reducing sugars and tannins. Probably, the phytochemicals in the extract did not interfere with the cell cycle (A. cepa) nor caused damage to the DNA (A. cepa and mice), and exhibited protective effect in both studied species. The observed data indicate the importance of P. bracteosa bark extract for the inhibition of damage and chemoprevention. However, more studies should be carried out to ensure its protective effect on the genetic material.

Mosaicism, the presence of subpopulations of cells bearing somatic mutations, is associated with disease and aging and has been detected in diverse tissues, including apparently normal cells adjacent to tumors. To analyze mosaicism on a large scale, we surveyed haplotype-specific somatic copy number alterations (sCNAs) in 1,708 normal-appearing adjacent-to-tumor (NAT) tissue samples from 27 cancer sites and in 7,149 blood samples from The Cancer Genome Atlas. We find substantial variation across tissues in the rate, burden and types of sCNAs, including those spanning entire chromosome arms. We document matching sCNAs in the NAT tissue and the adjacent tumor, suggesting a shared clonal origin, as well as instances in which both NAT tissue and tumor tissue harbor a gain of the same oncogene arising in parallel from distinct parental haplotypes. These results shed light on pan-tissue mutations characteristic of field cancerization, the presence of oncogenic processes adjacent to cancer cells. A survey of copy number alterations in normal-appearing tissue in cancer samples reveals pan-tissue patterns of mosaicism.

Background Using fluorescence in situ hybridisation (FISH) to detect any gain of chromosomes 3, 7, or 17 and loss of the 9p21 locus has been proven to be sensitive in the diagnosis of pancreatobiliary tumors. However, both genetic and environmental factors contribute to the pathogenesis of pancreatobiliary tumors. Therefore, it is unknown whether this method is suitable for Chinese patients with pancreatobiliary tumors. This study aims to compare the sensitivity, specificity, predictive values and accuracy of cytology, ERCP/MRCP and FISH based on Chinese patients with pancreatobiliary tumors,and to analyze differences between brushing-based and formalin-fixed paraffin-embedded (FFPE)-based FISH. Methods A total of 66 brush cytology specimens obtained during ERCP were detected by FISH and cytology test respectively to compare the sensitivity, specificity, predictive values and accuracy. Besides, FFPE-based FISH was performed on 46 corresponding paraffin sections of pancreatobiliary tumors obtained by surgical resection. Results Our findings demonstrate that FISH greatly improves diagnostic sensitivity and negative predictive value compared to ERCP/MRCP and cytology without much reduction in specificity and positive predictive value. However, our results also indicate that FFPE-based FISH could not effectively identify the false-negative of brushing-based FISH. Conclusions We believe that FISH can effectively distinguish true positive and false positive results of cytological or radiological suspicions of malignancy. However, FFPE-based FISH still does not precisely recognize the false-negative of brushing-based FISH. Both cytology-based and PPFE-based FISH had limitation in some specimens.

Carcinoma of the ampulla of Vater is a relatively infrequent neoplasm, approximately six percent of periampullary tumours. The aim of the study is to identify the chromosomal alterations an...

Unbalanced translocations take place when two unequal chromosome sub-sequences swap, resulting in an altered genetic sequence. Such large-scale gene modification are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity. However, despite of their central role in genomic sequence analysis, little attention has been devoted to the problem of aligning sequences allowing for this kind of modification.

Fluorescence in situ hybridization (FISH) has been a revolutionary adjunct tool to traditional histopathological approaches for detecting genomic abnormalities in neoplasia that aid in diagnosis, prognosis, or prediction of response to therapy. With the rise of minimally invasive procedures for obtaining lesional material for evaluation, FISH studies performed on cytologic preparations have increased in use and demonstrated value in patient care. In this chapter, the qualitative and quantitative pre-analytic and analytic considerations of FISH as they relate to various cytology specimens are addressed. In addition, aspects of FISH validation as well as the principles and challenges inherent in the interpretation of FISH results are also presented.

Submitted by JAKELINE SANTOS OLIVEIRA (jakeline.oliveira@unesp.br) on 2019-01-29T12:48:18Z No. of bitstreams: 1 Dissertação_Jakeline_versão final (depositobiblioteca).pdf: 2812819 bytes, checksum: 7268b3b7d70527f0ee9242483a70f419 (MD5) Approved for entry into archive by Luciana Pizzani null (luciana@btu.unesp.br) on 2019-01-29T17:36:28Z (GMT) No. of bitstreams: 1 oliveira_js_me_bot_par.pdf: 791209 bytes, checksum: cdfa2f849b8dc51bdab77e31174a2d4e (MD5) Made available in DSpace on 2019-01-29T17:36:28Z (GMT). No. of bitstreams: 1 oliveira_js_me_bot_par.pdf: 791209 bytes, checksum: cdfa2f849b8dc51bdab77e31174a2d4e (MD5) Previous issue date: 2018-11-09 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) As ACs são alterações visíveis nos cromossomos, classificadas como numéricas e estruturais. Atualmente o grande desafio da genética clínica é classificar e associar a relevância clínica dos desequilíbrios genéticos ao fenótipo dos portadores. O trabalho tem como objetivo principal caracterizar desequilíbrio genômico sem diagnóstico sindrômico previamente descritos pelas técnicas de citogenética clássica, molecular visando apurar os pontos de quebras e genes inseridos na região cromossômica alterada por meio da citogenômica em estudos de casos. Foram feitas análises por citogenética (bandamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH) em três pacientes com malformações congênitas não-sindrômicas para definição diagnóstica e maior conhecimento sobre a correlação genótipo-fenótipo. Foram redigidos estudos de casos de três pacientes portadores de MCs, atraso do desenvolvimento e deficiência intelectual. O primeiro copilado de caso trata-se de paciente do sexo feminino com anomalias esqueléticas, deficiência intelectual e atraso do desenvolvimento. O cariótipo da paciente é 46,XX[11]/47,XX,+mar[9]. A análise de array-CGH revelou dois ganhos/duplicações nas bandas cromossômicas 6p11.2q12 (10.335 Mb de tamanho) e 6q14.1q14.3 (10.765 Mb de tamanho). Por meio da técnica da FISH e os resultados do array-CGH a região duplicada 6q14.1q14.3 encontra-se inserida em um cromossomo marcador, oriundo do cromossomo 6. Os sinais clínicos descritos na paciente foram semelhantes a outros pacientes com duplicação da região 6q14. Os genes PGM3, MYO6 e IMPG1 foram associados a alterações sensoriais, imunodeficiência e cardiomiopatia hipertrófica. Poucos são os casos na literatura com pacientes descritos com duplicação envolvendo as regiões 6q11-6q16. O segundo copilado de caso trata-se de paciente do sexo feminino com dimorfismo fácil, atraso do desenvolvimento e deficiência intelectual. O cariótipo apresentou o resultado: 46,XX, dup(12)(p13.1-p11.2). Por meio da técnica de array-CGH foi detectado o ganho genético de aproximadamente 28 Mb na região cromossômica 12p13.31-p11.1. A alteração cromossômica observada na paciente é descrita como duplicação 12p parcial. Os genes GRIN2B, ATF7IP, ALG10, SYT10, DNM1L, PKP2, PIK3C2G, SCNN1A, PIANP e SOX5 foram sobrepostos a CNVs de ganho, classificadas como patogênicos correlacionadas aos fenótipos de face dismórfica, convulsões, disfunção cognitiva e distúrbios do neurodesenvolvimento. A alteração presente na paciente é similar aos sinais clínicos descritos em indivíduos na literatura. O terceiro copilado de caso trata-se de paciente do sexo feminino com hemiface, incisivo central único, deficiência intelectual, atraso do desenvolvimento e deficiência na fala. O cariótipo apresentou o resultado: 46,XX, t(1;14)(p36.2;q23). A translocação aparentemente equilibrada t(1;14) presente na paciente e do tipo de novo, com pouco casos recorrentes na literatura. Por meio da técnica de array-CGH foram caracterizadas duas perdas/deleções cromossômicas, nas regiões cromossômicas 14q13.1-q13.3 (2,1 Mb de tamanho) e Xp22.31 (1,7 Mb de tamanho). A deleção da região cromossômica 14q13 é descrita como menor região sobreposta (SRO) ao locus HPE8 para o espectro de holoprosencefalia (HPE). Os genes EAPP, SNX6, TULIP1 e NKX2, são descritos na literatura como potenciais genes candidatos a HPE e doenças neurológicas. A microdeleção da região cromossômica Xp22.1 apresenta os genes VCX3A e STS xii descritos na literatura alterados em doenças neurológicas. Os sinais clínicos presentes em nossa paciente em similaridade com os descritos na literatura e alteração nas bandas cromossômicas 14q13.1-q13.3 permitem associação com a microforma de HPE. No geral, a técnica de array-CGH que dispõem de resoluções a nível de kb, foi fundamental para a elucidação dos achados genômicos em todos os pacientes. Este estudo contribui com a correlação genótipo-fenótipo e consequentemente com a literatura científica a respeito das alterações cromossômicas não sindrômicas descritas nos copilados de caso. The ACs are visible changes in the chromosomes, classified as numerical and structural. Currently the great challenge of clinical genetics is to classify and associate the clinical relevance of genetic imbalances with the phenotype of the carriers. The main objective of this work is to characterize genomic imbalance without syndromic diagnosis previously described by the classical and molecular cytogenetic techniques, in order to determine the breakpoints and genes inserted in the chromosomal region altered by cytogenetics in case studies. Cytogenetics (GTG banding), molecular cytogenetics (FISH) and cytogenetics (array-CGH) were performed in three patients with non-syndromic congenital malformations for diagnostic definition and greater knowledge on genotype-phenotype correlation. Case studies of three patients with MCs, developmental delay and intellectual disability were written. The first case file is a female patient with skeletal anomalies, intellectual disability and developmental delay. The patient's karyotype is 46, XX [11] / 47, XX, + sea [9]. The array-CGH analysis revealed two gains / doublings in the chromosomal bands 6p11.2q12 (10,335 Mb in size) and 6q14.1q14.3 (10,765 Mb in size). Through the FISH technique and the results of the array-CGH the duplicate region 6q14.1q14.3 is inserted in a chromosome marker, coming from chromosome 6. The clinical signs described in the patient were similar to other patients with duplication of the region 6q14. The genes PGM3, MYO6 and IMPG1 were associated with sensory alterations, immunodeficiency and hypertrophic cardiomyopathy. There are few cases in the literature with patients described with duplication involving the 6q11-6q16 regions. The second case file is a female patient with easy dimorphism, developmental delay and intellectual disability. The karyotype presented the result: 46, XX, dup (12) (p13.1-p11.2). Using the array-CGH technique, the genetic gain of approximately 28 Mb was detected in the chromosomal region 12p13.31-p11.1. The chromosomal abnormality observed in the patient is described as partial duplication. The genes GRIN2B, ATF7IP, ALG10, SYT10, DNM1L, PKP2, PIK3C2G, SCNN1A, PIANP and SOX5 were superimposed on gain CNVs, classified as pathogenic correlated to dysmorphic face phenotypes, convulsions, cognitive dysfunction and neurodevelopmental disorders. The present alteration in the patient is similar to the clinical signs described in individuals in the literature. The third case file is a female patient with hemiface, single central incisor, intellectual disability, developmental delay and speech deficiency. The karyotype presented the result: 46, XX, t (1; 14) (p36.2; q23). The apparently balanced translocation t (1; 14) present in the patient is of the new type, with few recurrent cases in the literature. By means of the array-CGH technique, two losses / chromosomal deletions were characterized, in the chromosomal regions 14q13.1-q13.3 (2.1 Mb in size) and Xp22.31 (1,7 Mb in size). The deletion of the 14q13 chromosomal region is described as a reduced overlap region (ORS) at the HPE8 locus for the holoprosencephaly (HPE) spectrum. EAPP, SNX6, TULIP1 and NKX2 genes are described in the literature as potential candidate genes for HPEs and neurological diseases. The microdeletion of chromosomal region Xp22.1 presents the genes VCX3A and STS described in the literature altered in neurological diseases. The clinical signs present in our patient in similarity to those described in the literature and alteration in the xiv 14q13.1-q13.3 chromosomal bands allow association with the microform of HPE. In general, the array-CGH technique that has resolutions at kb level was fundamental for the elucidation of genomic findings in all patients. This study contributes to the genotype-phenotype correlation and consequently to the scientific literature regarding the non-syndromic chromosomal changes described in the case files.

Submitted by THÁRSIS GABRYEL GOMES (tharsisgabryel@gmail.com) on 2018-07-06T16:46:28Z No. of bitstreams: 1 Dissertação_Final_Thársis_Gabryel.pdf: 4039823 bytes, checksum: 786e56454b91f984beac8c52b11764a5 (MD5) Approved for entry into archive by Sulamita Selma C Colnago null (sulamita@btu.unesp.br) on 2018-07-13T16:41:35Z (GMT) No. of bitstreams: 1 gomes_tg_me_bot_par.pdf: 757634 bytes, checksum: 9fc78887fcb72f8a3df38d43599df0d0 (MD5) Made available in DSpace on 2018-07-13T16:41:35Z (GMT). No. of bitstreams: 1 gomes_tg_me_bot_par.pdf: 757634 bytes, checksum: 9fc78887fcb72f8a3df38d43599df0d0 (MD5) Previous issue date: 2018-05-04 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) As cardiopatias congênitas (CCs) podem ser definidas como qualquer anormalidade na estrutura e/ou na função cardiocirculatória presente ao nascimento. Constituem as malformações congênitas mais comuns entre recém-nascidos vivos, podendo se apresentar de duas formas: isoladas (ou não sindrômicas) e sindrômicas. De caráter multifatorial, o surgimento de CCs envolve fatores ambientais, genéticos e epigenéticos. A etiologia genética de CCs ainda é pouco conhecida. Entre as causas genéticas conhecidas, podemos destacar: aneuploidias, alterações na estrutura dos cromossomos, desequilíbrios citogenômicos (perdas e ganhos genômicos ou variações no número de cópias genômicas – CNVs), mutações pontuais, variações em um único nucleotídeo, entre outras. Dentre essas, as CNVs contribuem com aproximadamente 10% na etiologia genética de CCs não sindrômicas, e cerca de 20% entre as sindrômicas. O objetivo deste trabalho foi investigar possíveis desequilíbrios citogenômicos em pacientes diagnosticados com CCs sindrômicas e não sindrômicas idiopáticas. Foram recrutados 31 pacientes, sendo 13 sindrômicos e 18 não sindrômicos. Todos foram submetidos à avaliação genético-clínica. As amostras foram coletadas a partir do sangue periférico, e realizou-se o cariótipo convencional para todos os sindrômicos. A análise por MLPA foi realizada em 27 pacientes. O DNA genômico dos pacientes sindrômicos selecionados foi submetido a duas plataformas de CMA (array-CGH/SNP arrays): SNP-array 850K HumanCytoSNP (Illumina®) e SurePrint G3 Human CGH Microarray Kit, 4x180K (Agilent Technologies®). Os resultados foram analisados através de bancos de dados online. A análise pela MLPA na região cromossômica 22q11.2 não evidenciou alterações, exceto para uma paciente não sindrômica que apresentou duplicação envolvendo o gene TOP3B, uma alteração sem relevância clínica até o momento. Dos 6 pacientes analisados pela CMA, 4 foram normais e 2 apresentaram alterações (pacientes 8325 e 8362). O paciente 8325 apresentou uma deleção de 159,11 kb em 1p36.11 envolvendo 4 genes, e uma ausência de heterozigosidade (AOH) em 2p13.2p12, abrangendo 45 genes e indicando uma dissomia uniparental. A deleção encontrada é benigna, enquanto a AOH possui genes que, quando em presença de mutações recessivas, podem ser causais. Já o paciente 8362 apresentou trissomia parcial de 15q25.2q26.3 (tamanho de 18,4 Mb e envolvendo 124 genes) e simultânea monossomia parcial de 18p11.32p11.22 (tamanho de 8,7 Mb, contendo 40 genes). Na região de 15q25.2q26.3 foram identificados 12 genes possivelmente candidatos à CC encontrada no paciente, entre eles ADAMTSL3, MCTP2, MESF2A, MESP1, MESP2 e NTRK3. Outros 6 genes nessa região podem estar associados às alterações neurológicas encontradas no paciente. Em relação à perda genômica em 18p11.32p11.22, apenas um gene (TYMS) parece estar relacionado à CC, enquanto outros 10 genes apresentam relação com algumas alterações extracardíacas. Os resultados evidenciam a contribuição de fatores genéticos na gênese das anomalias congênitas observadas. Entretanto, não explicam todas as alterações de forma holística, havendo a necessidade de mais investigações para a definição de uma correlação genótipo-fenótipo mais robusta e mais sinérgica. Congenital heart defects (CHD) can be defined as any abnormality in the structure and /or cardiocirculatory function present at birth. Congenital malformations are more common among live newborns. CHD can be presented at two forms: isolated (or non syndromic) and syndromic ones. Of multifactorial spectrum, the emergence of CHD involves environmental, genetic and epigenetic factors. The genetic etiology of CHD is still poorly understood. Among the known genetic causes, we can highlight: aneuploidies, changes in chromosome structure, cytogenetic imbalances (losses and genomic gains, can be also called copy number variations - CNVs), point mutations, variants in a single nucleotide, among others. Among these, CNVs contribute to approximately 10% in the genetic etiology of non-syndromic CHD, and about 20% among syndromic ones. The aim of this study was to investigate possible cytogenetic imbalances in patients diagnosed with idiopathic syndromic and non-syndromic CHD. Thirty one patients were recruited, of which 13 syndromic and 18 non-syndromic. Each patient were submitted to genetic-clinical evaluation. Only patients with an undefined syndromic condition were included in cytogenetic investigations. Samples were collected from the peripheral blood, and the conventional karyotype was performed for all syndromic patients. MLPA analysis was performed in 27 patients. The genomic DNA of the selected patients was analyzed into two CMA (array-CGH / SNP arrays) platforms: SNP-array 850K HumanCytoSNP (Illumina®) and SurePrint G3 Human CGH Microarray Kit, 4x180K (Agilent Technologies®). All results were analyzed through online databases. The MLPA analysis in the 22q11.2 chromosomal region did not show alterations, except for a non-syndromic patient who presented a duplication involving the TOP3B gene, an alteration with no known clinical relevance. Of the 6 patients analyzed by CMA, 4 were normal and 2 presented alterations (patients 8325 and 8362). Patient 8325 had a deletion of 159.11 kb in 1p3611 involving 4 genes, and an absence of heterozygosity (AOH) in 2p13.2p12, spanning 45 genes and indicating an uniparental disomy (UPD). The deletion found is benign, whereas AOH has genes that, if they are carriers of recessive mutations, may be causal. Patient 8362 presented partial trisomy of 15q25.2q26.3 (size of 18.4 Mb and involving 124 genes) and simultaneous partial monosomy of 18p11.32p11.22 (size of 8.7 Mb, containing 40 genes). In the region of 15q25.2q26.3 we identified 12 possibly candidate CHD genes in the patient, among them we can highlight: ADAMTSL3, MCTP2, MESF2A, MESP1, MESP2 and NTRK3. Another 6 genes in this region may be associated with the neurological changes found in the patient. Regarding genomic loss in 18p11.32p11.22, only one gene (TYMS) appears to be related to CHD, while another 10 genes are related to some extracardiac features. Results evidenced the contribution of genetic factors (in this case, cytogenetic imbalances) in the genesis of the observed congenital anomalies. However, they do not fully explain all the clinical phenotype. It is necessary to perform further investigations to define a more robust and synergistic genotype-phenotype correlation. CNPq: 134183/2016-9

Resumen Objetivo: evaluar efecto genotóxico y mutagénico en linfocitos humanos expuestos a nanotubos de carbono (NTC) prístinos y dopados con Nitrógeno. Métodos: linfocitos humanos fueron expuestos a NTC dopados y prístinos (0.08, 0.09, 0.1mg/mL), se evaluó alteraciones cromosómicas e intercambio de cromátidas hermanas (ICH). Resultados: se presentaron rupturas cromatídicas y cromosómicas en linfocitos expuestos a 0.1mg/mL y 0.08mg/mL de NTC prístinos. NTC dopados, indujeron cromosomas dicéntricos y anillos cromosómicos. Se presentó diferencia significativa en el porcentaje de ICH de células tratadas con NTC dopados versus control negativo y NTC prístinos (p

Background Primary amenorrhea (PA) is proposed to have multiple etiological factors that include genetic factors, intrauterine malformations, endocrine dysfunction and environmental factors, as revealed by previous studies pertaining to amenorrhea. However, among the various proposed etiologies, genetic factors appear to be highly associated with PA as approximately 40% of PA cases have been found to have genetic causes. Aim of the study The present study was proposed to establish the frequency and pattern of chromosomal abnormalities in PA cases of Kashmir. Subjects and methods A total of 108 females within the age group of 14–33 years and having a history of amenorrhea were included in the study. Peripheral blood lymphocyte cultures were set for each subject according to standard protocol and chromosomal analysis was carried out on well spread metaphases by the help of Cytovision software Version 3.9. Results The results of the present study reveal that the incidence of chromosomal abnormalities in PA cases of this region is almost similar with those of many reports around the world. However, we report two unique chromosomal alterations viz., 46,XX, dup2q(13) and 46,XX, t(2,5)(p11.2;q34) that have not been found elsewhere in the literature. Conclusion The results of the present study indicate that chromosomal analysis of females with PA, after the exclusion of non-genetic causes, should be essentially considered for the precise diagnosis and the development of more successful treatment. The study being the first of its kind in this part of the world forms the basis for further studies of the PA cases of this region. The precise molecular characterization of the unique breakpoint regions reported in our study can possibly help in the identification of new genes involved in primary amenorrhea.

In chronic lymphatic leukemia (CLL), detection and characterization of prognostic relevant chromosomal alterations is optimally done by interphase-fluorescence in situ hybridization (iFISH). Interphase nuclei derived from blood smears, bone marrow smears or from cultivated and conventionally prepared blood or bone marrow cells can be used. In CLL heterozygous or even homozygous deletion of RB1 can be found. Interestingly an iFISH diagnostic result with RB1 deletion as sole aberration is indicative for a favorable course of the disease. Here we describe the best way how to detect RB1 deletion in CLL.

El presente estudio tuvo como objetivo determinar la prevalencia de las alteraciones cromosómicas en Canis familiaris con neoplasias clínicas. Se trabajó con 25 pacientes de una clínica veterinaria en Lima, Perú en 2015-2016. Para el cultivo de sangre periférica y el análisis cromosómico se colectaron muestras por punción venosa, las cuales se almacenaron por 3±1 horas como máximo. Se realizó el procesamiento citogenético y el bandeo GTG convencional. El reporte se realizó según las recomendaciones del Committee for the Standardized Karyotype of the Dog. El promedio de edad fue de 9.5 años (4-17 años) y los grupos raciales con mayor frecuencia fueron el mestizo (20%), Golden Retriever (16%) y Shi-tzu (11.5%). El 72% presentaba alteraciones cromosómicas. De estas, 9 (36%) fueron trisomías, 9 (36%) heterocromatinas constitutivas, 2 (8%) translocaciones, 2 (8%) deleciones y 1 (4%) cromosoma en anillo. Se observaron alteraciones mixtas en 9 pacientes (36%), donde la trisomía del cromosoma 13 fue la más frecuente (28%), seguida de heterocromatina del cromosoma 9 (24%). El análisis de riesgo mediante regresión logística múltiple demostró que perros de 10 o más años tuvieron 2.4 veces más riesgo de cáncer que perros de menor edad (p

Genetic alterations can negatively impact male reproductive function in a number of ways. The hypothalamic-pituitary–gonadal axis can be negatively impacted by various chromosomal abnormalities (O'Flynn et al., 2010). Men with decreased sperm concentration are more likely to have chromosomal rearrangements (Clementini et al., 2005). In addition to impacting the quantity of sperm, chromosomal alterations can result in abnormal chromosomal segregation during meiosis, which can result in higher rates of sperm aneuploidy (Piomboni et al., 2014). Understanding chromosomal alterations and their impact on male fertility is important for all reproductive healthcare providers.

Most patients with pancreatic ductal adenocarcinoma (PDAC) die within 6 months of diagnosis. However, 20% to 25% patients undergoing total tumor resection remain alive and disease-free 5 years after diagnostic surgery. Few studies on tumor markers have predicted patient prognosis and/or survival. We evaluated the effect of tumor cytogenetic copy number changes detected by interphase fluorescence in situ hybridization on overall survival (OS) of 55 PDAC patients. The prognostic value of copy number changes showing an effect on OS was validated in an external cohort of 44 surgically resected PDAC patients by comparative genomic hybridization arrays, and the genes coded in altered chromosomes with prognostic value were identified by high-density single-nucleotide polymorphism arrays in 20 cases. Copy number changes of chromosomes 4 and 9q34 with gains of 8q24 were independently associated with shorter OS. On the basis of these three chromosomal alterations, a score is proposed that identifies patients with significantly different (P 0.001) 5-year OS rates: 60% ± 20%, 16% ± 8%, and 0% ± 0%, respectively. Our results show an association between tumor cytogenetics and OS of PDAC patients and provide the basis for further prognostic stratification of patients undergoing complete tumor resection. Further studies to identify specific genes coded in these chromosomes and their functional consequences are necessary to understand the clinical effect of these changes.

Background. The use of cytogenetic assays in the surveillance of populations occupationally exposed to a variety of xenobiotics originates from the assumption that chromosomal alterations might be causally involved in early stages of carcinogenesis. Materials and methods. This study was designed to assess genotoxic damage in somatic cells of workers contacting with harmful factors after the accident in metallurgical plant. The study was conducted on 29 workers (with the mean age of 44 ± 2.5) performing various jobs with harmful factors. Control group was recruited from occupationally unexposed individuals and comprised 18 persons with the mean age of 30 ± 2.2 and inplant control was 5 employees from metallurgical plant (accountants) with the mean age of 32 ± 5.9. Chromosome aberration analysis was performed on peripheral blood lymphocytes, cultures were incubated for 48h. Results. Among the residents with occupational hazards, a statistically significant increase of the frequency of the cells with chromosome aberrations in comparison with the control group (5.2 ± 0.3 and 2.4 ± 0.3, respectively). The highest frequency of cells with structural abnormalities was observed among steel plant workers (6.3 ± 0.6). Conclusion. Our findings suggest that in peripheral blood lymphocytes of residents contacting with harmful factors may induce clastogenic effects, indicating a potential health risk in populations of workers. A high average frequency of metaphases with aberrations and characterization of quality spectrum of cytogenetically violations is an indication of adverse environmental conditions which have developed after the accident.

FADD was initially described as an adaptor molecule for death receptor-mediated apoptosis, but subsequently it has been implicated in nonapoptotic cellular processes such as proliferation and cell cycle control. During the last decade, FADD has been shown to play a pivotal role in most of the signalosome complexes, such as the necroptosome and the inflammasome. Interestingly, various mechanisms involved in regulating FADD functions have been identified, essentially posttranslational modifications and secretion. All these aspects have been thoroughly addressed in previous reviews. However, FADD implication in cancer is complex, due to pleiotropic effects. It has been reported either as anti- or protumorigenic, depending on the cell type. Regulation of FADD expression in cancer is a complex issue since both overexpression and downregulation have been reported, but the mechanisms underlying such alterations have not been fully unveiled. Posttranslational modifications also constitute a relevant mechanism controlling FADD levels and functions in tumor cells. In this review, we aim to provide detailed, updated information on alterations leading to changes in FADD expression and function in cancer. The participation of FADD in various biological processes is recapitulated, with a mention of interesting novel functions recently proposed for FADD, such as regulation of gene expression and control of metabolic pathways. Finally, we gather all the available evidence regarding the clinical implications of FADD alterations in cancer, especially as it has been proposed as a potential biomarker with prognostic value., This work was supported by the Spanish Ministry of Economy and Competitiveness (RTI2018-093330-B-I00 and BES-2013-065740 to J.F.-P.); Fundación Ramón Areces to J.F.-P.; the Autonomous Community of Madrid, Spain (B2017/BMD-3778 LINFOMAS-CM to J.F.-P.); the Scientific Foundation of the Spanish Association against Cancer (AECC 2018 PROYE18054PIRI to J.F.-P.); the Instituto de Salud Carlos III (ACCI-CIBERER-17 ISCIII to J.F.-P.), and the Universidad Autónoma de Madrid, Faculty of Sciences (grants for final Master’s dissertation to M.V.-M.). L.V.-M. is the recipient of a Master’s fellowship from the Universidad Autónoma de Madrid

9576 Background: The incidence of melanoma subtypes differs significantly among ethnicities. Ultraviolet (UV) radiation-driven melanomas are common in Caucasians, while non-cutaneous melanomas including acral and mucosal melanomas are more frequent in Asians. It will be of great interest and clinical relevance to decipher the molecular pathogenesis of different melanoma subtypes. Methods: We retrospectively studied a cohort of 89 Chinese melanoma patients who underwent surgical resection of their primary tumors followed by chemotherapy. Genomic profiling of primary melanomas was performed using next generation sequencing by targeting 422 cancer-relevant genes. The Kaplan-Meier method and logrank test were used for survival analysis, and a cox model was used for multivariate survival analysis. Results: Acral melanomas (54/89, 60%) were the most common subtype of this cohort, while cutaneous and mucosal subtypes accounted for 25% and 15%, respectively. Mutation profiling revealed that BRAF was most frequently mutated in cutaneous melanomas, but aberrant BRAF, RAS, KIT, and NF1 were almost evenly represented in acral and mucosal melanomas; of note, mucosal melanomas had a propensity for concurrent driver mutations. Chromosomal alterations were detected across all subtypes, and chr7p amplification significantly correlated with poor prognosis while independently of melanoma subtypes. Furthermore, acral and mucosal melanomas demonstrated higher rates of focal copy number variations (CNVs) than cutaneous melanomas. The amplification of CDK4/CCND1 and NOTCH2 was observed predominantly in acral melanomas , and RAD51 loss was significantly enriched in mucosal melanomas correlating with poor survival. In addition, the tumor mutation burden (TMB) was significantly lower in acral or mucosal melanomas than in cutaneous melanomas. Conclusions: Our findings revealed distinct patterns of driver mutations and chromosomal alterations in acral and mucosal melanomas in contrast to cutaneous melanoma, and highlighted the association of chromosome 7p amplification and RAD51 deletion with unfavourable survival in melanoma patients treated with standard chemotherapy.

Genetic causes can be directly responsible for various clinical conditions of male infertility and spermatogenic impairment. With the increased use of assisted reproduction technologies our understanding of genetic basis of male infertility has large implications not only for understanding the causes of infertility but also in determining the prognosis and management of such couples. For these reasons, the genetic investigations represent today an essential and useful tool in the treatment of male infertility. Several evidences are available for the clinical practice regarding the diagnosis; however, there are less information relative to the treatment of the genetic causes of male infertility. Focus of this review is to discuss the main and more common genetic causes of male infertility to better direct the genetics investigation in the treatment of spermatogenic impairment.

Malignant Pleural Mesothelioma (MPM) is a cancer whit a poor prognosis. The landscape of the chromosomal rearrangements in MPM was approached by several authors but robust conclusions could not be made, given the limited sample sets analyzed within each study. In order to improve the knowledge on the field, we retrieved and pooled all the results deriving from published studies where comparative genomic hybridization (CGH) was employed. A total of 283 tissues (149 epithelioid, 53 sarcomatoid, 78 biphasic, and 3 unclassified) were analysed, 179 with classical chromosome CGH (cCGH), and 104 with arrayed-CGH (aCGH). Some chromosomal bands were involved in aberrations with a frequency exceeding 20% (-1p21, -9p, -14q, and -22q for the epithelioid, -4, +5p, +8q21ter, -9p, -13, and -14q for the sarcomatoid, and -9p, -14q, and -22q for the biphasic type). We found a statistical significant association between contemporary losses at 9p21 and 1p21-1p22 (21% of the samples showed losses at both bands, P=7.74x10-8), whose significance should be elucidated with further studies. Candidate cancer genes involved in MPM were suggested. Finally, 15% of epithelioid, 13% of sarcomatoid, and 13% of biphasic MPM tissues did not show any genomic alteration. Only two previous studies suggested a less aggressive behavior of MPM in relation to a low degree of chromosomal alterations. Thus, more work is warranted to understand whether chromosomal rearrangements could be included as prognostic biomarker in the clinical practice.

There are many instances in which the cancer patient and its nursing staff may be exposed to toxins and/or require barriers. Although the beneficial effects of chemotherapy against the cancer generally outweigh the potential side effects in skilled hands, almost all anticancer drugs have side effects. Toxicity is the most significant treatment-limiting factor in cytotoxic drug use. In addition, multiple studies have shown multiple potential dangers to staff handling cytotoxic drugs, including increased chromosomal alterations, hepatotoxicity and abnormal reproductive outcomes to be associated with exposure to various chemotherapeutic drugs. For these reasons, it is important that written safety protocols be established and followed in the any veterinary clinic administering chemotherapy. There must also be written instructions to pet owners for at-home administration, handling of drugs and for dealing with drug-contaminated excreta. Veterinary nurses have a vital role to play in the care of chemotherapy patients, and in maintaining the health and safety of both patient and staff. Careful administration of cytotoxics and subsequent patient monitoring should avoid many potential complications of using these drugs. If guidelines are followed, the safe use of cyto-toxic drugs should be possible for the majority of veterinary practices, with minimal risk to all staff involved. Practices and personnel should not become complacent with cytotoxic drug use and regular risk assessment, and updates to Control of Substances Hazardous to Health (COSHH) local rules.

Lipomas and leiomyomas are highly frequent benign tumors of mesenchymal origin. Both tumor entities are often characterized by recurrent chromosomal abnormalities. They share those cytogenetic deviations affecting chromosomal band 6p21 or 12q14~15 targeting either of the two gene loci of the human high mobility group AT-hook proteins. However, the most frequent genetic alterations in uterine leiomyomas apparently constituting a distinct pathogenetic entity are gain-of-function mutations of the Mediator subcomplex 12 gene which often do not coincide with microscopically visible chromosomal alterations and apparently never coincide with rearrangements of the gene encoding high mobility group AT-hook 2 protein.

Background: The broad spectrum of neuroblastoma (NB) clinical behavior depends on a genomic landscape of tumor cells. The amplification of MYCN oncogene is the most powerful negative prognostic marker in NB. Moreover, segmental chromosomal alterations are also associated with a poor outcome. Therefore, the comprehensive characterization of tumor genetic features is obligatory for NB patients. These features determine the risk stratification and therapeutic decisions in treatment. Purpose: Our report focuses on a possibility to use standard microarray procedure to demonstrate critical structural chromosomal alteration in archival samples of NB tumors. Methods and Findings: Formalin-fixed paraffin-embedded tissue samples from 8 NB primary tumors have been analyzed by cytogenetic microarrays. It achieved a very good quality of genomic DNA from fixed samples. Chromosomal abnormalities were detected in 7 out of 8 cases. It was not an incidence of MYCN amplification. Conclusion: The results demonstrate that it is possible to obtain reliable and highquality microarray data from archival samples.