ArrayCGH on a cohort of pediatric T-ALL cases characterized by TCRAD-MYC translocation
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ABSTRACT:
PROVIDER: PRJNA417967 | ENA |
REPOSITORIES: ENA
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Project description:ArrayCGH was performed on a cohort of 25 specimens collected from children with newly diagnosed T-ALL characterized by TCRAD-MYC translocation ArrayCGH analyses were perfomed to study genomic aberrations occurring in the rare subgroup of TCRAD-MYC rearranged T-ALL
2018-07-01 | GSE106773 | GEO
Project description:ArrayCGH was performed on a cohort of 36 specimens collected from children with newly diagnosed T-ALL treated on contemporary clinical trials. The data was used to investigate mechanisms of primary chemotherapy resistance in T-ALL.
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Project description:Conventioal cytogenetic on 2 sinonasal sarcoma (SNS) cases showed t(2;4)(q37.1;q31.3) translocation previously. The aim of this whole transcriptome analysis is to determine potential candidate genes involved in this translocation. Total RNA extracted from frozen cultured primary tumor cells from a SNS characterized at the cytogenetics level was subjected to Illumina whole transcriptome RNA-sequencing anslysis.
2014-04-17 | E-GEOD-52257 | biostudies-arrayexpress
Project description:MALT lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/BCL10-IGH and t(14;18)(q32;q21)/IGH-MALT1, which commonly activate the NF-κB pathway. Gastric MALT lymphomas harboring such translocation do not respond to H. pylori eradication, while those without translocation can be cured by antibiotics. To understand the molecular mechanism of these different MALT lymphoma subgroups, we performed gene expression profiling analysis of 24 MALT lymphomas (15 translocation-positive, 9 translocation-negative). Gene set enrichment analysis (GSEA) of the NF-κB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions showed that translocation-positive MALT lymphomas are characterized by an enhanced expression of NF-κB target genes, particularly TLR6, CCR2, CD69 and BCL2, while translocation-negative cases were featured by active inflammatory and immune responses, such as IL8, CD86, CD28 and ICOS. Separate analyses of the genes differentially expressed between translocation-positive and negative cases and measurement of gene ontology term in these differentially expressed genes by hypergeometric test reinforced the above findings by GSEA. Finally, expression of TLR6, in the presence of TLR2, enhanced both API2-MALT1 and BCL10 mediated NF-κB activation in vitro. Our findings provide novel insights into the molecular mechanism of MALT lymphomas with and without translocation, potentially explaining their different clinical behaviors. This study compares MALT with other lymphomas namely follicular and mantle cell lymphomas, and investigates the molecular mechanisms of the lymphomagenesis between translocation positive versus negative MALT lymphoma cases in order to derive the pathways leading to MALT lymphoma pathogenesis using GSEA, GO, dynamic pathway analysis as well as other bioinformatics analysis. Samples were run on the Affymetrix HG-U133A and HG-U133 plus2 GeneChips.
2010-05-31 | E-GEOD-18736 | biostudies-arrayexpress
Project description:Acute lymphoblastic leukemia (ALL) is characterized by the accumulation of somatic genetic alterations in B- or T-lymphoid precursor cells eventually resulting in overt leukemia. Contrary to paediatric ALL, its adult counterpart is rather scarcely researched. Early studies demonstrated that gene expression profiling (GEP) is a valuable tool for subgroup identification and risk stratification. This submission of 192 ALL (137 B-cell ALL [B-ALL] and 55 T-cell ALL [T-ALL]) cases characterized on gene expression microarrays serves as a repository for multiple studies examining the leukemogenic mechanisms underlying overt ALL establishment. After informed consent, bone marrow aspirates or peripheral blood samples of a representative cohort of 192 adult ALL patients were collected. Eligible patients had a diagnosis of primary ALL confirmed by cytological examination and immunophenotyping of blood and bone marrow. The majority of these cases were treated following the HOVON (Dutch-Belgian Hematology-Oncology Co-operative group) protocols (http://www.hovon.nl). All studies were approved through the institutional ethics review board and all patients provided written informed consent in accordance to the declaration of Helsinki. Survival data for these patients are captured but not shared publicly for data protection purposes, and will only be available on a case-by-case basis upon specific request, which are likely to be made in a collaborative structure. Blasts and mononuclear cells were purified by Ficoll-Hypaque (Nygaard, Oslo, Norway) centrifugation and cryopreserved. All samples contained 80-to-100 percent blast cells after thawing, regardless of the blast count at diagnosis. RNA isolation was performed as previously described (Valk et al., Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia, New England Journal of Medicine, 2004). <br>Complementary genotyping data from the same study have also been deposited at ArrayExpress, under accession number E-MTAB-5036 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5036/ ). A supplementary file 'DNA_RNA_link_numbers.xlsx' is also provided allowing RNA samples in this submission to be mapped against equivalent DNA sample in E-MTAB-5036.</br>
2017-01-31 | E-MTAB-5035 | biostudies-arrayexpress
Project description:Identification of miRNA differentially expressed between MYC-translocation positive and and MYC-translocation negative Burkitt Lymphoma and their impact on gene expression profile Study of microRNA profile of MYC-translocation positive and MYC-translocation negative Burkitt Lymphoma cases in order to uncover possible differences at the molecular level
2015-08-05 | E-GEOD-71471 | biostudies-arrayexpress
Project description:Pediatric acute myeloid leukemia (AML) is a heterogeneous disease characterized by non-random genetic aberrations related to outcome. Detecting these aberrations however still lead to failures or false negative results. Therefore, we focused on the potential of gene expression profiles (GEP) to classify pediatric AML. Gene expression microarray data of 237 children with AML were generated and cases were split into a discovery cohort (n=157) and an independent validation cohort (n=80). Next, a double-loop cross validation approach was used to generate a subtype-predictive GEP in the discovery cohort which was then tested for its true predictive value in the independent validation cohort.
2010-10-21 | GSE17855 | GEO
Project description:genomic analysis using arrayCGH to gain insight into chromosomal copy number in mucoepidermoid carcinoma (MEC). Results suggest that two types of MECs can be distinguished: (i) a group of MECs without t(11;19)(q21;p13) translocation with many copy number aberrations (> 6), independent of histological grade, and (ii) a group of MECs with the t(11;19)(q21;p13) translocation with no or a few copy number aberrations (<6 ) with two exceptions classified as low and intermediate grade.
2017-11-01 | GSE87353 | GEO
Project description:Childhood acute lymphoblastic leukemia (ALL) comprises a large group of genetic subtypes with a favorable prognosis characterized by a TEL-AML1-fusion, hyperdiploidy (>50 chromosomes) or E2A-PBX1 fusion and a smaller group with unfavorable outcome characterized by either a BCR-ABL-fusion, MLL-rearrangement or T-ALL. About 25% of precursor B-ALL are currently genetically unclassified and have an intermediate prognosis. The present study used genome-wide strategies to reveal new biological insights and advance the prognostic classification of childhood ALL. A double-loop cross validation was used to construct a classifier based on gene expression in ALL cells from 190 newly diagnosed cases (COALL cohort, GEO GSE13425) with a prediction accuracy of 90%. T-ALL, TEL-AML1-positive, hyperdiploid and E2A-rearranged cases were identified with 100% sensitivity and â¥94% specificity. The classifier accuracy was confirmed in an independent cohort of 107 cases (87.9%, DCOG cohort, GEO GSE13351). Experiment Overall Design: 190 bone marrow and peripheral blood samples were collected at diagnosis and frozen. They were later thawed and hybridized to Affymetrix U133A arrays.
2009-01-31 | E-GEOD-13425 | biostudies-arrayexpress