GEO DataSets

(Submitter supplied) Lymphoblastic lymphoma (LBL) is one of the most frequent occurring pediatric non-Hodgkin lymphomas. In the WHO classification scheme pediatric LBL is considered to be the same disease entity as pediatric acute lymphoblastic leukemia (ALL). However, it is unclear whether the genetic basis of pediatric LBL development is similar to that of pediatric ALL. We performed genome-wide analyses of copy number aberrations in 12 T-LBL and 7 precursor B-cell LBL pediatric cases using high-resolution SNP-based array CGH. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL3718

25 Samples

Download data: CEL, CHP

(Submitter supplied) Acute lymphoblastic leukemia (ALL) is an heterogeneous disease comprising several subentities that differ for both immunophenotypic and molecular characteristics. Over the years, the biologic understanding of this neoplasm has largely increased. Gene expression profiling has recently allowed to identify specific signatures for the different ALL subsets and permitted identification of pathways deregulated by a given lesion. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL570 GPL8191

39 Samples

Download data: CEL, XLS

(Submitter supplied) Gene expression analyses, were performed on 121 consecutive childhood leukemias (87 B-lineage acute lymphoblastic leukemias (ALLs), 11 T-cell ALLs, and 23 acute myeloid leukemias; AMLs), investigated during an 8-year period at a single center. The supervised learning algorithm k-nearest neighbor (k-NN) was utilized to build gene expression predictors that could classify the ALLs/AMLs according to clinically important subtypes with high accuracy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4861

127 Samples

Download data: TXT

(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the predominant sites of disease in T-ALL and T-LL are observed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

29 Samples

Download data: CEL

(Submitter supplied) In this study, we performed an inventory of copy number changes present in childhood acute lymphoblastic leukemias. The cohort contains a total of 40 diagnosis samples, including 7 T-lineage ALLs and 33 precursor B-cell ALLs. High resolution genomic profiling was perfomed using Affymetrix SNP arrays. We detected multiple de novo genetic lesions, including gross aneuploidies and segmental gains and losses, some of which were subtle and affected single genes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL2004 GPL3718 GPL2005

45 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Despite increased knowledge about genetic aberrations in pediatric T-cell acute lymphoblastic leukemia (T-ALL), no clinically feasible treatment-stratifying marker exists at diagnosis. Instead patients are enrolled in intensive induction therapies with substantial side effects. In modern protocols, therapy response is monitored by minimal residual disease (MRD) analysis, and used for post-induction risk group stratification. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

65 Samples

Download data: TXT

(Submitter supplied) Acute lymphoblastic pediatric leukemia specimens without known genetic hallmarks are examined for hidden genomic aberrancies and related gene expression profiles Integration of genomic variation and gene expression profiling identifies hidden genetic lesions and novel pathways involved in BP-ALL pathogenesis Keywords: expression data

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL570 GPL2004 GPL2005

160 Samples

Download data: CEL, CHP, PDF

(Submitter supplied) We consider a data set consisting out of 27 arrayCGH dye-swap experiments (54 arrays) of individuals with T-ALL versus normal individuals. Aim was to detect novel unbalanced genomic rearrangements in T-ALL. Analysis of the patients was done using an array with genomic BAC and PAC probes with an overall resolution of 1Mb over the entire genome and with additional probes around known and candidate oncogenes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4939

54 Samples

Download data: GPR

(Submitter supplied) Abstract: To investigate the effect of l-asparaginase on acute lymphoblastic leukemia (ALL), we used cDNA microarrays to obtain a genome-wide view of gene expression both at baseline and after in vitro exposure to l-asparaginase in cell lines and pediatric ALL samples. In 16 cell lines, a baseline gene expression pattern distinguished l-asparaginase sensitivity from resistance. However, for 28 pediatric ALL samples, no consistent baseline expression pattern was associated with sensitivity to l-asparaginase. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

5 related Platforms

109 Samples

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(Submitter supplied) Time series of in vitro 2 IU/ml L-asparaginase exposure in acute lymphoblastic leukemia cell lines. Groups of assays that are related as part of a time series. Keywords: time_series_design

Organism:

Homo sapiens

Type:

Expression profiling by array

5 related Platforms

55 Samples

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(Submitter supplied) Samples of pediatric acute lymphoblastic leukemia. All samples contain at least 90% blasts. Each sample was split into two flasks, one of which was exposed to 2IU/ml of L-asparaginase. The other flask served as a control. Cells were lysed at the times indicated. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3322

22 Samples

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(Submitter supplied) Samples of pediatric acute lymphoblastic leukemia obtained from patients at diagnosis. All samples contain at least 77% blasts. Asparaginase LC50 values were determined for each of these samples. (LC50 was determined on a different aliquot of the same sample.) Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3271 GPL3254

32 Samples

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(Submitter supplied) We present here a genome-wide map of abnormalities found in diagnostic samples from 45 adults and adolescents with acute lymphoblastic leukemia (ALL). 500K single nucleotide polymorphism (SNP) array analysis uncovered frequent genetic abnormalities, with cryptic deletions constituting half of the detected changes, implying that microdeletions are a characteristic feature of this malignancy. Importantly, the pattern of deletions resembled that recently reported in pediatric ALL, suggesting that adult, adolescent, and childhood cases may be more similar on the genetic level than previously thought. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL3720 GPL2641 GPL3718

165 Samples

Download data: CEL, TXT

(Submitter supplied) Chromosomal aberrations are a hallmark of acute lymphoid leukaemia (ALL) but alone fail to induce leukaemia. To identify cooperating oncogenic lesions, we performed genome-wide analysis of leukaemic blasts from 242 paediatric ALL patients using high-resolution single nucleotide polymorphism arrays and genomic DNA sequencing. Our analyses revealed deletion, amplification, point mutation and structural rearrangement in genes encoding key regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL2005 GPL3720 GPL2004

1099 Samples

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(Submitter supplied) GEP class prediction in association with CI-FISH (42 candidate genes) and patient MRD stratification

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

72 Samples

Download data: CEL

(Submitter supplied) The goals of this study are to determine whether alterations in the 3D genome organization are associated with the malignant transformation of T-ALL. We report integrated analyses of 3D genome alterations and differentially expressed genes (DEGs) in 18 newly diagnosed T-ALL patients and 4 healthy T cell controls. We found that 3D genome reorganization at the compartment, topologically associated domains (TAD), and loop levels in different subtypes of T-ALL. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL20795

52 Samples

Download data: BEDPE, BW, H5, HIC, TXT, XLS

(Submitter supplied) Infant T-cell acute lymphoblastic leukaemia (iT-ALL) is a very rare and poorly defined entity with a poor prognosis. We assembled a unique series of 13 infants with T-ALL, which allowed us to identify genotypic abnormalities and to investigate prenatal origins. Matched samples (diagnosis/remission) were analysed by single nucleotide polymorphism-array to identify genomic losses and gains. In three cases, we identified a recurrent somatic deletion on chromosome 3. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

13 Samples

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(Submitter supplied) PAPER 1:"Identification of novel subgroups of high-risk pediatric precursor B acute lymphoblastic leukemia (B-ALL) by unsupervised microarray analysis: clinical correlates and therapeutic implications. A Children's Oncology Group (COG) study." ABSTRACT We examined gene expression profiles of pre-treatment specimens from 207 patients from the COG P9906 study to identify signatures of children with high risk B-precursor acute lymphoblastic leukemia (ALL) and to determine whether the resulting clusters are associated with either specific clinical features or treatment response characteristics. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

207 Samples

Download data: CEL, CHP, MSK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

20 Samples

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(Submitter supplied) Precursor T-cell lymphoblastic neoplasms are aggressive haematological neoplasm that most often manifest with extensive marrow and blood affectation (T-cell acute lymphoblastic leukaemia or T-ALL) or less commonly as a thymic mass with limited bone marrow infiltration (T-cell lymphoblastic lymphoma or T-LBL). Here we show data from small-RNA-Seq in a sample series of T-LBL from Spanish patients.The goal was to determine the levels of expression of coding genes and microRNAs, and to identify all genetic variants including SNVs, indels, and fusion transcripts.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

10 Samples

Download data: XLSX