GEO DataSets

(Submitter supplied) Chromosomal aneuploidy and translocations are hallmarks of acute lymphoblastic leukemia (ALL), but many patients lack a recurring chromosomal alteration. Here we report a recurring interstitial deletion of the pseudoautosomal region 1 of chromosomes X and Y in B-progenitor ALL that results in the expression of a novel fusion that juxtaposes the first non-coding exon of P2RY8 to the coding region of the CRLF2 (cytokine receptor like factor 2, or thymic stromal lymphopoietin receptor) gene. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8737

2 Samples

Download data: TXT

(Submitter supplied) DS-ALL is a highly heterogeneous disease with predominance of an aberrant exp. of CRLF2 cooperating with mutated JAK2 Acute lymphoblastic pediatric leukemia specimens of Down's syndrome are examined for gene expression profiles and specific genetic aberrations. Gene expression profiling and specific genetic variation analysis identify novel pathways involved in DS-ALL pathogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL570

119 Samples

Download data: CEL, PDF

(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) Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia We report two novel, cryptic chromosomal abnormalities in precursor B-cell acute lymphoblastic leukemia (BCP-ALL): a translocation, either t(X;14)(p22;q32) or t(Y;14)(p11;q32), in 33 patients and an interstitial deletion, either del(X)(p22.33p22.33) or del(Y)(p11.32p11.32), in 64 patients, involving the pseudoautosomal region (PAR1) of the sex chromosomes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL8876 GPL4091

16 Samples

Download data: TXT

(Submitter supplied) Deregulated expression of the type I cytokine receptor, CRLF2 (CRLF2-d), is observed in 5-15% of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL), is associated with activation of the JAK/STAT pathway and has an inferior outcome compared to those with good risk cytogenetics. We aimed to determine the clinical and genetic landscape of CRLF2-d ALL using genomic approaches including karyotyping, fluorescence in situ hybridisation, whole genome and whole exome sequencing. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

41 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL97 GPL570

316 Samples

Download data: CEL

(Submitter supplied) Philadelphia-like B-cell precursor acute lymphoblastic leukemia (Ph-like ALL) is characterized by distinct genetic alterations and inferior prognosis in children and younger adults. The purpose of this study was the genetic and clinical characterization of Ph-like ALL in adults. Among 207 adult B-cell precursor ALL patients, 26 (13%) were classified as Ph-like using Affymetrix microarrays. The incidence of this subtype was 25% among 105 B-cell precursor ALL patients negative for BCR-ABL1 and MLL-translocations (B-other). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL97

109 Samples

Download data: CEL

(Submitter supplied) Philadelphia-like B-cell precursor acute lymphoblastic leukemia (Ph-like ALL) is characterized by distinct genetic alterations and inferior prognosis in children and younger adults. The purpose of this study was the genetic and clinical characterization of Ph-like ALL in adults. Among 207 adult B-cell precursor ALL patients, 26 (13%) were classified as Ph-like using Affymetrix microarrays. The incidence of this subtype was 25% among 105 B-cell precursor ALL patients negative for BCR-ABL1 and MLL-translocations (B-other). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

109 Samples

Download data: CEL

(Submitter supplied) Philadelphia-like B-cell precursor acute lymphoblastic leukemia (Ph-like ALL) is characterized by distinct genetic alterations and inferior prognosis in children and younger adults. The purpose of this study was the genetic and clinical characterization of Ph-like ALL in adults. Among 207 adult B-cell precursor ALL patients, 26 (13%) were classified as Ph-like using Affymetrix microarrays. The incidence of this subtype was 25% among 105 B-cell precursor ALL patients negative for BCR-ABL1 and MLL-translocations (B-other). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

98 Samples

Download data: CEL

(Submitter supplied) Xenograft models represent an excellent method for expanding primary leukemias, but their ability to preserve the gene expression profile of the parent leukemia may also depend on providing microenvironmental factors that are not cross-reactive between human and mouse. Here we focused on leukemias with a CRLF2 mutation, and the ability of human TSLP to stimulate these cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

5 Samples

Download data: XLSX

(Submitter supplied) The cytokine TSLP stimulates in vitro proliferation of human fetal B cell progenitors. Genetic alterations that cause overexpression of the TSLP receptor component, CRLF2, lead to B cell acute lymphoblastic leukemia (CRLF2 B-ALL) with poor outcome. The in vivo role of TSLP in normal human B cell development and its contribution to CRLF2 B-ALL are unknown. In classic xenograft models CRLF2-mediated signaling is unlikely to be activated by mouse TSLP, based on data from engineered cellular models. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

18 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL18573

21 Samples

Download data

(Submitter supplied) Gene expression profiling was performed to characterise transcriptional programs associated with response to type I JAK2 inhibitor ruxolitinib, type II JAK2 inhibitor CHZ868 or shRNA-mediated JAK2 knockdown in MHH-CALL4 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) RNA-seq was performed to compare the transcriptional programmes of murine Eµ-Crlf2/Jak2R683G-expressing B-ALL cells subjected to short-term (2 days) versus long-term (21 days) shRNA-mediated Jak2 knockdown in vivo.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: CSV

(Submitter supplied) This experiment comprises 283 CEL files generated on the Affymetrix U133 Plus 2.0 gene expression microarray platform, using patient peripheral blood and bone marrow samples from the first cohort of patients accrued to Children's Oncology Group Study AALL0232. No clinical covariate data is provided at this time as the clinical study is not yet published. Researchers who would like to request outcome or other covariate data are asked to contact Dr. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

283 Samples

Download data: CEL

(Submitter supplied) We studied the in vitro and in vivo efficacy of the HDAC inhibitor Givinostat/ITF2357 in BCP-ALL with CRLF2 rearrangements. We used BCP-ALL CRLF2- rearranged MHH-CALL4 and MUTZ5 cell lines as well as blasts from CRLF2 rearranged BCP-ALL patients and patients’ derived xenograft samples. We conclude that Givinostat may represent a novel and effective tool, in combination with current chemotherapy, to treat this subsets of ALL with poor prognosis and chemotherapy-related toxicity.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

10 Samples

Download data: CEL

(Submitter supplied) Inherited non-coding genetic variants confer significant disease susceptibility in many cancers. However, the molecular processes by which germline variants contribute to somatic lesions are poorly understood. We performed targeted sequencing in 5,008 patients and identified a key regulatory germline variant in GATA3 strongly associated with Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9052

74 Samples

Download data: COOL, NARROWPEAK, TXT

(Submitter supplied) Seventeen T-ALL patients out of 120 (14.2%) presented CRLF2 expression 5 times higher than the median (‘CRLF2-high’) with a significantly inferior 5-y EFS and an increased CIR compared to CRLF2-low patients.GEP of 15 T-ALL patients with (‘CRLF2-high’) were compared to 15 CRLF2-low patients. GSEA identified cell cycle deregulating gene sets.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

30 Samples

Download data: CEL

(Submitter supplied) Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features. Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched. To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 35 non-Down syndrome (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression, and methylation analyses. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6986 GPL8490 GPL570

233 Samples

Download data: CEL, TXT

(Submitter supplied) SNP profiling can reveal copy number abnormalities and loss of heterozygosity associated with distinct biologic subtypes of acute lymphoblastic leukemia (ALL). We performed SNP profiling of Down syndrome ALL cases and controls to identify unique biologic features of this ALL subgroup.

Organism:

Homo sapiens

Type:

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

Platform:

GPL6986

161 Samples

Download data: TXT