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Illumina SNP-array data for 2 ETV6/RUNX1-positive Acute Lymphoblastic Leukemia samples and corresponding normal samples

ABSTRACT: Acute lymphoblastic leukemia (ALL), the most common malignant disorder in childhood, is typically associated with numerical chromosomal aberrations, fusion genes or small focal deletions, thought to represent important pathogenetic events in the development of the leukemia. Mutations, such as single nucleotide changes, have also been reported in childhood ALL, but these have only been studied by sequencing a small number of candidate genes. Herein, we report the first unbiased sequencing of the whole exome of two cases of pediatric ALL carrying the ETV6/RUNX1 (TEL/AML1) fusion gene (the most common genetic subtype) and corresponding normal samples. A total of 14 somatic mutations were identified, including four and seven protein-altering nucleotide substitutions in each ALL. Twelve mutations (86%) occurred in genes previously described to be mutated in other types of cancer, but none was found to be recurrent in an extended series of 29 ETV6/RUNX1-positive ALLs. The number of single nucleotide mutations was similar to the number of copy number alterations as detected by single nucleotide polymorphism arrays. Although the true pathogenetic significance of the mutations must await future functional evaluations, this study provides a first estimate of the mutational burden at the genetic level of t(12;21)-positive childhood ALL.

ORGANISM(S): Homo sapiens

PROVIDER: GSE25102 | GEO | 2012/07/03

SECONDARY ACCESSION(S): PRJNA142779

REPOSITORIES: GEO

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Affymetrix SNP-array data for 2 ETV6/RUNX1-positive Acute Lymphoblastic Leukemia samples and corresponding normal samples

Project description:Acute lymphoblastic leukemia (ALL), the most common malignant disorder in childhood, is typically associated with numerical chromosomal aberrations, fusion genes or small focal deletions, thought to represent important pathogenetic events in the development of the leukemia. Mutations, such as single nucleotide changes, have also been reported in childhood ALL, but these have only been studied by sequencing a small number of candidate genes. Herein, we report the first unbiased sequencing of the whole exome of two cases of pediatric ALL carrying the ETV6/RUNX1 (TEL/AML1) fusion gene (the most common genetic subtype) and corresponding normal samples. A total of 14 somatic mutations were identified, including four and seven protein-altering nucleotide substitutions in each ALL. Twelve mutations (86%) occurred in genes previously described to be mutated in other types of cancer, but none was found to be recurrent in an extended series of 29 ETV6/RUNX1-positive ALLs. The number of single nucleotide mutations was similar to the number of copy number alterations as detected by single nucleotide polymorphism arrays. Although the true pathogenetic significance of the mutations must await future functional evaluations, this study provides a first estimate of the mutational burden at the genetic level of t(12;21)-positive childhood ALL. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 2 leukemic bone marrow samples and two corresponding normal blood samples.

2012-07-02 | E-GEOD-25116 | biostudies-arrayexpress

Affymetrix SNP-array data for 2 ETV6/RUNX1-positive Acute Lymphoblastic Leukemia samples and corresponding normal samples

2012-07-03 | GSE25116 | GEO

Illumina SNP-array data for 2 ETV6/RUNX1-positive Acute Lymphoblastic Leukemia samples and corresponding normal samples

Project description:Acute lymphoblastic leukemia (ALL), the most common malignant disorder in childhood, is typically associated with numerical chromosomal aberrations, fusion genes or small focal deletions, thought to represent important pathogenetic events in the development of the leukemia. Mutations, such as single nucleotide changes, have also been reported in childhood ALL, but these have only been studied by sequencing a small number of candidate genes. Herein, we report the first unbiased sequencing of the whole exome of two cases of pediatric ALL carrying the ETV6/RUNX1 (TEL/AML1) fusion gene (the most common genetic subtype) and corresponding normal samples. A total of 14 somatic mutations were identified, including four and seven protein-altering nucleotide substitutions in each ALL. Twelve mutations (86%) occurred in genes previously described to be mutated in other types of cancer, but none was found to be recurrent in an extended series of 29 ETV6/RUNX1-positive ALLs. The number of single nucleotide mutations was similar to the number of copy number alterations as detected by single nucleotide polymorphism arrays. Although the true pathogenetic significance of the mutations must await future functional evaluations, this study provides a first estimate of the mutational burden at the genetic level of t(12;21)-positive childhood ALL. Illumina SNP-array genotyping was performed according to the manufacturer's directions on DNA extracted from 2 leukemic bone marrow samples and two corresponding normal blood samples. The genotype data from the arrays were used for quality assesment of genotype data from high throughput sequencing.

2012-07-02 | E-GEOD-25102 | biostudies-arrayexpress

Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

Project description:Genome binding/occupancy profiling of ETS Variant Transcription Factor 6- Runt Related Transcription Factor 1 fusion protein (ETV6-RUNX1) in REH cells by high throughput sequencing. ETV6-RUNX1 is expressed in pediatric t(12;21) ETV6-RUNX1 B cell precursor acute lymphoblastic leukemia.

2022-04-01 | GSE176084 | GEO

Affy SNP-array data for 23 ETV6/RUNX1-positive ALL patient samples and one cell line

Project description:The ETV6/RUNX1 fusion gene, present in 25% of B-lineage childhood acute lymphoblastic leukemia (ALL), is thought to represent an initiating event, which requires additional genetic changes for leukemia development. To identify additional genetic alterations, 24 ETV6/RUNX1-positive ALLs were analyzed using 500K single nucleotide polymorphism arrays. The results were combined with previously published data sets, allowing us to ascertain genomic copy number aberrations (CNAs) in 164 cases. In total, 45 recurrent CNAs were identified with an average number of 3.5 recurrent changes per case (range 0-13). Twenty-six percent of cases displayed a set of recurrent CNAs identical to that of other cases in the data set. The majority (74%), however, displayed a unique pattern of recurrent CNAs, indicating a large heterogeneity within this ALL subtype. As previously demonstrated, alterations targeting genes involved in B-cell development were common (present in 28% of cases). However, the combined analysis also identified alterations affecting nuclear hormone response (24%) to be a characteristic feature of ETV6/RUNX1-positive ALL. Studying the correlation pattern of the CNAs allowed us to highlight significant positive and negative correlations between specific aberrations. Furthermore, oncogenetic tree models identified ETV6, CDKN2A/B, PAX5, del(6q), and +16 as possible early events in the leukemogenic process. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 23 leukemic bone marrow samples and one ETV6/RUNX1-positive cell line.

2010-07-07 | E-GEOD-19996 | biostudies-arrayexpress

Refining the set of ETV6-RUNX1-specific genes by employing gene expression profiles of patients in remission

Project description:The chromosomal translocation t(12;21) resulting in the ETV6-RUNX1 fusion gene is the most common genetic abnormality in childhood acute lymphoblastic leukemia (ALL). As the emergence of microarray technology, finding subtype-specific genes becomes one of the main objectives in most ALL studies. However, the list of differentiated genes derived by comparing patients in the subtype versus the others contains many false positives, which are not really subtype-specific. In order to refine the list of subtype-specific genes for ALL with ETV6-RUNX1, this study conducted microarray experiments on patients in both diagnosis and remission status.

2019-02-01 | GSE74335 | GEO

Affy SNP-array data for 23 ETV6/RUNX1-positive ALL patient samples and one cell line

2010-07-07 | GSE19996 | GEO

ChIP-seq for RUNX1 and ETV6-RUNX1 in an induced pluripotent stem cell model of ETV6-RUNX1 pre-leukaemia

Project description:ETV6-RUNX1 is a first-hit mutation in childhood B cell precursor acute lymphoblastic leukaemia. ETV6-RUNX1 is a fusion protein which inherits the DNA-binding runt domain from RUNX1. Here we performed chromatin precipitation for native RUNX1 and ETV6-RUNX1 using RUNX1 antibodies and specifically for the ETV6-RUNX1 fusion using a V5-tag pull down.

2022-10-31 | E-MTAB-12208 | biostudies-arrayexpress

Genome wide mapping of ETV6 binding sites in pre-B leukemic cells

Project description:Background: Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies. Notably, the t(12;21) translocation leading to an ETV6-AML1 fusion gene is the most common genetic alteration found in childhood acute lymphoblastic leukemia. Moreover, most of these patients also lack ETV6 expression, suggesting a tumor suppressor function. Results: To gain insights on ETV6 DNA-binding specificity and genome wide transcriptional regulation capacities, we performed chromatin immunoprecipitation experiments coupled to deep sequencing in a t(12;21)-positive pre-B leukemic cell line. This strategy led to high quality ETV6-bound regions. ETV6 binding is mostly cell type-specific as only few regions are shared with other blood cell subtypes. Peaks localization and motif enrichment analyses revealed a unique binding profile that is associated with the presence of the ETV6-AML1 fusion product. Conclusions: We described the first ETV6 binding map in the t(12;21) background. This study highlighted the complex and unique interplay between ETV6 and ETV6-AML1 and underscored the highly regulated mechanisms of ETV6 binding. ETV6 inactivation observed in this context could induce specific transcriptional changes promoting leukemic transformation.

2017-11-15 | GSE102785 | GEO

Co-expression of long non-coding RNAs and protein-coding genes in pediatric B-cell acute lymphoblastic leukemia

Project description:Long non-coding RNAs (lncRNAs) play important roles in numerous diseases and represent an emerging layer of cancer biology. However, the role that lncRNAs play in the pathogenesis of pediatric B-cell leukemia (B-ALL) with t(12;21) (ETV6-RUNX1) translocation is largely unknown. In this study, we assessed the lncRNA expression profiles of 42 pediatric B-ALL (24 with and 18 without the t(12;21) translocation) and 4 bone marrows from healthy donors. We identified 117 lncRNAs that were differentially expressed (fold change> 1.5 and FDR > 0.05) between the B-ALL subgroups (ETV6-RUNX1-positive and ETV6-RUNX1-negative). The most upregulated lncRNAs in ETV6-RUNX1 positive B-ALL were TCL6, RP4-697K14.3, LOC100292680, RP11-345I18.1, LINC00599 and TRAF3IP2-AS1, while the most downregulated were RP11-135F9.1, RP11-561B11.1, AK095221, RP11-463H12.1, AC007283.4 and CCDC26. Coding-non-coding gene co-expression networks were constructed to identify lncRNAs with potential functions in ETV6-RUNX1 translocation. Levels of representative lncRNA-mRNA pairs were further detected by RT-qPCR in patients with pediatric B-ALL. Importantly, pediatric B-ALL patients who expressed low levels of the lncRNA TCL6 had lower disease-free survival than patients with high levels of TCL6. Thus, these findings provide the first detailed description of lncRNA expression profiles related to t(12;21) translocation in pediatric B-ALL. Such lncRNAs profiles might play important roles in driving normal cells to leukemic cells. These lncRNAs may provide novel molecular biomarkers and offer new basis for combating pediatric B-ALL.

2019-12-10 | GSE128254 | GEO

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