Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Henrik Lilljebjörn

PROVIDER: E-GEOD-19996 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias.

Lilljebjörn Henrik H Soneson Charlotte C Andersson Anna A Heldrup Jesper J Behrendtz Mikael M Kawamata Norihiko N Ogawa Seishi S Koeffler H Phillip HP Mitelman Felix F Johansson Bertil B Fontes Magnus M Fioretos Thoas T

Human molecular genetics 20100531 16

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 ...[more]

PMID: 20513752

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Dataset Information

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

Publications

The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias.

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