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E-GEOD-17195 - Germline genomic variations associated with childhood acute lymphoblastic leukemia

Status
Released on 16 August 2009, last updated on 2 June 2014
Organism
Homo sapiens
Samples (44)
Array (1)
Protocols (7)
Description
We identified germline single nucleotide polymorphisms (SNPs) associated with childhood acute lymphoblastic leukemia (ALL) and its subtypes. Using the Affymetrix 500K Mapping array and publicly available genotypes, we identified 18 SNPs whose allele frequency differed (P<1x10-5) between a pediatric ALL population (n=317) and non-ALL controls (n=17,958). Six of these SNPs differed (P≤0.05) in allele frequency among four ALL subtypes. Two SNPs in ARID5B not only differed between ALL and non-ALL groups (rs10821936, P=1.4x10-15, odds ratio[OR]=1.91; rs10994982, P=5.7x10-9, OR=1.62) but also distinguished B-hyperdiploid ALL from other subtypes (rs10821936, P=1.62 x10-5, OR=2.17; rs10994982, P=0.003, OR 1.72). These ARID5B SNPs also distinguished B-hyperdiploid ALL from other subtypes in an independent validation cohort (n=124 children with ALL) (P=0.003 and P=0.0008, OR 2.45 and 2.86, respectively) and were associated with methotrexate accumulation and gene expression pattern in leukemic lymphoblasts. We conclude that germline genomic variations affect susceptibility to and characteristics of specific ALL subtypes. We used microarrays to detail the global program of gene expression in primary leukemic blasts cells from children diagnosed with acute lymphoblastic leukemia.
Experiment type
transcription profiling by array 
Contacts
Geoffrey Neale <geoffrey.neale@stjude.org>, Geoffrey A Neale, Mary V Relling
Citation
Germline genomic variants associated with childhood acute lymphoblastic leukemia. Trevi�o LR, Yang W, French D, Hunger SP, Carroll WL, Devidas M, Willman C, Neale G, Downing J, Raimondi SC, Pui CH, Evans WE, Relling MV. , PMID:19684603
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-17195.idf.txt
Sample and data relationshipE-GEOD-17195.sdrf.txt
Raw data (1)E-GEOD-17195.raw.1.zip
Processed data (1)E-GEOD-17195.processed.1.zip
Array designA-AFFY-33.adf.txt
Links