Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Distinctive genotypes in infants with T-cell acute lymphoblastic leukaemia      
dateReleased:
07-30-2015
description:
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 thirteen cases of infants with T-ALL which allowed us to identify genotypic abnormalities and to investigate prenatal origins. Matched samples (diagnosis/remission) were analysed by SNP-array to identify genomic losses and gains. In three cases, we identified a recurrent somatic chromosome 3 deletion. These losses, confirmed by FISH, result in the complete deletion of MLF1, not previously described in T-ALL. We observed two cases with an 11p13 deletion (LMO2-related), one of which also harboured a deletion of RB1. Another case presented a large 11q14.1-11q23.2 deletion that included ATM and only five patients (38%) showed deletions of CDKN2A/B. Four cases showed NOTCH1 mutations, in one case FBXW7 was the sole mutation and three cases showed alterations in PTEN. MLL rearrangements (MLL-r) were detected in three out of thirteen cases. For three patients, mutations and CNAs could be backtracked to birth using neonatal blood spot DNA, demonstrating an in utero origin. Overall, our data indicates iT-ALL has a diverse but distinctive profile of genotypic abnormalities when compared to T-ALL in older children and adults. Affymetrix SNP6.0 arrays were performed according to the manufacturer's directions on DNA extracted from diagnostic bone marrow or peripheral blood samples. Copy number analyses of Affymetrix SNP6.0 arrays were performed for 13 infant T-ALL samples.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-67271
refinement:
raw
alternateIdentifiers:
67271
keywords:
functional genomics
dateModified:
08-19-2015
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-AFFY-142
name:
Affymetrix GeneChip Genome-Wide Human SNP 6.0 [GenomeWideSNP_6]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-67271/E-GEOD-67271.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-67271/E-GEOD-67271.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67271
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.