E-GEOD-10387 - Genotyping and transcription profiling OF human T-cell prolymphocytic leukemia patients identifies novel chromosomal imbalances AND candidate genes IN T-PLL

Status
Submitted on 5 February 2008, released on 10 April 2008, last updated on 2 May 2014
Organism
Homo sapiens
Samples (12)
Array (1)
Protocols (5)
Description
T-cell prolymphocytic leukemia (T-PLL) is a rare aggressive lymphoma derived from mature T cells, which is, in most cases, characterized by the presence of an inv(14)(q11q32)/t(14;14)(q11;q32) and a characteristic pattern of secondary chromosomal aberrations. DNA microarray technology was employed to compare the transcriptomes of eight immunomagnetically purified CD3+ normal donor-derived peripheral blood cell samples, with five highly purified inv(14)/t(14;14)-positive T-PLL blood samples. Between the two experimental groups, 734 genes were identified as differentially expressed, including functionally important genes involved in lymphomagenesis, cell cycle regulation, apoptosis and DNA repair. Notably, the differentially expressed genes were found to be significantly enriched in genomic regions affected by recurrent chromosomal imbalances. Upregulated genes clustered on chromosome arms 6p and 8q, and downregulated genes on 6q, 8p, 10p, 11q and 18p. High-resolution copy-number determination using single nucleotide polymorphism chip technology in 11 inv(14)/t(14;14)-positive T-PLL and 1 without the inv(14) including those analyzed for gene expression, refined chromosomal breakpoints as well as regions of imbalances. In conclusion, combined transcriptional and molecular cytogenetic profiling identified novel specific chromosomal loci and genes that are likely to be involved in disease progression and suggests a gene dosage effect as a pathogenic mechanism in T-PLL. Each Sample has its raw data file linked as a supplementary file. Experiment Overall Design: 12 T-cell prolymphocytic leukaemia samples were hybridized to 50K_Xba SNP arrays.
Experiment types
genotyping by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-10387.idf.txt
Sample and data relationshipE-GEOD-10387.sdrf.txt
Raw data (1)E-GEOD-10387.raw.1.zip
Processed data (1)E-GEOD-10387.processed.1.zip
Array designA-AFFY-70.adf.txt
Links