An integrated genomic and expression analysis of 7q deletion in SMZL (Oligo aCGH)

ABSTRACT: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown. In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data. High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region. Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation. In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas. Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL. Keywords: Genome variation profiling by genome tiling array For aCGH. 21 fresh frozen splenic samples from patients with SMZL were hybridized against a reference control of pooled PBMC genomic DNA from 10 normal subjects. High-resolution oligonucleotide analysis of copy number variations in splenic marginal zone lymphoma (SMZL) in regions of recurrent alteration. Regions included on the array: 7q (2k resolution) and regions of interest on chromosomes 3q, 6q and 9q at 12k resolution.

ORGANISM(S): Homo sapiens

SUBMITTER: Alan Watkins 

PROVIDER: E-GEOD-35425 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress