Comparative genomic hybridization of kidney samples from Wilms tumor patients to accurately map 1p13 breakpoints

ABSTRACT: Wilms tumour karyotypes frequently exhibit recurrent, large-scale chromosomal imbalances, among the most common of which are concurrent loss of 1p and gain of 1q. We have previously identified a novel breakpoint at 1p13 by 1Mb-spaced array CGH, and undertook a fine-tiling oligonucleotide array approach to accurately map the region in four tumours exhibiting rearrangements at this locus. The use of a 10 bp–spaced platform revealed that all four tumours in fact harboured different breakpoints, which were mapped to target four distinct genes – PHTF1, DCLRE1B, TRIM33 and NRAS. The precise breakpoint interval was confirmed for one case to lie within intron 3 of DCLRE1B by quantitative copy number PCR and RT-PCR. In addition, expression profiling revealed a pattern of down- and up-regulation of genes either side of the breakpoint in all cases. Although it appears that no single gene is the driver of this rearrangement, this study highlights the power of fine-tiling oligonucleotide arrays to delineate breakpoint regions identified by other genome-wide screens. Processed data is provided as one archive per processed data file obtained via clicking on the ftp link. Related experiment E-TABM-164.

ORGANISM(S): Homo sapiens

DISEASE(S): Wilms tumour

SUBMITTER: Anita Grigoriadis 

PROVIDER: E-TABM-155 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress