Figure 2
From: Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness
The 5q21 deletion targets CHD1. (a) Left, Agilent 44K CGH array heatmap view of deletions spanning 5q21 in prostate tumors with deletion. Blue intensity (scale shown) identifies CBS-called deletions. Right, Agilent custom-tiling CGH array heatmap view of raw copy number ratios (scale indicated) for selected samples with informative deletions. Tumor samples no. 538 and no. 362 (asterisked) define the 120-kb smallest region of shared deletion (bracketed by yellow-dashed lines), which affects only CHD1. The exon structure of CHD1, and the only other nearby gene, RGMB, are shown. Note, for some samples, apparent deletion boundary discrepancies between the Agilent 44K CGH array and the custom tiling array data reflect the lower resolution and CBS-based smoothing in the former. The Agilent high-density custom CGH 15K array was designed using eArray 6.5 software, with probes spanning a subregion of 5q15–q21.1 (96.0–102.0 Mb; build 18) tiled on average every 500 bp. (b) Transcript levels of CHD1, measured by oligonucleotide microarray, are reduced in tumor samples with 5q21 deletion compared with samples without 5q21 deletion, and compared with normal prostate. Box plots show 25th, 50th (median) and 75th percentiles of sample-set expression. P-values (two-sided Mann–Whitney U-test) are shown. CHD1 transcript levels were obtained by HEEBO oligonucleotide microarray (http://www.microarray.org/sfgf/heebo.do) profiling, carried out in parallel on 63 of the same tumor samples, and, for a subset, matched adjacent-normal tissue. Values are reported as log2 ratios, normalized to the sample-set mean. The full gene-expression dataset will be detailed separately (Gulzar and Brooks; manuscript in preparation).
