A. Metaphase preparation and interphase nucleus from a clinically healthy dog to which canine bacterial artificial chromosome (BAC) clones representing the genes ABL (yellow signal) and BCR (green signal) showing the localization of these loci to CFA 9 and 26, respectively (see inset). B) Hybridization of the same BCR and ABL BAC clones to a metaphase preparation and interphase nuclei derived from a CML patient. In the metaphase spread, while one copy each of CFA 9 and 26 appear normal (lower right) the presence of a derivative chromosome showing co-localization of yellow and green signal (inset) indicates the presence of the ‘Raleigh’ chromosome. Similarly, juxtaposition of one green and one yellow signal in each of the two interphase nuclei conform this translocation event
Reproduced from Breen and Modiano (2008) with kind permission of Springer Netherlands, Dr. Matthew Breen and Dr. Jaime Modiano.

A) Single homologues of two example chromosomes; on the left the larger submetacentric chromosome has been divided in regions A and B on the p-arm and regions C-H on the q-arm; on the right the smaller metacentric chromosome has regions 1 and 2 comprising the p-arm and regions 3 and 4 comprising the q-arm. B and C shows balanced chromosome aberrations in which the organization of the segments has altered but their copy number has not changed; in B a reciprocal translocation between the two chromosomes has resulted in two new derivative chromosomes, in which the q arms have been exchanged; in C a paracentric inversion in the q arm of the larger chromosome has resulted in a change of segment order. These changes would go undetected in comparative hybridization analysis and would require cytogenetic evaluation to identify these changes. Panels D, E and F shows structural changes that are associated with gain or loss of chromosomal segments of the larger chromosome; D shows deletion of region E, E shows a pericentric inversion with loss of region A, F shows a duplication of region E. All three of these aberrations change the DNA content of the cell and would be readily detected using CGH analysis. All three would also be visualized using molecular cytogenetic evaluation with suitable probes.

A) Scan data resulting from the use of a small 3,840 feature cDNA spotted microarray. RNA from two samples were differentially labeled (reference = red; tumor = green) and c-hybridized to the array. Following hybridization the microarray was scanned at 5 μM resolution, acquiring the two color planes. The strength of the hybridization signal on each spot relates the abundance of mRNA population of the corresponding gene. On the right a merged image is shown to visually compare gene expression levels of both samples. B) Hierarchical cluster analysis 100 genes identified as showing differential regulation of 60 canine cancer specimens. Each column represents a different patient and each row represents a different gene. Blue represents increased expression and yellow represents reduced expression, relative to non-neoplastic cells. Despite being of the same tumor type, it is evident that these 60 cases of the same histological type have quite distinct gene expression profiles and associating these with response to therapy and survival will lead to more sophisticated cancer patient management.

A) aCGH data of a canine tumor sample using a 1Mb BAC array [24] indicates genome wide DNA copy number variation of 2,200 canine BAC clones. There is indication of copy number increase for regions of dog chromosomes (CFA) 6,9, 21 and 26 and evident of copy number decrease for segments of CFA 8, 19, 26 and 28. There is evidence of a homozygous deletion of a single BAC clone in the distal half of CFA 8 (circled). B) genome wide aCGH analysis of the same case on a high resolution oligonucleotide array, assessing copy number at 385,000 points in the canine genome and with an effective resolution of 50Kb. It is evident that the overall copy number aberrations visible in panel B are grossly comparable to those in panel A although additional copy number changes are evident that lay between the loci assessed on the BAC array. C) aCGH data specifically from CFA 8 of panel B); when the copy number data are evaluated at this resolution it is evident that the copy number aberration at the distal end of the chromosome may now be further refine to a region that spans fewer than 1.5 Mb between 45 Mb and 46.5 Mb (red lines). Interestingly, this higher resolution platform also identified a smaller deletion of less than 1 Mb at the proximal end of CFA8 within the region ~5.5 Mb-6.0 Mb. This deletion lay between BAC clones on the 1 Mb array and so was not detected in panel A.