ATMKO.CD3εKO B-cell lymphomas exhibit chromosomal instability and a gain of a 4.48-Mb region on MMU18. (A) SKY image of a metaphase chromosome spread prepared from an early-passage (6 weeks) ATMKO.CD3εKO B-cell lymphoma (16508) identifies structural and numerical aberrations, including deletions (MMU6 and MMU12), unbalanced translocations [T(14;6), T(15;1), T(16;18;14), and T(19;1)], and an aberrant MMU18 with an amplified homogeneous staining region (Hsr). (B) SKY images from 3 ATMKO.CD3εKO tumors (39317 and 180764 (left) and 141645 at day 0 and early passage (right) provide examples of structural aberrations that contributed to copy number gains of MMU18 sequences in these tumors. Metaphase images (15 per sample) of day 0 (n = 5) and early-passage tumors (n = 11) were collected at room temperature using a Leica DMRBE epifluorescence microscope fitted with a charge-coupled device camera, a 63× oil-immersion lens, and SpectraCube SD200 acquisition software (Applied Spectral Imaging). Analysis was performed using SKYview software (Applied Spectral Imaging). Array CGH analysis of genome-wide copy number alteration changes in day 0 (n = 9) (C) and early-passage (n = 12) ATMKO.CD3εKO tumors (D) using Nexus Copy Number software (BioDiscovery). Identification of the minimal region of genomic amplification on MMU18 (black arrow) that is present in day 0 (n = 9) (E) or early-passage (n = 12) samples (F). Copy number alteration gains are to the right of the chromosome (blue) and losses are to the left (red). (G) Gene expression profiling from Figure 3 was mined for the expression of genes found in the recurrent amplicon on MMU18 in these B-cell tumors. Relative differences in expression are indicated by the color bar; * indicates a technical replicate of that sample.