Unexpected aCGH results. (A) Hidden unbalanced der(7)t(3;7) rearrangement in patient #22. Plots for chromosomes 3 and 7 reveal a 3q gain and 7q loss. Using a homebrew breakapart probe set for EVI1 (bottom right), metaphase FISH confirmed the presence of both EVI1/3q26.2 FISH signals on both chromosome 3 homologues and a single EVI1 (green) telomeric probe to the der(7) chromosome at band 7q21.3 (upper right). This patient also showed a "cryptic" RUNX1 deletion (not shown). (B) Non-contiguous CNAs of chromosome 7 resulted in four distinct deletions (one in 7p and three in 7q) in patient #15. The 7 centromere was detected by FISH but is not represented on the BAC array. Using a commercially available 7cen/7q31 FISH probe set, a normal FISH result was reported in this patient because the 7 centromere and 7q31 (arrow) were present in two copies. (C) Complex 12p aCGH plot in patient #15 with normal-appearing pair of chromosomes 12. The dup/del/dup 12p CNAs detected by aCGH were not visible by cytogenetics. I-FISH confirmed gain in 12p13.31 with RP11-433J6, deletion at 12p13.2 using RP11-36K5, and duplication of 12p12.1 using RP11-34A16.