PTEN deletions in T-ALL. (A) Array CGH was performed with genomic DNA from diagnostic specimens collected from 47 children with T-ALL. The data are shown as a dChip plot of CGH segmented log₂ copy number ratios at the PTEN locus. The red box denotes the location of the PTEN coding sequence. White arrowheads point to cases with segmented log₂ copy number ratios of less than −0.5 involving the PTEN coding sequence. Two samples on which CGH was unsuccessful (T-ALL 36 and 37) were excluded from analysis. (B-D) Raw CGH data from representative patient samples. Red lines represent the segmented log₂ copy number ratio shown in panel A. (E-G) FISH analysis of representative cases confirmed the deletions identified by CGH. Orange, PTEN probe; green, centromere 10 probe. Images were obtained with an Axio Imager A1 fluorescence microscope (Carl Zeiss) using a 100× Alpha Apochromatic Plan oil-immersion objective (Carl Zeiss), a JAI CV-M4+CL progressive scan camera (JAI Inc), and Genus acquisition software version 3.92 build 7 (Genetix USA). Note that the Genus cytogenetic image acquisition software applies an automated “thresholding” algorithm that sets a signal intensity threshold below which any signal is considered background and thus excluded from the final composite image. During image acquisition, all images generated by the software were compared to the view from the microscope to confirm that they were fully representative. (B,E) Homozygous deletions had log₂ ratios of −1.26 (case 44) and −4.11 (case 45). Cells were available for FISH on case 44 and clearly showed homozygous loss of PTEN. (C,F) The CGH detection of a heterozygous deletion in case 34 (log₂ ratio, −0.54) correlated with the detection of PTEN deletion by FISH on 1 allele in 21% of the cells examined. (D,G) Case 21 retained both PTEN alleles intact by FISH and CGH.