LEF1 microdeletions and truncating mutations are recurrent genetic alterations in T-ALL. Array CGH was performed on genomic DNA from diagnostic specimens collected from 47 children with T-ALL. (A) dChip plot of the segmented CGH log₂ copy number ratios at the LEF1 genomic locus. Recurrent microdeletions involving LEF1 and no other known genes were identified in 5 (11%) of the 47 primary T-ALL samples. Note that cases 36 and 37 were excluded because CGH quality controls failed. (B-D) Raw CGH log₂ copy number ratio data (black dots) shown for 3 representative cases, together with the genomic location of LEF1 exons. The segmented data plotted in panel A are shown as red lines. The y-axis is log₂ of the copy number ratio (0 = no copy number change). (E) Sequencing of LEF1 genomic coding sequence identified heterozygous nonsynonymous sequence alterations in 3 (7%) of the 44 T-ALL cases analyzed. Black arrowheads denote the location of predicted truncating mutations, whereas the white arrowhead denotes the missense mutation identified. (F) Sequence chromatograms for representative mutant and wild-type samples, showing the presence of a heterozygous frameshift mutation in sample T-ALL 13.