Nonsynonymous mutations detected by WES and amplicon sequencing. Nonsynonymous mutations detected by WES in (A) patient 2073 and (B) patient 2279. The first column shows gene symbols, the second column shows detected mutations. Mutations with homozygous variant allele frequencies are displayed in dark red. These include hemizygous mutations of PHF6, MED12, and CLDN34 on chromosome X and the mutation of a single RREB1 allele on chromosome 6 (the second RREB1 allele is completely lost because of a monoallelic deletion on 6p identified by SNP array; supplemental Table 6). Mutations with the heterozygous variant allele frequency are displayed in light red, and subclonal mutations with variant allele frequencies <15% are displayed in pink. Genes that are recurrently mutated in T-cell acute lymphoblastic leukemia are in bold. Mutated alleles that were detectable in the RNAseq data are marked in black. The positions of the remaining mutations that were not detected in the RNAseq data were either not covered at all or were covered by only a low number of reads (supplemental Table 5). (C) Levels of 6 different mutated WT1 alleles and of germline allele were determined by amplicon sequencing in patient 2279. The y-axis shows the proportion of mutated and/or germline reads within the total number of reads, which was set to 100%. M, myeloid subpopulation in patient 2073 and preT-myeloid subpopulation in patient 2279; T, preT subpopulation.