Sequencing coverage and SNP Array 6.0 analysis reveal copy number variations in region with RAD21 mutations. (A) DNA sequence chromatograms of tumor and remission samples show tumor-specific frameshift mutations in RAD21: insertions */+TTAG (chr8: 117866622) and */+TT (chr8: 117866620) affecting 1 RAD21 allele in a patient with t(8;21)–positive CBF-AML. (B) Analysis of the coverage variation across the genome (indicated on the horizontal axis) reveals a gain of chromosome 8 (chr 8). The coverage of the tumor sample was normalized by subtracting the coverage of the remission sample; each point corresponds to the scaled and normalized median read number in a 300-bp-wide target region. (C) SNP 6.0 copy number variation analysis confirms the diagnosis-specific gain of chr 8 in the patient. Top line (in blue) indicates plot of chr 8 from diagnosis sample; and bottom line (in green) corresponds to chr 8 in matched remission sample. (D) Somatic nonsense mutation in exon 9 of RAD21 (chr8: 117864815, c.C1294T:p.Q432X) confirmed by Sanger DNA sequencing of tumor and remission samples in a patient with CK-AML. (E) Coverage variation indicates a gain of the long arm of chr 8. The plot is generated as described in panel B. (F) 250K SNP array analysis reveals the diagnosis-specific gain on the long arm of chr 8.