LETTER TO THE EDITOR Analysis of BCR–ABL1 tyrosine kinase domain mutational spectra in primitive chronic myeloid leukemia cells suggests a unique mutator phenotype Leukemia advance online publication, 26 August 2010; doi:10.1038/leu.2010.179 Chronic myeloid leukemia (CML) is a clonal hematopoietic stem cell disorder characterized by a BCR–ABL1 fusion gene, usually resulting from a reciprocal t(9;22) translocation. 1 The identifica- tion of this abnormality led to the development of therapies that selectively inhibit the activity of the BCR–ABL1 tyrosine kinase (TK) oncoprotein. 2 Imatinib mesylate (IM), the first such inhibitor, has shown considerable effectiveness in chronic Drug Naïve Imatinib Resistant Upper & Lower Critical Values Number of mutations Number of mutations Expected Value Acceptance region 20 30 40 50 60 70 80 10 0 Number of Mutations 40 60 80 100 120 140 160 180 0 20 Codon Position Upper & Lower Critical Values Expected Value Acceptance region Number of Mutations Deviation from Expected No. of Mutations Drug Naïve, 1st Position Deviation from Expected No. of Mutations Drug Naïve, 2nd Position Deviation from Expected No. of Mutations Drug Naïve, Total G A C T A A G G T T C C to A to to T to A to A to G to G to T to T to C to C to G A C T A A G G T T C C 0 5 10 15 20 -10 -5 to A to G C to T T to C to T to C to C to T to A to G to A to G Deviation from Expected Number of Mutations Deviation from Expected Number of Mutations Deviation from Expected Number of Mutations Deviation from Expected Number of Mutations -5 0 5 10 15 20 -15 -10 to A to G to T to C to T to C to C to T to A to G to A to G Deviation from Expected Number of Mutations Deviation from Expected Number of Mutations 0 10 20 30 40 -20 -10 to A to G C to T to C to T to C to C to T to A to G to A to G Deviation from Expected No of Mutations Imatinib Resistant, 1st Position Deviation from Expected No of Mutations Imatinib Resistant, 2nd Position Deviation from Expected No of Mutations Imatinib Resistant, Total G to A A to G T to C A to T A to C G to C G to T T to A T to G C to A C to G t A t C T A A G G T T C C G to A A to G T T to C A to T A to C G to C G to T T to A T to G C to A C to G -15 -10 -5 0 5 10 15 20 -25 -20 -5 0 5 10 15 20 25 -15 -10 A to to to to to to to to to to to to G T C T C C T A G A G 10 -5 0 5 10 15 20 25 -20 -15 A G T C T C C T A G A G 1 3 2 1 3 2 Codon Position 1 3 2 to C to T G C C G Key Transitions - Purine Transitions - Pyrimidine Transversions NH Rejection Level Key Transitions - Purine Transitions - Pyrimidine Transversions NH Rejection Level Figure 1 Distribution of BCR–ABL1 TK domain mutations across codon positions in cells from IM-naı ¨ve and IM-resistant CML patients. (a) Assuming H 0 , the central dashed line shows the expected number of mutations at all three codon positions, the uniform lines show the upper and lower critical values of the test outside which H 0 is rejected, with the shaded area representing the acceptance region. The P-values corresponding to codon positions 1, 2 and 3 for the IM-naı ¨ve cell data are 0.0191, 1.1x10 7 and 1.5  10 22 , respectively, and for the IM-resistant cell data are 0.0158, 1.1  10 11 and 4.2  10 24 , respectively. (b) Comparative deviation of each mutation type from the expected frequency derived from unselected regions of the human genome. Transi- tions and transversions are shaded and the rejection levels of H 0 beyond which the observed numbers of mutations are deemed significant are represented by black dashed lines. Two-tailed tests were performed using a 5% cutoff to reject H 0 , in which n obs was significantly different from n exp . Critical test values were generated by a short program in Mathematica (Wolfram Research, http://www.wolfram.com/products/mathematica/index.html). The modified conditional rebalancing/reweighting P-value 9 was employed in the calculation of critical values to correct for asymmetry in the binomial distribution. Leukemia (2010), 1–5 & 2010 Macmillan Publishers Limited All rights reserved 0887-6924/10 www.nature.com/leu