Genome-wide LOH analysis in JMML. The SNP array preparation is described in the legend to Figure 1. Genotypes were derived from the scanned array image using proprietary software (GCOS/GTYPE, Affymetrix) at default settings except for a more stringent cutoff level for equivocal genotypes (call confidence P-value <0.05 instead of <0.25 as preselected in the software). Genotype information was generated for 85 425–109 880 polymorphic markers in each sample. (Hybridization of sample D102 to the XbaI array failed; therefore, 45 654 HindIII SNPs were used for further analysis of D102.) Information on genomic position was missing for 851 SNPs; these SNPs were excluded from further analysis. Since paired constitutional DNA for each leukemia sample was not available, LOH was analysed through the statistical inference model implemented in dChip software (Lin et al., 2004). The inferred probability of LOH at 1955 SNP loci on chromosome 17 is displayed for JMML samples D003, D102, D115, D126 and D127. Each of the five samples was obtained from a patient with NF-1. Four of the five samples show LOH of a large segment on chromosome arm 17q. The genomic position of the NF1 gene is indicated with an arrow.