Figure 3

Classification of ALL samples with undefined cytogenetic subtypes. (A) Each sample (n = 210) is represented as a vertical bar positioned in its corresponding subtype ‘track’ according to its allocation by the classifier. The color key to the right of panel (A) shows the estimated subtype probability scores. Probability scores <0.5 are not shown. (B) The distribution of probability scores ≥0.5 in the 210 patients. Eighty-three patients were not classified, 106 patients were unequivocally assigned to one subtype, 17 patients were classified into multiple subtype groups, and four patients had high reference scores. (C) The distribution of the number of patients with ‘normal’, ‘no result’, and ‘non-recurrent’ karyotypes into subtype-groups. The subtype distribution in the known sample group is also shown. (D) Hierarchical clustering of the original 546 ALL patients of known subtype and the patients newly classified as one unequivocal subtype (n = 106). Patients are clustered on the horizontal axis and the 215 autosomal subtype-specific consensus CpG sites are clustered on the vertical axis and color-coded by subtype classifier. The darker color indicates samples with previously established cytogenetic subtype, and the corresponding lighter color and asterisk (*) indicates newly classified samples. The color key for the patient samples is shown to the left of the heatmap. In the heatmap, blue indicates low and red indicates high methylation levels. (E) Hierarchical clustering and heatmap of the ALL patients of known subtype (n = 546), those newly classified and unequivocally assigned to one subtype (n = 106), patients without classification (n = 83, gray), and patients classified into multiple subtypes (n = 17, black). Four patients with suspected low blast count are not shown.