Clustering pattern based on gene expression and chromosome 21 copy number variation of iAMP21-ALL. (A) t-distributed stochastic neighbor embedding plot showing gene expression profiling of 1493 B-ALL samples, including 92 iAMP21-ALL samples. Each dot represents a sample. The top 1000 most variable genes (on the basis of median absolute deviation) were selected and processed by the t-distributed stochastic neighbor embedding algorithm with a perplexity score of 30. Eighty-seven cases clustered together, forming an iAMP21-ALL cluster. One carrier of rob(15;21)c with a tetraploid clone clustered with the ETV6::RUNX1 cases (SJALL062722), 1 typical case clustered with the ZEB2 plus CEBPE group (SJBALL030771), and 1 typical case with gains of chromosomes 14 and 21 clustered with high hyperdiploidy (SJBALL021031), whereas 2 cases were located within the DUX4 cluster. (B) Heatmap showing DNA copy number profiles of chromosome 21 derived from WGS data of 102 cases. The log₂ ratio of copy number was calculated based on the tumor and germ line samples for each case, with red and blue showing copy number amplification/gain and deletion, respectively. Each row represents a sample. The ideogram for chromosome 21 as well as GISTIC scores for copy number amplification and deletion is shown across the top. Subgroup information and the number of copies in the most highly amplified region (HighestCN) are shown on the left. The highlighted region between the 2 dashed lines represents the common region of gain derived from GISTIC analysis including all patients (32.8-40.6 Mb, between TIAM1 and HMGN1). RUNX1 is located within this common region. Typical 1 cases (n = 32) exhibit the deletion of the chromosome 21 sub-telomeric region without juxta-centromeric deletions. The size of the sub-telomeric deletions ranged from 0.1 Mb to 6.9 Mb. Typical 2 cases (n = 34) exhibit the deletion of both sub-telomeric and juxta-centromeric regions of chromosome 21. Typical 3 cases (n = 10) exhibit deletions of only juxta-centromeric regions.