Figure 4.

Identification of distinct subtypes of ALL through gene expression profiling. (A) Representative break-apart FISH for KMT2A::AFF1 fusion. The upper panel shows a cell with DNA FISH for KMT2A 5′ and 3′ showing 1 intact allele and 1 disrupted allele. The lower panel shows a second hybridization added on top of the first with AFF1 3′, which confirms disruption of KMT2A and fusion to AFF1 3′. (B) Illustration showing overexpression of CRLF2 and detection by flow cytometry. The image was created in Biorender (https://biorender.com/). (C) Schematic representation of NUTM1 rearrangements with multiple fusion partners and multiple breakpoints detected by WTS and visualized in ProteinPaint (https://proteinpaint.stjude.org/). Ex, exon. The approach in parenthesis (WGS) is alternative to WTS. (D) Integrative Genomics Viewer visualization of BCL11B Enhancer Tandem Amplification (BETA), observed in 20% of BCL11B-activated lineage ambiguous leukemia.¹⁶² (E) t-distributed stochastic neighbor embedding (t-SNE) representation from WTS data of B-ALL subtypes highlighted in different colors. Each dot represents a sample (N = 2004). Image is from Kimura et al.¹⁹¹