Table 2.
Proposed BCP ALL subgroups based on gene expression and gene fusion/sequence mutation patterns
| RNA-seq data-based subgroups | Frequency in the study cohort (n = 1,223), no. of patients (%) | Most frequently mutated genes (%) |
| MEF2D fusions (G1) | 39 (3) | MEF2D–BCL9 (67), MEF2D–HNRNPUL1 (21), NRAS (13), KMT2A (10) |
| TCF3–PBX1 (G2) | 76 (6) | TCF3–PBX1 (100), TP53 (8) |
| ETV6–RUNX1/–like (G3) | 161 (13) | ETV6–RUNX1 (82), WHSC1 (9), KRAS (7), NRAS (6) |
| DUX4 fusions (G4) | 63 (5) | DUX4–IGH (78), NRAS (30), MYC (11), TP53 (11), PTPN11 (11), KMT2D (11), CTCF (8), FLT3 (8), PAX5 (8) |
| ZNF384 fusions (G5) | 74 (6) | EP300–ZNF384 (53), TCF3–ZNF384 (12), TAF15–ZNF384 (11), SMARCA2–ZNF362 (4), NRAS (14), KRAS (12), |
| FLT3 (14), PTPN11 (14), SETD1B (9), ZEB2 (8), EZH2 (8), KMT2D (7) | ||
| BCR–ABL1/Ph–like (G6) | 167 (14) | BCR–ABL1 (31), IGH–CRLF2 (10), JAK2 fusions (10), ABL1 fusions (7), IGH–EPOR (7), P2RY8–CRLF2 (5), KRAS (6), JAK2 (7), RUNX1 (5) |
| Hyperdiploidy (G7) | 408 (33) | NRAS (19), KRAS (18), FLT3 (13), PTPN11 (8), KMT2D (7), CREBBP (6) |
| KMT2A fusions (G8) | 56 (5) | KMT2A–AFF1 (29), KMT2A–MLLT1 (25), KMT2A–MLLT3 (13), KRAS (13), NRAS (14), FLT3 (7) |
| PAX5 and CRLF2 fusions (G9) | 111 (9) | P2RY8–CRLF2 (12), PAX5–NOL4L (8), PAX5–AUTS2 (6), NRAS (23), KRAS (23), PAX5 (12), FLT3 (11), JAK1 (8) |
| PAX5 (p.P80R) mutation (G10) | 23 (2) | PAX5 (96), PTPN11 (26), NRAS (22), KRAS (17), FLT3 (13), IL7R (9), SETD2 (9) |
| IKZF1 (p.N159Y) mutation (G11) | 6 (<1) | IKZF1 (100), KRAS (17), KMT2D (17) |
| ZEB2 (p.H1038R)/IGH–CEBPE (G12) | 8 (<1) | ZEB2 (75), NRAS (62), KMT2D (25), KRAS (12), KMT2A (12), CDKN2A (12) |
| TCF3/4–HLF (G13) | 11 (<1) | TCF3/4–HLF (64), KRAS (18), NRAS (9), ZEB2 (9), ASXL2 (9) |
| NUTM1 fusions (G14) | 20 (2) | NUTM1 fusions (30), TP53 (15), KRAS (10), CREBBP (15), KMT2D (10), SETD1B (10) |