Somatic coding variants differ between initial diagnosis and relapse
| Patient . | Age at diagnosis (y) . | Time to relapse (y) . | Germ line tissue available . | Presentation variants . | Relapse variants . | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| SNV/indel . | CDKN2A . | SV . | Noncoding . | SNV/indel . | CDKN2A . | SV . | Noncoding . | ||||
| P003 | 1 | 5 | Yes | AKT1 I447M, CNOT3 D218fs, GNB1 K89E, LEF1 T237fs, NF1 E1787G, PBRM1 S25P, PTEN R233fs, SMARCA4 K1365E | 68-kb HetDel | IL7R E47A, FAT1 N3678D, NOTCH1 Q2444∗, RB1 E693K | 137-kb HomDel | ||||
| P042 | 6 | 6 | No | IL7R T244fs, LEF1 Q80, NOTCH1 P2514fs, RPL22 L86H, USP7 A571fs | 1.9-Mb HomDel | t(7;11) (TRB-LMO2) | TAL1 intron 1 SNV | IL7R L242C, NOTCH1 Q2409fs, NOTCH1 L2408R, NOTCH1 F1592C, STAT5B D475N | 110-kb HomDel | t(11;14) (LMO2-TRA) | TAL1 intron 1 SNV |
| P044 | 5 | 6 | No | FBXW7 R609W, NOTCH1 Q2444∗, USP7 V256fs | 10-Mb HomDel | DNM2 G358R, MED12 Y204∗, NOTCH1 L1574P, NRAS G12D, U2AF1 E143K | |||||
| P046 | 12 | 6 | No | PTEN N228fs | 85-bp LMO2 intron 1 duplication TAL1 neo-enhancer | PTEN R233fs | 55-kb HomDel | STIL-TAL1 deletion | 85-bp LMO2 intron 1 duplication | ||
| P047 | 1 | 5 | Yes | ASXL1 G646fs, CNOT3 S245fs, FAT1 F3135L, IKZF1 V20fs, MED12 R2015K, NOTCH1 L1678P, PBRM1 K1373E, PHF6 N222fs, PTEN T319S, PTPRC L372P, STAT5B A529S, SUZ12 H620R | DNM2 I524T, DNMT3A M548V, EP300 M2227V, FBWX7 R393fs, FBWX7 L221P, JAK3 H962R, KMT2A I1393fs, KMT2D S1037P, MED12 L1446P, NOTCH1 L1678P, NOTCH1 S797P, NF1 L216P, NF1 L303P, PHF6 Y301H, PTPRC L834P, SETD2 K1020R, SMARCA4 L1035Q, SMARCA4 S1475G, TRRAP Y376C, ZFP36L2 S257G | 550-kb HetDel | |||||
| P048 | 6 | 7 | Yes | KMT2D Q3905L, NOTCH1 F1592S, USP7 D305H, WT1 P141del | 2.8-Mb HomDel | STIL-TAL1 deletion | 84-bp LMO2 intron 1 duplication | IDH2 N211S, NOTCH1 T2466fs | 800-kb HetDel | STIL-TAL1 deletion (alternative breakpoints) | 84-bp LMO2 intron 1 duplication |
| P049 | 2 | 6 | Yes | CREBBP Q3761A, FAT1 F3478S, KMT2D C3132∗, PTEN R233fs | 19-kb HomDel | 89-bp LMO2 intron 1 duplication TAL1 Neo-enhancer | ARID1A G655V, ATM T1985A, DNM2 N282D, KMT2A G3716A, PTEN M239_Y240insE, USP7 T592fs | 5-kKb HetDel | STIL-TAL1 deletion | 89-bp LMO2 intron 1 duplication | |
| Patient . | Age at diagnosis (y) . | Time to relapse (y) . | Germ line tissue available . | Presentation variants . | Relapse variants . | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| SNV/indel . | CDKN2A . | SV . | Noncoding . | SNV/indel . | CDKN2A . | SV . | Noncoding . | ||||
| P003 | 1 | 5 | Yes | AKT1 I447M, CNOT3 D218fs, GNB1 K89E, LEF1 T237fs, NF1 E1787G, PBRM1 S25P, PTEN R233fs, SMARCA4 K1365E | 68-kb HetDel | IL7R E47A, FAT1 N3678D, NOTCH1 Q2444∗, RB1 E693K | 137-kb HomDel | ||||
| P042 | 6 | 6 | No | IL7R T244fs, LEF1 Q80, NOTCH1 P2514fs, RPL22 L86H, USP7 A571fs | 1.9-Mb HomDel | t(7;11) (TRB-LMO2) | TAL1 intron 1 SNV | IL7R L242C, NOTCH1 Q2409fs, NOTCH1 L2408R, NOTCH1 F1592C, STAT5B D475N | 110-kb HomDel | t(11;14) (LMO2-TRA) | TAL1 intron 1 SNV |
| P044 | 5 | 6 | No | FBXW7 R609W, NOTCH1 Q2444∗, USP7 V256fs | 10-Mb HomDel | DNM2 G358R, MED12 Y204∗, NOTCH1 L1574P, NRAS G12D, U2AF1 E143K | |||||
| P046 | 12 | 6 | No | PTEN N228fs | 85-bp LMO2 intron 1 duplication TAL1 neo-enhancer | PTEN R233fs | 55-kb HomDel | STIL-TAL1 deletion | 85-bp LMO2 intron 1 duplication | ||
| P047 | 1 | 5 | Yes | ASXL1 G646fs, CNOT3 S245fs, FAT1 F3135L, IKZF1 V20fs, MED12 R2015K, NOTCH1 L1678P, PBRM1 K1373E, PHF6 N222fs, PTEN T319S, PTPRC L372P, STAT5B A529S, SUZ12 H620R | DNM2 I524T, DNMT3A M548V, EP300 M2227V, FBWX7 R393fs, FBWX7 L221P, JAK3 H962R, KMT2A I1393fs, KMT2D S1037P, MED12 L1446P, NOTCH1 L1678P, NOTCH1 S797P, NF1 L216P, NF1 L303P, PHF6 Y301H, PTPRC L834P, SETD2 K1020R, SMARCA4 L1035Q, SMARCA4 S1475G, TRRAP Y376C, ZFP36L2 S257G | 550-kb HetDel | |||||
| P048 | 6 | 7 | Yes | KMT2D Q3905L, NOTCH1 F1592S, USP7 D305H, WT1 P141del | 2.8-Mb HomDel | STIL-TAL1 deletion | 84-bp LMO2 intron 1 duplication | IDH2 N211S, NOTCH1 T2466fs | 800-kb HetDel | STIL-TAL1 deletion (alternative breakpoints) | 84-bp LMO2 intron 1 duplication |
| P049 | 2 | 6 | Yes | CREBBP Q3761A, FAT1 F3478S, KMT2D C3132∗, PTEN R233fs | 19-kb HomDel | 89-bp LMO2 intron 1 duplication TAL1 Neo-enhancer | ARID1A G655V, ATM T1985A, DNM2 N282D, KMT2A G3716A, PTEN M239_Y240insE, USP7 T592fs | 5-kKb HetDel | STIL-TAL1 deletion | 89-bp LMO2 intron 1 duplication | |
Mutations shared at diagnosis and relapse shown in bold. SV, structural variant; HetDel, heterozygous deletion; HomDel, homozygous deletion.