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Mullighan Lab > Supplemental Data

Genomic Landscape of Relapsed Acute Lymphoblastic Leukemia





Patient Sample type Lineage R1 RemTime R2 RemTime D Subtype D D Subtype 2 Evolution D unique Common D-R1 R1/S unique Lin Switch Result IgTCR HyperMT group HyperCNA Tumor after BMT
SJBALL006 D-G-R1 B 4.8 na B-other MEF2D Second Primary Tumor CDKN2A del MEF2D-BCL9 fusion RB1 del N Second Primary Tumor N N na
SJBALL013 D-G-R1-R2 B 4.3 2.1 nd nd Minor (D-R1), Major (R1-R2) CREBBP and ADD3 subclonal VPREB1, PAX5del, ETV6del EPOR (subclonal), CREBBP, RB1 and CDKN2A/B del Y, R=biphenotypic na N N na
SJBALL017 D-G-R1 B 6.4 na Ph-like P2RY8-CRLF2 Minor JAK1, PAX5 PAX3, PTCH1, P2RY8-CRLF2 JAK1, KRAS (subclonal), PAX5del, CDKN2A/B del N na N N no
SJBALL021924 D-G-R1 B 0.7 na Hyper nd Major None IKZF1del, PTCH1, ETV6, IKZF1 G183S, KRAS, CREBBP MLL2x2 sub, MLL3 sub N na N N na
SJBALL022426 D-G-R1 B 2.7 na B-other iAMP21 Minor SETD2 Few, none recurrent PICALM, IKZF1, CDKN2A/B N Clonally related major clone N N no
SJBALL022427 D-G-R1 B 2.8 na Ph-like nd Minor SOCS3 VPREB1, PAX5, ETV6, CDKN2A/B dels; FGFR1 and DDX6 muts ETV6del homo, EBF1 amp, PAX5-TP63 fusion N na N N na
SJBALL022428 D-G-R1 B 0.3 na B-other nd Polyclonal TP53 sub becomes clonal; CCND3 TP53, B2M, DDX3X, BCL6, BTG1 (multiple), TCF3 (multiple) TP53 N na Y, Diagnosis N na
SJBALL022429 D-G-R1 B 4.5 na DUX4 nd Minor None unique; TP53 sub becomes clonal VPREB1, IKZF1 dels; NRAS G13V, IGH-DUX4 fusion TBL1XR1 del N na N N no
SJBALL022430 D-G-R1 B 7.2 na DUX4 nd Minor MLL2, FLT3 IKZF1, ARID2 dels, IGH-DUX4 fusion AKAP9; MLL2x2 sub N na N N no
SJBALL022431 D-G-R1 B 3.7 na Ph-like P2RY8-CRLF2, iAMP21 Major FLT1 VPREB1, BTG1 dels; ATM, ABL1, ELF4, P2RY8-CRLF2 fusion NR3C1, CDKN2/B CNA; CHEK2, ROS1 N na N Y no
SJBALL022432 D-G-R1-R2 B 2.9 6.8 Ph-like P2RY8-CRLF2 Minor (D-R2) None VPREB1, IKZF1, ETV6, CDKN2A/B CNA; CREBBP, P2RY8-CRLF2 fusion nd N na Y, Group 2 N na
SJBALL022477 D-G-R1 B 3.3 na Hyper nd Minor None ARID5B del; PDGFRA CREBBP N na N N no
SJBALL022478 D-G-R1 B 1.9 na MLL Ph-like Minor IL7R sub (lost); NRAS (rises) VPREB1, PAZ5, IKZF1, CDKN2A/B, KMT2A-TNS3;IKZF1-KMT2A;TNS3-IKZF1 fusions NRAS now clonal; DDX3X N na N N na
SJBALL022479 D-G-R1 B 4.3 na Ph-like nd Minor LEF1 del, U2AF1 IKZF1, EBF1 dels; H3F3B mut; PAX5-JAK2 fusion SLX4IP, FHIT and ETV6 del; QKI and ADAR mut N na N N na
SJBALL022480 D-G-R1 B 2.1 na Ph nd Polyclonal ERG sub, rises MLLT6 MED12, MECOM; MLLT10 and KDM6B (sub) N na N N no
SJBALL022481 D-G-R1 B 3.2 na Hyper nd Minor CDKN2A/B, ADD3 del; PTPRT, CREBBP falls, CREBBP and MLH3 rise None clonal KRAS, ALK, SETD2, NCOR2, PBX1 N na N N na
SJBALL022482 D-G-R1-R2 B 3.3 0.3 B-other TCF3-HLF Minor (D-R1), Minor (R1-R2) RB1, PAX5, BTG1 delns BRD4, TCF3-HLF fusion VPREB1, PAX5, APC2, RB1 CNAs; TBL1XR1, MEF2C, HLF muts sub, become clonal at R2; DMD (lost) N Clonally related minor clone D->R1; Clonally related major clone R1 ->R2 N N na
SJBALL022483 D-G-R1-R2 B 4.2 2.1 Hyper nd Polyclonal (D-R1), Polyclonal (R1-R2) FOXO1, RET sub, rise; NRAS, HOXA11, ROS1, ALK fall PAX5del, ARID5Bdel KRAS sub falls, CDKN2A/B 2copy del N na Y, Diagnosis N na
SJBALL022484 D-G-R1 B 4.8 na Ph-like CRLF2 high Minor none recurrent SLX4IP, IKZF1 del IKZF1 del homo, RB1, NF1, CDKN2A/B del; NF1 homo N na N N no
SJBALL031 D-G-R1-S B 7.9 1.1 nd nd Major (D-R1) FLT3 falls VPREB1, RN1, ETV6 dels; EZH2, CDKN2A, PTPN11 NF1, CDKN2A/B del; FANCC mut; TCF3-ZNF384 fusion Y, R= biphenotypic S=AML na N N S, not in study
SJBALL032 D-G-R1 B 3.4 na Ph-like PAX5amp Major None recurrent (MAU2) PAX5amp, CDKN2A/Bdel, PAX5fs, BCL3, NRAS, MN1 RUNX1, MEF2C, BTLA del N na N N na
SJBALL036 D-G-R1 B 4.0 na B-other ETV6-RUNX1-like Minor NF1, IKZF1 dels; TSC2, CREBBPx3 sub that rise; ETV6-EXTL1 fusion RAG1, PAX5, ETV6, ADD3 dels; ETV6-SRRM1 fusion IKZF1 del homo N na N N no
SJBALL074 D-G-R1 B 5.1 na nd nd Minor CDKN2A/B del; KRAS sub x2, fall BRCA2, ZEB2 SNV NR3C2 CNA; KRAS, TBL1XR1 clonal SNVs N na N N no
SJBALL113 D-G-R1-R2 B 4.3 1.3 B-other nd Polyclonal (D-R1), Polyclonal (R1-R2) FANCA SNV sub at D and R1, clonal R2 PAN3del, VPREB1del ATF7IP, TCF3 clonal R1 and R2; PTEN, RUNX1 SNV sub at R1 and fall. Y, R2=biphenotypic Clonally related major clone D->R1; Clonally related minor clone R1->R2 Y, Group 1 N no
SJBALL182 D-G-R1 B 5.7 na B-other ZNF384 Minor NF1 del; NF1 and MLL2 SNVs sub and fall IKZF1, BTLA CNA, TAF15-ZNF384 fusion VPREB1 and CDKN2A/B del N na N N na
SJBALL192 D-G-R1-R2 B 0.5 0.3 B-other nd Minor (D-R1), Minor (R1-R2) PTPN11 and XPO1 sub rise CDKN2A/B 2 copy del; PAX5 biallelic, IL7R NT5C2 (lost R2) N na N N na
SJBALL199 D-G-R1 B 1.0 na DUX4 nd Major PAX5 SNV sub falls; IGH-DUX4 fusion ETV6 del; NR3C1 SNV VPREB1 del; FGFR1, BCL9, P2RY8 SNV sub N na N N R1
SJERG003 D-G-R1 B 5.3 na DUX4 nd Minor NRAS, NF1x2, KLF4 SNV sub fall; IGH-DUX4 fusion IKZF1 del; VPREB1, ERG, CDKN2A/B del; HNRNPA2B1, KIT SNV N na N N na
SJERG009 D-G-R1 B 3.3 na DUX4 nd Minor NRAS SNV sub falls; NRAS SNV sub stays sub, RAD21 sub rises VPREB1, CDKN2A/B, ARID2 del, IGH-DUX4 fusion IKZF1, APC2 del; IKZF1, NR3C2 SNV sub N Clonally related major clone N N no
SJERG023 D-G-R1 B 5.9 na DUX4 nd Major ERG, CDKN2A/B, ARID2 del; U2AF1, PIK3CA SNV fall None recurrent RB1, ERG, ARID2 del; FAM58A, FUS, MLL SNV clonal N Clonally related major clone N N na
SJERG025 D-G-R1 B 9.9 na DUX4 nd Major MLL2 SNV falls IKZF1, ERG del MLL2 NCOR2 clonal N Clonally related minor clone N N no
SJETV010 D-G-R1-R2 B 0.6 0.3 ETV6-RUNX1 nd Polyclonal (D-R1), Polyclonal (R1-R2) ARID2, CCND3 SNV sub fall; ETV6-RUNX1 fusion VPREB1, TBL1XR1, RAG1, FHIT, CDKN2A/B dels; KDM5C SNV, ETV6-RUNX1 fusion NR3C1x2, CTCF, PTEN, TP53 SNV clonal persist to R2; many SNV sub low MAF and increase MAF but stay sub at R2 e.g. GATA3 N na Y, Group 1 N na
SJETV043 D-G-R1 B 3.3 na ETV6-RUNX1 nd Minor None recurrent VPREB1, TBL1XR1, SLX4IP, NR3C1, FHIT, CDKN2A/B, BTLA, BTG1, ATF7IP del; ETV6-RUNX1 fusion RAG1 del; PTPN11 and MLLT4 SNV clonal N na N Y no
SJETV047 D-G-R1-R2 B 8.1 2.6 ETV6-RUNX1 nd Major (D-R1), Minor (R1-R2) Multiple SNV lost, ZNF697 sub rises ROR1 SNV, ETV6-RUNX1 fusion NR3C1 del; PER1 SNV N Clonally related minor clone D->R2; R1 sample failed N N no
SJETV048 D-G-R1 B 4.2 na ETV6-RUNX1 nd Minor CDKN2A/B del; SETD2, NRAS sub fall VPREB1, PAX5, ATF7IP, ADD3 dels; ATF7IP SMV SLX4IP, CDKN2A/B, BTG1 del; ZNF384, CREBBBP, EP300, FAT3 SNV clonal; ETV6-RUNX1, P2RY8-CRLF2, RUNX1-APOLD1, RUNX1-DDX47 fusions N na Y, Group 2 N na
SJETV138 D-G-R1 B 4.2 na ETV6-RUNX1 Hyper Minor VPREB1 del; multiple non-recurrent fall and sub rise TBL1XR1, SLX4IP, NF1 del; GRIN2A SNV Multiple non-recurrent N na N N no
SJHYPER009 D-G-R1 B 4.1 na Hyper nd Major None No R CNA data; NRAS None N na N N na
SJHYPER017 D-G-R1 B 4.5 na Hyper nd Minor MLL2 SNV sub rises; ERBB4 SNV sub falls CDKN2A/B del; NRAS SNV TP63 N na N N no
SJHYPER021925 D-G-R1 B 4.0 na Hyper nd Major GC, CXCR3 SNV sub fall PAX5, CDKN2A/B del; FLT3, CREBBP, PDGFRA SNV EVI5 SNV N na N N na
SJHYPER021999 D-G-R1 B 4.0 na Hyper nd Minor CDKN2A/B del; NRAS and KRAS sub rise; NRAS sub falls CREBBP, ARID5B, HNRNPA2B1, CHD4 SNV CDKN2A/B del; TLX3 SNV. N na N N na
SJHYPER022 D-G-R1 B 2.5 na Hyper nd Minor KRAS SNV sub rises at R, NRAS clonal falls CREBBP (LOH at R) MSH6 SNV sub N na Y, Group 1 N no
SJHYPER022423 D-G-R1 B 8.8 na Hyper nd Major None recurrent MET, NRAS, APC2, PLAG1x2 SNVs; CREBBP SNV LOH at R CTCF, PIK3CA N na Y, Diagnosis N na
SJHYPER022424 D-G-R1 B 7.0 na Hyper nd Major FLT3, ERG SNV sub fall None recurrent ETV6 SNV clonal; TCF7L2, NRAS sub N na N N na
SJHYPER027 D-G-R1-R2 B 4.4 2.1 Hyper nd Major (D-R1), Major (R1-R2) None recurrent TRRAP SNV CDKN2A/B del N na Y, Preserved N na
SJHYPER098 D-G-R1 B 1.3 na Hyper nd Minor IKZF1 del; NRASx2 1 clonal 1 sub fall CDKN2A/B del; SETD2 SNV IKZF1 del; BCL11A, NT5C2 SNV N na N N no
SJHYPER127 D-G-R1 B 1.8 na Hyper nd Minor WHSC1 and BCL11A SNV sub rises, PMS1 SNV sub falls NR3C1, BTLA del Mant SNV absent at D: BCL11A, KLF6, EZH2, CDKN2A… N na Y, Group 3 N R1
SJHYPO117 D-G-R1-R2 B 1.2 0.5 Hypo iAMP21 Polyclonal (D-R1), Polyclonal (R1-R2) CREBBP sub falls PML, CREBBP None N na Y, Group 1 N R2
SJHYPO126 D-G-R1 B 0.4 na Hypo nd Polyclonal FANCA, BCL11A SNV low MAF, rise at R; ETV6-HBB fusion IKZF2 del TET1, MLLT1 SNV N na Y, Group 4 N no
SJHYPO146 D-G-R1-R2 B 5.0 0.6 Hypo Ph-like Polyclonal (D-R1), Polyclonal (R1-R2) PAX5 sub falls PLAG1, CREBBP and NF1 rises None N na Y, Group 4 N R2
SJINF001 D-G-R1 B 2.6 na MLL INF Minor None recurrent KRAS SNV; KMT2A-AFF1 fusion IL21R, NR3C2 SNV UTR N na N N na
SJINF002 D-G-R1 B 2.8 na MLL INF Minor None recurrent KMT2A-AFF1 fusion APC2 del; PAX5 SNV N na N N no
SJINF003 D-G-R1 B 0.8 na MLL INF Minor KMT2A-AFF1 fusion None recurrent RPL22 SNV sub N Clonally related minor clone N N no
SJINF060 D-G-R1 B 1.1 na MLL INF Major None recurrent KMT2A-MLLT1 fusion; ID2-IGK fusion PICALM del; WHSC1, CREBBPx2 SNV; SERINC3-ZCCHC7 fusion , CREBBP-DNAJA3 fusion N na N N na
SJINF061 D-G-R1 T 0.8 na TALL INF Minor KRAS SNV sub rises at R ; BICD2-JAK2 fusion PICALM CNA TBX3 SNV sub N na N N na
SJINF065 D-G-R1 B 0.5 na MLL INF Minor TBA TBA KMT2A-AFF1, AFF1-BSX fusions N na N N no
SJINF068 D-G-R1 B 0.3 na MLL INF Major TBA KMT2A-AFF1 fusion TBA N na N N no
SJINF073 D-G-R1 B 0.3 na MLL INF Minor TBA KMT2A-MLLT3 fusion, JMJD1C-TSN fusion TBA N na N N no
SJMLL006 D-G-R1 B 1.6 na MLL nd Major KRAS SNV clonal falls; KMT2A-AFF1 fusion CDKN2A/B del CDKN2A/B del; KDM6A SNV N na N N R1
SJMLL022031 D-G-R1-R2 B 1.2 0.7 MLL nd Major (D-R2) KMT2A-MLLT1 fusion IKZF1 del nd N na N N R2
SJMLL026 D-G-R1 B 0.5 na MLL nd Minor IKZF1 del; IL9R SNV sub falls ERG SNV, KMT2A-AFF1 fusion IKZF1, CDKN2A/B del; RUNX1 SNV sub; ZEB2-TXLNG fusion, NR3C1-TMEM241 fusion N na N N na
SJMLL039 D-G-R1 B 1.2 na MLL nd Major HLF SNV sub falls KMT2A-AFF1 fusion TP53, RUNX1T1 SNV clonal N na N N na
SJPHALL002 D-G-R1 B 2.5 na Ph nd Minor None recurrent (IGF2BP1 defines minor clone) PAX5, IKZF1, CDKN2A/B del; CCNE1 SNV sub MTOR SNV sub N na N N R1
SJPHALL005 D-G-R1 B 4.5 na Ph HYPER Precursor None BCR-ABL1 fusion? RUNX1, NCOR1 SNV clonal; BCORL1, RUNX1 SNV sub Y, R=biphenotypic Second Primary Tumor N N na
SJPHALL013 D-G-R1 B 2.9 na Ph nd Minor None recurrent (CDH7 defines minor rising clone); BCR-ABL1 fusion VPREB1, SLX4IP, MEF2C, CDKN2A/B, BTLA, ABI1 CNA; SPOP SNV None recurrent N na N N na
SJPHALL018 D-G-R1 B 1.2 na Ph nd Minor SLIT3 SNV sub rises VPREB1, IKZF1, CDKN2A/B del PRDM1 SNV sub N na N N na
SJPHALL020 D-G-R1 B 0.7 na Ph nd Major BCR-ABL1 fusion TBA TBA N na N N na
SJPHALL022425 D-G-R1 B 2.6 na Ph nd Precursor Multiple but none recurrent all fall IKZF1 different lesions; BCR-ABL1 fusion?, MAGIX SNV clonal Multiple non-recurrent N Second Primary Tumor N N no
SJPHALL029 D-G-R1-S B 3.3 0.8 Ph nd Minor (D-R1) Multiple SNV sub fall none recurrent; BCR-ABL1 fusion IKZF1, CDKN2A/B del; multiple SNV none recurrent VPREB1 del; multiple SNV none recurrent N na N N S, not in study
SJTALL001 D-G-R1-R2 T 1.1 1.0 ETP nd Minor (D-R1) ETV6 del; PTPN11, KRAS, ATF7IP SNV sub rise; FNBP1 + other SNV fall; MED14-HOXA9 fusion, ABCC9-ITPR2 fusion None recurrent CEBPA SNV clonal, NT5C2 subclonal (not at D) Y, R1=biphenotypic na N N R2
SJTALL003 D-G-R1 T 0.8 na ETP nd Minor IL7R, FBXW7x2, NOTCH1 SNV sub lost CDKN2A/B del; GATA3, PAX7, FBXW7x2, NOTCH1 RUNX1 SNV clonal N na N N na
SJTALL007 D-G-R1 T 3.0 na ETP nd Minor JAK3, EP300, KDM6A, NOTCH1x2 SNV sub fall; IL7R, NOTCH1 SNV sub rise CDKN2A/B del; GATA3, ECT2L SNV KDM6A, NT5C2 SNV clonal; NT5C2 SNV sub N na Y, Preserved N na
SJTALL008 D-G-S T 2.4 na ETP nd Polyclonal None recurrent SMARCA4, NRAS SNV clonal None recurrent Y, S=AML na N N S
SJTALL013 D-G-R1 T 6.2 na ETP nd Minor DNM2, EZH2, NOTCH1x2, JAK1x2 SNV sub fall; NOTCH1 SNV sub low MAF rise PHF6, DNM2 SNV Many, none recurrent N na N N no
SJTALL023 D-G-R1-R2 T 1.9 0.5 TALL nd Polyclonal (D-R1), Polyclonal (R1-R2) FOXP1 sub becomes clonal at R2 CDKN2A/B 2 copy del MSH2 2 copy del, many key genes that rise and fall N na Y, Group 3 Y R2
SJTALL045 D-G-R1 T 1.7 na TALL nd Major QKI SNV clonal persists, NOTCH1, BCL11B, MTOR, ERCC4 clonal and fall LEF1, CDKN2A/B del NRAS SNV clonal; NT5C2, NOTCH1x2, NR3C1, SMARCA4 SNV sub N na N N no
SJTALL049 D-G-R1-S T 8.5 5.6 TALL TAL1 Precursor (D-R1), Second Primary Tumor (R1-S) CDKN2A 2 copy del, CDKN2Bdel; PTENx2, AUTS2, PAX5 SNV fall STIL del? LEF1del, CDKN2A/B 2 copy del, RB1 SNV sub Y, S=CML Second Primary Tumor 2x N N na
SJTALL050 D-G-R1-R2 T 0.7 0.6 TALL TLX3 Minor (D-R1) NOTCH1 SNVx2 sub fall TLX3, CDKN2A/B CNA; WT1x2, DNM2 SNV clonal MYB gain N na N N R2
SJTALL054 D-G-R1 T 2.9 na TALL nd Minor BCL11B, WT1x2 SNV minor fall VRPEB1, CDKN2A/B del; WHSC1, PHF6, NOTCH1, AKT1, DNM2 SNV clonal MLL, ETV6 gain N na N N na
SJTALL055 D-G-R1 T 1.2 na TALL nd Major TCF3 SNV sub fall None recurrent NOTCH1, PDGFB, CREBBP, TERT, HNF1A SNV clonal N Clonally related major clone N N na
SJTALL057 D-G-R1 T 1.8 na TALL TAL1 Polyclonal PTEN SNVx2 clonal fall; several non-recurrent sub rise to be clonal STIL, CDKN2A/B del; MN1 Many SNV, biallelic MSH2 N na Y, Group 3 N na
SJTALL058 D-G-R1 T 4.7 na TALL nd Minor IL7R clonal SNV fall CDKN2A/B IKZF1 del; FANCA, ITK SNV; WT1 homo, NRAS N na N N no
SJTALL091 D-G-R1 T 1.9 na TALL nd Minor Multiple non-recurrent SNV fall NOTCH1, U2AF1, PTCH1, PTPN11, STAG2, KRAS, ETV6, RPL5, ARID1A (clonal) WT1 and SRSF3 (sub) Highest MAF clone none recurrent; 2nd highest RARA, SH2B3, 3rd ROS1, 4th none recurrent. N na Y, Group 2 N na
SJTALL092 D-G-R1 T 1.6 na TALL nd Major MYCN, ATRX SNV clonal lost, NOTCH1, PLCG1 SNV sub lost CDKN2A/B del; ZFHX3 SNV clonal Many SNV none recurren N na N N na
SJTALL093 D-G-R1 T 0.4 na TALL nd Polyclonal None recurrent CDKN2A/B del, NCOA4, IKZF1, STAT5B, LIFR SNV None recurrent N na N N na
SJTALL094 D-G-R1 T 1.3 na TALL nd Major None recurrent CDKN2A/B del; ROS1, PAX3, BRD4 SNV None recurrent N na N N na
SJTALL098 D-G-R1 T 1.0 na TALL nd Polyclonal FBXW7 SNV fall RUNX1 del; JAK3, TP53, LRPB1, LZTR1, NOTCH1 SNV None recurrent N na N N na
SJTALL124 D-G-S T 1.2 na TALL nd Minor NOTCH1x2 SNV fall CDKN2A/B del, TP53, KIT, DDX3X, FUS SNV None recurrent Y, S=AML na N N na
SJTALL139 D-G-R1-R2 T 2.7 1.0 TALL TAL1 Major (D-R1), Minor (R1-R2) CTCF, MYC, NOTCH1, FAT4 SNV sub fall STIL, CDKN2A/B del SF3B1, SMARCA4, LEF1 SNV, lost at R2 N na Y, Group 4 N R2
SJTALL142 D-G-S T 2.4 na TALL nd Second Primary Tumor CDKN2A/B del, MTOR, CCND3 SNV fall SIRT2 KRAS SNV sub Y, S=AML Second Primary Tumor N N no
SJTALL152 D-G-R1 T 0.9 na TALL TAL1/TLX3 Polyclonal FAT4, FBXW7, NOTCH1x2, IL7R fall TLX3, STIL, CDKN2A/B del; FBXW7 SNV NT5C2 sub N na N N na
SJTALL161 D-G-R1 T 1.9 na ETP nd Minor None NF1 del; ETV6, NRAS, NOTCH1, FAT4, CCND3, PHF6, XPO1 SNV BTG1 N na N N R1
SJTALL164 D-G-S T 1.5 na ETP nd Major None recurrent NF1, ATF7IP None recurrent Y, S=AML na N N no