Table 3

Copy number gain lesions detected by SNP-A and affected candidate genes (N = 26)

Patient no.DiseaseChromosomeStartStopLength, MbAffected candidate genes
40 Myeloid BP 1p22.2p13.3 90311409 107802971 17.49 HFM1, CDC7, TGFBR3, BRDT, GLMN, RPAP2, GFI1, EVI5, PTBP2, DPYD, SNX7, AGL, VCAM1, EXTL2, DPH5 
44 Myeloid BP 1q21.2q44 148187512 247169378 98.98 VPS45, APH1A, ECM1, MCL1, ENSA, ARNT, SETDB1, GABPB2, PIP5K1A, PI4KB, TCHH, PGLYRP4, ILF2, INTS3, IL6R, MUC1, ARHGEF2, CD1, SLAMF6, ATF6, NOS1AP, DDR2, NUF2, PBX1, MPZL1, NME7, PRRX1, RABGAP1L, FmABL2, MR1, DHX9, EDEM3, HMCN1, UCHL5, TROVE2, KCNT2, ASPM, CRB1, PTPRC, NR5A2, PKP1, PTPN7, PTPRV, LGR6, PPP1R12B, JARID1B, BTG2, SOX13, MDM4, PCTK3, ELK4, SRGAP2, IKBKE, RASSF5, MAPKAPK2, IRF6, TRAF5, RD3, PTPN14, USH2A, RRP15, TGFB2, DUSP10, TLR5, TP53BP2, FBXO28, WDR26, WNT9A, NUP133, ARID4B, CEP170, AKT3, SMYD3, AHCTF1, NLRP3 
40 Myeloid BP 1q25.3q41 183864117 218274672 34.41 HMCN1, UCHL5, TROVE2, KCNT2, ASPM, CRB1, PTPRC, NR5A2, PKP1, PTPN7, PTPRV, LGR6, PPP1R12B, JARID1B, BTG2, SOX13, MDM4, PCTK3, ELK4, SRGAP2, IKBKE, RASSF5, MAPKAPK2, IRF6, TRAF5, RD3, PTPN14, USH2A, RRP15, TGFB2 
23 AP 2q33.1q37.3 202918925 242678246 39.76 NRP2, FASTKD2, IDH1, IKZF2, IGFBP2, USP37, WNT6, PTPRN, EPHA4, PAX3, CUL3, PID1, FBXO36, PSMD1, ECEL1, GIGYF2, INPP5D, USP40, SH3BP4, MLPH, HES6, HDAC4 
27 AP 6q11.1q12 61949077 63513069 1.56 KHDRBS2 
34 Myeloid BP 8 166818 146263890 146.1 Trisomy 8 
44 Myeloid BP 8 166818 146263890 146.1 Trisomy 8 
40 Myeloid BP 8 166818 146263890 146.1 Trisomy 8 
40 Myeloid BP 9q34.12q34.3 132658747 140164310 7.51 ABL1, MED27, SETX, TTF1, DDX31, VAV2, NOTCH1 
19 AP 9q34.12q34.3 132672428 140164310 7.49 ABL1, MED27, SETX, TTF1, DDX31, VAV2, NOTCH1 
25 AP 10q11.21 43543186 44823480 1.28 CXCL12, RASSF4 
36 Myeloid BP 11p15.2p12 13226368 43097900 29.87 SOX6, PTPN5, BBOX1, LGR4, METT5D1, ELP4, PAX6, WT1, HIPK3, COMMD9, TRAF6 
25 AP 15q21.1 43920344 46958155 3.04 SEMD6D, DUT, SEP152 
34 Myeloid BP 17p11.2q25.3 22095317 78640854 56.55 Whole 17q duplication 
23 AP 17q21.31q25.3 41700840 78640854 36.94 WNT3, WNT9B, CDC27, SP2, CDK5RAP3, CBX1, HOXB family, ABI3, SPOP, SAMD14, ABCC3, CROP, SPAG9, HLF, AKAP1, SEPT4, RPS6KB1, BRIP1, MAP3K3, SMURF2, AXIN2, PRKCA, MAP2K6, SOX9, SDK2, NUP85, GRB2, LLGL2, CDK3, JMJD6, BIRC5, SOCS3, CARD14, RAPTOR, AATK 
47 Myeloid BP 17q24.3 66201540 66965287 0.76 BC039327 
16 AP 18 79 140 76117153 76.04 Trisomy 18 
30 Myeloid BP 18p11.21 12321501 13522208 1.2 SLMO1, SPIRE1, CEP76, PTPN2, SEH1L, SEP192 
27 AP 18q12.2q12.3 33414141 41421419 8.01 KC6, PIK3C3, RIT2, SETBP1 
40 Myeloid BP 22q11.1q11.23 14449498 21959552 7.51 GAB4, BID, HIRA, GNB1L, MED15, PI4KA, CRKL, BCR, MAPK1 
19 AP 22q11.1q11.23 14919628 21880556 6.96 GAB4, BID, HIRA, GNB1L, MED15, PI4KA, CRKL, BCR, MAPK1 
Patient no.DiseaseChromosomeStartStopLength, MbAffected candidate genes
40 Myeloid BP 1p22.2p13.3 90311409 107802971 17.49 HFM1, CDC7, TGFBR3, BRDT, GLMN, RPAP2, GFI1, EVI5, PTBP2, DPYD, SNX7, AGL, VCAM1, EXTL2, DPH5 
44 Myeloid BP 1q21.2q44 148187512 247169378 98.98 VPS45, APH1A, ECM1, MCL1, ENSA, ARNT, SETDB1, GABPB2, PIP5K1A, PI4KB, TCHH, PGLYRP4, ILF2, INTS3, IL6R, MUC1, ARHGEF2, CD1, SLAMF6, ATF6, NOS1AP, DDR2, NUF2, PBX1, MPZL1, NME7, PRRX1, RABGAP1L, FmABL2, MR1, DHX9, EDEM3, HMCN1, UCHL5, TROVE2, KCNT2, ASPM, CRB1, PTPRC, NR5A2, PKP1, PTPN7, PTPRV, LGR6, PPP1R12B, JARID1B, BTG2, SOX13, MDM4, PCTK3, ELK4, SRGAP2, IKBKE, RASSF5, MAPKAPK2, IRF6, TRAF5, RD3, PTPN14, USH2A, RRP15, TGFB2, DUSP10, TLR5, TP53BP2, FBXO28, WDR26, WNT9A, NUP133, ARID4B, CEP170, AKT3, SMYD3, AHCTF1, NLRP3 
40 Myeloid BP 1q25.3q41 183864117 218274672 34.41 HMCN1, UCHL5, TROVE2, KCNT2, ASPM, CRB1, PTPRC, NR5A2, PKP1, PTPN7, PTPRV, LGR6, PPP1R12B, JARID1B, BTG2, SOX13, MDM4, PCTK3, ELK4, SRGAP2, IKBKE, RASSF5, MAPKAPK2, IRF6, TRAF5, RD3, PTPN14, USH2A, RRP15, TGFB2 
23 AP 2q33.1q37.3 202918925 242678246 39.76 NRP2, FASTKD2, IDH1, IKZF2, IGFBP2, USP37, WNT6, PTPRN, EPHA4, PAX3, CUL3, PID1, FBXO36, PSMD1, ECEL1, GIGYF2, INPP5D, USP40, SH3BP4, MLPH, HES6, HDAC4 
27 AP 6q11.1q12 61949077 63513069 1.56 KHDRBS2 
34 Myeloid BP 8 166818 146263890 146.1 Trisomy 8 
44 Myeloid BP 8 166818 146263890 146.1 Trisomy 8 
40 Myeloid BP 8 166818 146263890 146.1 Trisomy 8 
40 Myeloid BP 9q34.12q34.3 132658747 140164310 7.51 ABL1, MED27, SETX, TTF1, DDX31, VAV2, NOTCH1 
19 AP 9q34.12q34.3 132672428 140164310 7.49 ABL1, MED27, SETX, TTF1, DDX31, VAV2, NOTCH1 
25 AP 10q11.21 43543186 44823480 1.28 CXCL12, RASSF4 
36 Myeloid BP 11p15.2p12 13226368 43097900 29.87 SOX6, PTPN5, BBOX1, LGR4, METT5D1, ELP4, PAX6, WT1, HIPK3, COMMD9, TRAF6 
25 AP 15q21.1 43920344 46958155 3.04 SEMD6D, DUT, SEP152 
34 Myeloid BP 17p11.2q25.3 22095317 78640854 56.55 Whole 17q duplication 
23 AP 17q21.31q25.3 41700840 78640854 36.94 WNT3, WNT9B, CDC27, SP2, CDK5RAP3, CBX1, HOXB family, ABI3, SPOP, SAMD14, ABCC3, CROP, SPAG9, HLF, AKAP1, SEPT4, RPS6KB1, BRIP1, MAP3K3, SMURF2, AXIN2, PRKCA, MAP2K6, SOX9, SDK2, NUP85, GRB2, LLGL2, CDK3, JMJD6, BIRC5, SOCS3, CARD14, RAPTOR, AATK 
47 Myeloid BP 17q24.3 66201540 66965287 0.76 BC039327 
16 AP 18 79 140 76117153 76.04 Trisomy 18 
30 Myeloid BP 18p11.21 12321501 13522208 1.2 SLMO1, SPIRE1, CEP76, PTPN2, SEH1L, SEP192 
27 AP 18q12.2q12.3 33414141 41421419 8.01 KC6, PIK3C3, RIT2, SETBP1 
40 Myeloid BP 22q11.1q11.23 14449498 21959552 7.51 GAB4, BID, HIRA, GNB1L, MED15, PI4KA, CRKL, BCR, MAPK1 
19 AP 22q11.1q11.23 14919628 21880556 6.96 GAB4, BID, HIRA, GNB1L, MED15, PI4KA, CRKL, BCR, MAPK1 

BP indicates blast phase; and AP, accelerated phase.

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