Frequency and description of novel CNAs
| Cytoband . | Type of CNA . | Number of patients (%) . | MCR size . | Genes in MCR . | Significant by GISTIC algorithm . |
|---|---|---|---|---|---|
| 22q11.22 | Loss | 4 (10.2) | 304 kb | 4 (ZNF280B, ZNF280A, PRAME, GGTLC2) | Yes |
| 3p14.2-p14.1 | Loss | 3 (7.6) | 4.1 Mb | 11 | |
| 3p14-p12.3 | Loss | 3 (7.6) | 8.5 Mb | 8 (EIF4E3,GPR27,PROK2,SHQ1,PPP4R2,PDZRN3,CNTN3,ROBO2) | |
| 4p15.2-p14 | Loss | 3 (7.6) | 10 Mb | 7 (SLC34A2,RBPJ,CCKAR,TBC1D19,STIM2,PCDH7,ARAP2) | |
| 7q34 | Loss | 3 (7.6) | 274 kb | 4 (UBN2,C7orf55,LUC7L2,KLRG2) | |
| 9p21.3 | Loss | 3 (7.6) | 2.6 Mb | 11 (including KLHL9, members of IFNA family, CDKN2A,CDKN2B) | Yes |
| 9p21.3-p21.1 | Loss | 3 (7.6) | 8.6 Mb | 15 | |
| 14q24.3-q31.3 | Loss | 3 (7.6) | 7.8 Mb | 7 (NRXN3,C14orf145,TSHR,GTF2A1,STON2,SEL1L,FLRT2) | |
| 3p12.3-q11.2 | Loss | 2 (5.1) | 13 Mb | 11 (VGLL3 and EPHA3) | Yes |
| 3q13.32-q13.33 | Loss | 2 (5.1) | 1.8 Mb | 18 (including CD80, GSK3B) | |
| 4q21.1-q21.23 | Loss | 2 (5.1) | 8.4 Mb | 34 | |
| 4q34 | Loss | 2 (5.1) | 3.1 Mb | 7 (GALNTL6,GALNT7,HMGB2,SAP30,SCRG1,HAND2,FBXO8) | |
| 6q23.3-q24 | Loss | 2 (5.1) | 2.9 Mb | 16 (including TNFAIP3) | |
| 9q34.3 | Loss | 2 (5.1) | 160 kb | 9 (TRAF2,FBXW5,C8G,LCN12,PTGDS,FLJ45224,C9orf142,CLIC3,ABCA2) | Yes |
| 9p22.1-p21.3 | Loss | 2 (5.1) | 1.4 Mb | 13 (including MLLT3 and members of IFNA family) | |
| 10q12.3-q13.3 | Loss | 2 (5.1) | 4.7 Mb | 15 | |
| 10q23.13 | Loss | 2 (5.1) | 215 kb | 7 (CH25H,LIPA,IFIT2,IFIT3,IFIT1L,IFIT1,IFIT5) | Yes |
| 10q23.32 | Loss | 2 (5.1) | 421 kb | 3 (BTAF1,CPEB3,MARCH5) | Yes |
| 15q13.3-q15.1 | Loss | 2 (5.1) | 9.1 Mb | 41 | |
| 15q15.1 | Loss | 2 (5.1) | 41 kb | MAPKB1, MGA | Yes |
| 8q24.21 | Gain | 4 (10.2) | 5.1 Mb | 9 (MTSS1,ZNF572,KIAA0196,NSMCE2,TRIB1,FAM84B,MYC,GSDMC,FAM49) | Yes |
| 6p25.3-p25.2 | Gain | 2 (5.1) | 3.7 Mb | 22 |
| Cytoband . | Type of CNA . | Number of patients (%) . | MCR size . | Genes in MCR . | Significant by GISTIC algorithm . |
|---|---|---|---|---|---|
| 22q11.22 | Loss | 4 (10.2) | 304 kb | 4 (ZNF280B, ZNF280A, PRAME, GGTLC2) | Yes |
| 3p14.2-p14.1 | Loss | 3 (7.6) | 4.1 Mb | 11 | |
| 3p14-p12.3 | Loss | 3 (7.6) | 8.5 Mb | 8 (EIF4E3,GPR27,PROK2,SHQ1,PPP4R2,PDZRN3,CNTN3,ROBO2) | |
| 4p15.2-p14 | Loss | 3 (7.6) | 10 Mb | 7 (SLC34A2,RBPJ,CCKAR,TBC1D19,STIM2,PCDH7,ARAP2) | |
| 7q34 | Loss | 3 (7.6) | 274 kb | 4 (UBN2,C7orf55,LUC7L2,KLRG2) | |
| 9p21.3 | Loss | 3 (7.6) | 2.6 Mb | 11 (including KLHL9, members of IFNA family, CDKN2A,CDKN2B) | Yes |
| 9p21.3-p21.1 | Loss | 3 (7.6) | 8.6 Mb | 15 | |
| 14q24.3-q31.3 | Loss | 3 (7.6) | 7.8 Mb | 7 (NRXN3,C14orf145,TSHR,GTF2A1,STON2,SEL1L,FLRT2) | |
| 3p12.3-q11.2 | Loss | 2 (5.1) | 13 Mb | 11 (VGLL3 and EPHA3) | Yes |
| 3q13.32-q13.33 | Loss | 2 (5.1) | 1.8 Mb | 18 (including CD80, GSK3B) | |
| 4q21.1-q21.23 | Loss | 2 (5.1) | 8.4 Mb | 34 | |
| 4q34 | Loss | 2 (5.1) | 3.1 Mb | 7 (GALNTL6,GALNT7,HMGB2,SAP30,SCRG1,HAND2,FBXO8) | |
| 6q23.3-q24 | Loss | 2 (5.1) | 2.9 Mb | 16 (including TNFAIP3) | |
| 9q34.3 | Loss | 2 (5.1) | 160 kb | 9 (TRAF2,FBXW5,C8G,LCN12,PTGDS,FLJ45224,C9orf142,CLIC3,ABCA2) | Yes |
| 9p22.1-p21.3 | Loss | 2 (5.1) | 1.4 Mb | 13 (including MLLT3 and members of IFNA family) | |
| 10q12.3-q13.3 | Loss | 2 (5.1) | 4.7 Mb | 15 | |
| 10q23.13 | Loss | 2 (5.1) | 215 kb | 7 (CH25H,LIPA,IFIT2,IFIT3,IFIT1L,IFIT1,IFIT5) | Yes |
| 10q23.32 | Loss | 2 (5.1) | 421 kb | 3 (BTAF1,CPEB3,MARCH5) | Yes |
| 15q13.3-q15.1 | Loss | 2 (5.1) | 9.1 Mb | 41 | |
| 15q15.1 | Loss | 2 (5.1) | 41 kb | MAPKB1, MGA | Yes |
| 8q24.21 | Gain | 4 (10.2) | 5.1 Mb | 9 (MTSS1,ZNF572,KIAA0196,NSMCE2,TRIB1,FAM84B,MYC,GSDMC,FAM49) | Yes |
| 6p25.3-p25.2 | Gain | 2 (5.1) | 3.7 Mb | 22 |
CNAs occurring in >2 samples. Genes in MCRs encompassing <10 genes are also listed.