Table 3.

Chromosomal regions harboring a different DNA copy number in triple-negative tumors compared with other tumor subtypes

LocationTriple negative (n = 35)
Triple negative tumors (n = 69)
PFDRGenes
Frequency gain (%)/lost (%)Frequency gain/lost
1q32.129/054/07E−44.9E−2SYT2
5q11.23/374/105E−44.6E−2ITGA1, PELO
5q13.2-5q14.10/433/205E−44.6E−2CRHBP, F2R, F2RL1, F2RL2, HEXB, HMGCR, ENC1, COL4A3BP, TINP1, IQGAP2, SV2C, KIAA0888, GCNT4, POLK, AGGF1, RGNEF, ZBED3, GFM2, C5orf37, S100Z, ANKRD31, LOC441086, LOC441087
5q14.2-5q14.30/433/208E−44.9E−2HAPLN1, VCAN, XRCC4, EDIL3, TMEM167, NBPF22P
5q21.10/463/172E−44.2E−2CHD1, ST8SIA4, RGMB, TMEM157
5q21.1-5q21.20/431/173E−44.2E−2PAM, HISPPD1, GIN1, NUDT12, C5orf30, SLCO6A1, LOC285708, SLCO4C1
6p25.120/64/108E−44.9E−2LY86, RP3-398D13.1
6p24.123/09/98E−44.9E−2
6p22.3-5p22.229/010/91E−42.2E−2E2F3, ID4, PRL, SOX4, TPMT, DEK, CDKAL1, MBOAT1, HDGFL1, AOF1, RNF144B, NHLRC1, FLJ22536, LOC729177
6p22.226/06/94E−44.2E−2SLC17A1
6p21.3326/06/77E−44.9E−2HCG9
6p21.3326/06/74E−44.2E−2ABCF1, GNL1, HLA-E, PPP1R10, DHX16, MDC1, NRM, MRPS18B, TRIM39, RPP21, C6orf134, PRR3, KIAA1949, TUBB, C6orf136
6p21.3326/04/74E−44.2E−2ATP6V1G2, CDSN, HLA-B, HLA-C, LTA, LTB, MICB, NFKBIL1, POU5F1, TCF19, TNF, BAT2, BAT1, LST1, HCP5, C6orf15, CCHCR1, PSORS1C1, PSORS1C2, HCG27, NCR3, MCCD1
6p21.33-6p21.3226/06/94E−44.2E−2CLIC1, CSNK2B, HSPA1A, HSPA1L, MSH5, NEU1, VARS, BAT4, BAT5, DDAH2, C6orf48, APOM, LSM2, C6orf47, LY6G5B, LY6G6D, C6orf27, C6orf25, C6orf21, C6orf26
6p21.3226/06/76E−44.6E−2AGER, CFB, C2, C4A, C4B, CREBL1, CYP21A2, DOM3Z, RNF5, SKIV2L, TNXB, RDBP, STK19, PPT2, AGPAT1, EHMT2, FKBPL, PRRT1, EGFL8, ZBTB12
6p21.3226/06/76E−44.6E−2HLA-DRA, NOTCH4, PBX2, C6orf10, BTNL2, GPSM3
6p21.3129/07/72E−44.2E−2KCTD20
6p21.231/07/94E−44.2E−2RNF8, KIAA0082, TBC1D22B, ZFAND3, BTBD9, C6orf129, MDGA1, FLJ45825
6p21.229/06/91E−42.2E−2DNAH8, GLO1, GLP1R, KCNK5, C6orf64, BTBD9
6p21.2-6p12.334/36/101E−42.2E−2(105), BYSL, RUNX2, CCND3, CDC5L, SLC29A1, HSP90AB1, MEP1A, NFKBIE, NFYA, PGC, POLH, PPP2R5D, PTK7, PRPH2, SRF, TBCC, VEGFA, TFEB, SUPT3H, NCR2, RCAN2, GNMT, TNFRSF21, PRICKLE4, XPO5, TTBK1, ABCC10, FOXP4, PTCRA, HCRP1
9p13.331/36/161E−42.2E−2C9orf23
11q14.311/61/331E−42.2E−2CHORDC1
11q22.36/90/384E−44.2E−2GRIA4, ICEBERG
11q22.36/90/393E−44.2E−2GRIA4, GUCY1A2, AASDHPPT, KIAA1826, KBTBD3
11q23.314/110/382E−44.2E−2C1QTNF5
15q13.3-15q140/406/176E−44.6E−2CHRM5, CHRNA7, RYR3, SCG5, ARHGAP11A, SLC12A6, DKFZP434L187, GREM1, TMEM85, C15orf24, AVEN, C15orf29, FAM7A3, FAM7A1, PGBD4, LOC283701, FMN1, LOC440268, C15orf45
15q140/376/168E−44.9E−2AGPAT7
15q140/376/168E−44.9E−2GOLGA8A, GJD2, GOLGA8B
15q140/376/168E644.9E−2AQR, ZNF770, ATPBD4, hCG_1787519, LOC723972
15q140/403/166E−44.6E−2C15orf41
15q22.20/299/98E−44.9E−2TLN2, MGC15885
15q22.2-15q22.310/2910/96E−44.6E−2CA12, PPIB, SNX1, TPM1, HERC1, USP3, DAPK2, RPS27L, RAB8B, CSNK1G1, SNX22, APH1B, FAM96A, LACTB, LOC145842, FBXL22
16q23.29/94/397E−44.9E−2
16q23.39/64/383E−44.2E−2OSGIN1, EFCBP2, LOC146167
16q24.16/34/363E−44.2E−2TMEM148, LOC727710
19q13.1231/06/37E−44.9E−2ZFP30, ZNF571, ZNF607, ZNF573, ZNF781, ZNF540, ZNF793, DKFZp761D1918
22q11.2117/90/177E−44.9E−2HIRA, UFD1L, CDC45L, MRPL40, LOC128977
22q11.2120/90/173E−44.2E−2ARVCF, COMT, GP1BB, SEPT5, RANBP1, TBX1, TXNRD2, HTF9C, ZDHHC8, DGCR8, GNB1L, RTN4R, C22orf29, DGCR6L, KIAA1652, C22orf25, FLJ32575, LOC284865, LOC440792