TABLE I.
GENERAL CHARACTERISTICS OF RECURRENTLY ALTERED REGIONS
| RAR | Clone | Chromosome | Map position1 | Size (Mb) | Cytoband | Number of cases | Cancer-related genes |
|---|---|---|---|---|---|---|---|
| G1 | RP11-326G21-RP5-936P19 | 1 | 142391262-183515789 | 41 | 1q21.1-1q32.1 | 49 | PDZK1, MCL1, ARNT, AF1Q, TPM3, ADAR, RPS27, HAX1, PYGO2, CKS1B, ADAM15, MUC1, HDGF, CCT3, PRCC, IFI16, AIM2, USF1, SELP, SELE, LAMC2, TPR, PTGS2, |
| G2 | RP11-572A16-RP11-438H8 | 1 | 198883756-244440465 | 46 | 1q32.1-1q44 | 45 | KIF14, ELF3, MDM4, ATF3, TGFB2, WNT3A, AKT3 |
| G3 | RP11-46C20-CTD-2291F22 | 5 | 27487154-35513594 | 8 | 5p14.1-5p13.2 | 19 | AMACR |
| G4 | CTB-55A14-CTB-73D21 | 5 | 167592449-174643724 | 7 | 5q34-5q35.2 | 16 | FGF18 |
| G5 | RP1-136B1-RP11-524H19 | 6 | 2316508-54856430 | 52 | 6p25.2-6p12.1 | 23 | DEK, ID4, E2F3, PRL, MICA, MICB, HMGA1, NOTCH4, MAPK14, PIM1, TFEB, CCND3, VEGF |
| G6 | RP5-1091E12-RP11-339F13 | 7 | 54851795-55154846 | 1 | 7p11.2 | 16 | EGFR |
| G7 | RP5-1057M1-RP11-212B1 | 7 | 79345845-86861115 | 7 | 7q21.11 | 20 | HGF, DMTF1, ABCB1 |
| G8 | RP5-1059M17-RP11-420H19 | 7 | 100783053-124638919 | 24 | 7q22.1-7q31.33 | 22 | EPO, EPHB4, PIK3CG, CAV1&2, MET, WNT2 |
| G9 | RP11-167E7-RP11-65A5 | 8 | 48736257-141551817 | 94 | 8q11.21-8q24.3 | 37 | PRKDC, MCM4, SNAI2, LYN, MOS, PLAG1, COPS5, TPD52, E2F5, MMP16, NBS1, EIF3S3, MYC, KCNK9, PTK2, EIF2C2, CCNE2 |
| G10 | RP11-472N13-RP11-505N10 | 10 | 31849328-33818450 | 2 | 10p11.22 | 15 | MAP3K8, NRP1, |
| G11 | RP11-95C14-RP11-265C7 | 13 | 91284427-112901415 | 21 | 13q31.3-13q34 | 16 | FGF14, ERCC5, |
| G12 | RP11-515O17-RP11-332H18 | 17 | 50654233-56847074 | 6 | 17q22-17q23.2 | 16 | HLF, MPO, PPM1D, BCAS3, TBX2 |
| G13 | CTD-2043I16-CTC-416D1 | 19 | 33293135-36979856 | 3 | 19q12 | 19 | CCNE1 |
| G14 | RP5-852M4-RP4-563E14 | 20 | 327036-61041280 | 61 | 20p13-20q13.33 | 26 | CDC25B, JAG1, SSTR4, BCL2L1, PLAGL2, DNMT3B, E2F1, MMP24, SRC, TOP1, MYBL2, MMP9, NCOA3, PTPN1, ZNF217, STK6, BMP7 |
| L1 | RP1-37J18-RP11-338N10 | 1 | 4487199-7719107 | 3.3 | 1p36.32-1p36.23 | 18 | CHD5, ICMT, CAMTA1 |
| L2 | RP11-285P3-RP4-560M15 | 1 | 14486429-15354152 | 0.9 | 1p36.21 | 24 | PRDM2, RIZ, CASP9 |
| L3 | RP11-8J9-RP11-412F21 | 1 | 46823997-69303906 | 23 | 1p33-1p31.2 | 17 | RAD54L, FAF1, S(T)IL, CDKN2C, TTC4, JUN, ARHI |
| L4 | RP11-118B23- RP5-1108M17 | 1 | 84667459-103923047 | 19 | 1p22.3-1p21.1 | 16 | BCL10, CLCA2, LMO4, GTF2B, TGFBR3, GFI1, EVI5 |
| L5 | RP11-213L8-RP11-553E4 | 4 | 172094998-190118103 | 18 | 4q33-4q35.2 | 34 | CASP3, FAT |
| L6 | RP1-273N12-RP11-347H8 | 6 | 99385861-102294657 | 3 | 6q16.2-6q16.3 | 17 | CCNC, GRIK2 |
| L7 | RP1-84N20-RP3-470B24 | 6 | 125389372-168197568 | 43 | 6q22.31-6q27 | 16 | CRSP3, PLAGL1, SASH1, LATS1, IGF2R, UNC93A, MLLT4 |
| L8 | RP11-336N16-RP11-75P13 | 8 | 2898583-34455078 | 31 | 8p23.2-8p12 | 34 | CSMD1, DEFB1, NAT1, NAT2, PSD3, TNFRSF10A, TNFRSF10B, TNFRSF10C, RHOBTB2 |
| L9 | RP11-48M17-RP11-48L13 | 9 | 2136329-29639069 | 27 | 9p24.2-9p21.1 | 26 | SMARCA2, MTAP, CDKN2B, CDKN2A, RECK, PAX5 |
| L10 | RP11-276H19-RP11-65B23 | 9 | 86827119-87654534 | 1 | 9q21.33 | 15 | GAS1, DAPK1 |
| L11 | RP11-92C4-RP11-31J20 | 9 | 98644250-104754734 | 6 | 9q22.33-9q31.1 | 16 | TGFBR1 |
| L12 | RP11-381K7-RP11-338L11 | 10 | 112963138-116971219 | 4 | 10q25.2-10q25.3 | 15 | CASP7 |
| L13 | RP11-153M24-RP11-359P14 | 13 | 27414161-59888914 | 32 | 13q12.2-13q21.2 | 19 | BRCA2, CCNA1, RB1, RFP2, DLEU1, DLEU2, DDX26 |
| L14 | RP11-353N19-RP11-68I8 | 14 | 91389738-99247779 | 8 | 14q32.12-14q32.2 | 15 | BCL11B |
| L15 | RP11-114I12-RP11-142A12 | 16 | 6846342-26727359 | 20 | 16p13.2-16p12.1 | 18 | SOCS1, ERCC4 |
| L16 | RP11-325K4-RP11-514D23 | 16 | 55369591-84922042 | 29 | 16q13-16q24.1 | 28 | CDH1, CDH3, BCAR1, WWOX, CDH13, WFDC1 |
| L17 | RP11-135N5-RP11-219A15 | 17 | 2312021-16718826 | 14 | 17p13.3-17p12 | 39 | TP53 |
| L18 | RP1-270M7-RP5-1031P17 | 21 | 15134621-39788380 | 14 | 21q11.2-21q22.2 | 15 | ADAMTS1 |
1
The mapping position refers to the UCSC genome browser (http://genome.ucsc.edu/; May 2004 freeze).