Table 2.
Most frequently detected minimal common regions (q-value < 0.01 and frequency > 40% of altered cases) of gain and loss in locally advanced rectal cancer tumors genotyped on the Affymetrix 6.0 SNP array platform (n = 39).
| Minimal Common Altered Regions (bp) | Region Length (bp) | N. of SNPs | Chr. Band | Event | Altered Cases (%) | Gene List |
|---|---|---|---|---|---|---|
| Chr18: 48351659-48920677 | 569018 | 2340 | 18q21.2 | Loss | 69 | RN7SL695P, SRSF10P1, RNU1-46P, MRO, ME2, MEX3C, ELAC1, SMAD4 |
| Chr20: 1560988-1585059 | 24071 | 18 | 20p13 | Gain | 56 | SIRPB1 |
| Chr1: 7829422-10869532 | 3040110 | 14577 | 1p36.23 | Loss | 56 | RNU1-7P, RN7SL729P, RNU6-991P, RPL7P11, RPL7P7, ENO1-IT1, ENO1-AS1, RNU6-304P, HMGN2P17, RN7SL451P, MIR34A, RNA5SP40, C1orf200, RN7SKP269, MIR5697, PGAM1P11, RNU6-828P, MIR1273D, RNU6-37P, RN7SL731P, RN7SL721P, CORT, RN7SL614P, VAMP3, UTS2, PARK7, ERRFI1, ENO1, CA6, SLC2A7, SLC2A5, SPSB1, SLC25A33, TMEM201, PIK3CD, LZIC, NMNAT1, RBP7, PGD, APITD1, APITD1-CORT, DFFA, PER3, TNFRSF9, RERE, GPR157, H6PD, CLSTN1, CTNNBIP1, UBE4B, KIF1B, PEX14, CASZ1, CAMTA1, SLC45A1 |
| Chr1: 26284282-31197400 | 4913118 | 20676 | 1p35.3 | Loss | 54 | RNU6-110P, SLC30A2, FAM110D, ZNF593, CD52, RN7SL490P, HMGN2, DPPA2P2, MIR1976, RN7SL679P, RN7SL501P, RN7SL165P, SFN, GPATCH3, NR0B2, OSTCP2, TRNP1, FAM46B, CHCHD3P3, NPM1P39, SNRPEP7, RNU6-48P, FCN3, CD164L2, IFI6, RNU6-949P, CHMP1AP1, RNU6-424P, RPEP3, RNU6-1245P, SCARNA1, THEMIS2, XKR8, RN7SL559P, SPCS2P4, RNU6-176P, RNU7-29P, ATPIF1, RNU6ATAC27P, SNORA73B, PRDX3P2, SNHG12, SNORD99, RAB42, RNU11, TMEM200B, PAFAH2, EXTL1, TRIM63, PDIK1L, CNKSR1, CATSPER4, CEP85, UBXN11, AIM1L, ZNF683, DHDDS, ARID1A, PIGV, ZDHHC18, GPN2, C1orf172, SLC9A1, WDTC1, SYTL1, MAP3K6, GPR3, FGR, FAM76A, STX12, PPP1R8, RPA2, SMPDL3B, PTAFR, DNAJC8, SESN2, MED18, TRNAU1AP, GMEB1, YTHDF2, OPRD1, MECR, SH3BGRL3, LIN28A, RPS6KA1, TMEM222, WASF2, AHDC1, PHACTR4, RCC1, SNHG3, TAF12, SRSF4, PTPRU, MATN1, MATN1-AS1, NUDC, EYA3, EPB41 |
| Chr1: 23401844-25226751 | 1824907 | 7976 | 1p36.11 | Loss | 54 | RNU6-514P, RNU6-135P, HTR1D, C1orf213, ID3, RN7SL532P, PITHD1, LYPLA2, GALE, RN7SL24P, MIR378F, PNRC2, RN7SL857P, RNU6-1208P, KDM1A, HNRNPR, ZNF436, ASAP3, MDS2, RPL11, TCEB3, HMGCL, FUCA1, SRSF10, MYOM3, IL22RA1, GRHL3, STPG1, RCAN3, SRRM1, RUNX3, LUZP1, TCEA3, E2F2, CNR2, IFNLR1, NIPAL3, NCMAP, CLIC4 |
| Chr8: 39235592-39384956 | 149364 | 964 | 8p11.22 | Gain | 51 | ADAM5, ADAM3A |
| Chr1: 20830489-20979684 | 149195 | 963 | 1p36.12 | Loss | 51 | MUL1, RPS4XP4, FAM43B, CDA, DDOST, PINK1, PINK1-AS |
| Chr1: 31457917-31735879 | 277962 | 1756 | 1p35.2 | Loss | 51 | SEPW1P, NKAIN1, SNRNP40, PUM1 |
| Chr15: 34670991-34830240 | 159249 | 1137 | 15q14 | Loss | 49 | MIR1233-1, HNRNPLP2, MIR1233-2, GOLGA8A, GOLGA8B |
| Chr15: 50557160-51352248 | 795088 | 3936 | 15q21.2 | Loss | 49 | MIR4712, AHCYP7, RNA5SP395, RN7SL354P, DCAF13P3, HDC, GABPB1-AS1, USP50, SPPL2A, GABPB1, USP8, TRPM7, AP4E1, TNFAIP8L3 |
| Chr1: 32278463-33614161 | 1335698 | 4306 | 1p35.1 | Loss | 48 | MIR5585, IQCC, DCDC2B, EIF3I, FAM167B, FAM229A, GAPDHP20, LRRC37A12P, RN7SL122P, FNDC5, TMEM54, SPOCD1, TMEM39B, TXLNA, CCDC28B, TMEM234, MTMR9LP, LCK, MARCKSL1, TSSK3, BSDC1, ZBTB8B, ZBTB8OS, RBBP4, KIAA1522, YARS, HPCA, AK2, TRIM62, PTP4A2, KPNA6, HDAC1, ZBTB8A, SYNC, S100PBP, RNF19B, KHDRBS1, ADC |
| Chr8: 2784419-6422612 | 3638193 | 44962 | 8p23.1 | Loss | 48 | RNA5SP251, RN7SL872P, PAICSP4, RN7SL318P, RPL23AP54, RN7SKP159, ANGPT2, CSMD1, MCPH1 |
| Chr8: 32577483-35655135 | 3077652 | 13569 | 8p12 | Loss | 48 | RNU6-663P, MTND1P6, MTND2P32, RANP9, RNU6-528P, SNORD13, RN7SL621P, RN7SL457P, VENTXP5, LSM12P1, TTI2, MAK16, DUSP26, FUT10, RNF122, NRG1, UNC5D |
| Chr1: 17005967-17253362 | 247395 | 1356 | 1p36.13 | Loss | 46 | EIF1AXP1, FAM231C, RNU1-4, CROCCP4, MIR3675, RNU1-2, MST1L, ESPNP, CROCC |
| Chr15: 35085898-35540410 | 454512 | 2309 | 15q14 | Loss | 46 | ACTC1, NANOGP8, PRELID1P4, ZNF770, AQR, ANP32AP1, DPH6 |
| Chr4: 113427910-113740790 | 312880 | 1219 | 4q25 | Loss | 46 | NEUROG2, MIR302B, MIR367, MIR302D, MIR302A, MIR302C, WRBP1, RPL7AP30, LARP7, OSTCP4, C4orf21, ANK2 |
| Chr4: 165303804-166130292 | 826488 | 5907 | 4q32.3 | Loss | 46 | RNU6-284P, RNU6-668P, TRIM60P14, FAM218BP, NACA3P, FAM218A, TRIM61, TRIM60, TMEM192, KLHL2, MARCH1 |
| Chr22: 29192671-29455689 | 263018 | 1166 | 22q12.1 | Loss | 46 | C22orf31, XBP1, ZNRF3-IT1, ZNRF3-AS1, ZNRF3 |
| Chr17: 44267864-44276547 | 8683 | 56 | 17q21.31 | Loss | 44 | KANSL1-AS1, KANSL1 |
| Chr14:1-20456201 | 20456200 | 4929 | 14q11.2 | Loss | 44 | RNU6-458P, OR11H12, ARHGAP42P5, NF1P4, MED15P1, RNU6-1239P, GRAMD4P3, DUXAP10, OR11H13P, GRAMD4P4, RNU6-1268P, MED15P6, ARHGAP42P4, OR11H2, OR4Q3, OR4H12P, OR4M1, OR4N1P, OR4K3, OR4K2, OR4K4P, OR4K5, OR4K1, OR4K16P, OR4K15, POTEG, BMS1P17, BMS1P18, POTEM, OR4N2, OR11K2P, OR4K6P |
| Chr4: 128751602-129198401 | 446799 | 1425 | 4q28.2 | Loss | 44 | RNU6-583P, FOSL1P1, PLK4, C4orf29, PGRMC2, HSPA4L, MFSD8, LARP1B |
| Chr1: 152552808-152586527 | 33719 | 100 | 1q21.3 | Loss | 41 | LCE3D, LCE3C, LCE3B |
| Chr1: 22455143-22963470 | 508327 | 2714 | 1p36.12 | Loss | 41 | MIR4418, ZBTB40-IT1, C1QA, WNT4, EPHA8, ZBTB40 |
| Chr15: 20586675-20717373 | 130698 | 443 | 15q11.1 | Gain | 41 | HERC2P3 |
| Chr8: 7290942-7771549 | 480607 | 514 | 8p23.1 | Gain | 41 | DEFB104B, DEFB105B, PRR23D1, FAM90A6P, FAM90A7P, FAM90A22P, OR7E157P, OR7E154P, FAM90A14P, FAM90A16P, FAM90A8P, FAM90A17P, FAM90A19P, FAM90A9P, FAM90A10P, PRR23D2, DEFB107A, DEFB105A, DEFB104A, DEFB103A, DEFB4A, SPAG11B, DEFB107B, FAM90A21, FAM90A23P, FAM90A18P, DEFB106A, SPAG11, HSPD1P2, DEFB106B |
Genes that have been commonly associated with colorectal cancer are shown in bold.