Table 2. Regional clone and copy number alterations and ccRCC tumor stage and grade.
| Chromosome arm | Clone with highest signal | Regions altered | Start (Mb) | End | P-valuea | Grade I, II (%) vs III, IV (%) | ORb | 95% CIb | P-value adjb |
|---|---|---|---|---|---|---|---|---|---|
| Grade | |||||||||
| 1p− | RP11-60J11 (1p36.2) | 1p36 | 7041.726 | 7 232 439 | 0.0041 | 14/33 | 2.94 | (1.66–5.21) | 0.00001 |
| 1q+ | RP11-104A2 (1q32-41) | 1q25, 31-41, 45 | 206 402.345 | 2.07E+08 | 1.58E-05 | 9/31 | 4.42 | (2.34–8.36) | 0.00001 |
| 3q+ | RP11-219P10 | 3q22-23 | 137 606.200 | 1.38E+10 | 0.0037 | 12/25 | 1.96 | (1.07–3.61) | 0.03 |
| 4p− | RP11-176I4 (4p15.1) | 4p14-16 | 33 086.961 | 33 087 410 | 5.85E-05 | 14/33 | 3.10 | (1.73–5.57) | 0.0001 |
| 4q− | RP11-6K22 (4q 26-27) | 4q11-13, 24,26-31,34,35 | 120 282.900 | 1.20E+08 | 7.79E-06 | 13/32 | 3.43 | (1.88–6.26) | 0.0001 |
| 6q− | RP-2202A14 (6q14) | 6q14 | 79 297.260 | 79 474 213 | 0.0034 | 19/37 | 2.09 | (1.22–3.56) | 0.007 |
| 7p+ | RP11-161C7 (7p22.3) | 7p13-14,21-22.3 | 6215.911 | 6 396 692 | 0.0002 | 2543 | 2.27 | (1.36–3.79) | 0.002 |
| 7q+ | RP11-10D8 (7q22.1) | 7q22.1-.3 | 98 067.790 | 98 216 726 | 3.78E-05 | 28/46 | 2.17 | (1.31–3.60) | 0.003 |
| 8p− | RP11-182G2 (8p22) | 8p22-23 | 4457.862 | 4 614 130 | 3.33E-06 | 30/53 | 2.59 | (1.56–4.27) | 0.0001 |
| 9p− | RP11-85J5 (9p21.3) | 9p21-22 | 24 524.208 | 24 524 427 | 1.97E-05 | 26/49 | 2.32 | (1.38–3.92) | 0.002 |
| 9q− | RP11-106O17 (9q22.3) | 9q21-33 | 94 882.444 | 94 882 881 | 8.72E-06 | 25/47 | 2.19 | (1.30–3.68) | 0.003 |
| 11q− | RP11-42L18 (11q22.3-23) | 11q22-23 | 107 422.086 | 1.08E+08 | 2.32E-05 | 8/25 | 3.81 | (1.93–7.53) | 0.0001 |
| 12q+ | RP11-89J2 (12q24.32) | 12q13-14, 24.32 | 124 666.600 | 1.25E+08 | 0.0005 | 17/29 | 1.81 | (1.26–3.68) | 0.04 |
| 13q− | RP11-11C5 (13q21.3) | 13q12-14.3, 21-tel | 72 013.886 | 72 183 774 | 2.34E-06 | 10/41 | 5.36 | (2.94–9.77) | 0.00001 |
| 14q− | RP11-26M6 (14q13) | 14q12-14, 21.3-32.2 | 34 404.822 | 34 591 592 | 2.34E-06 | 34/67 | 3.18 | (1.91–5.28) | 0.00001 |
| 17q+ | RP11-84E24 (17q24-25) | 17q24-25, tel | 67 512.626 | 67 693 011 | 3.78E-05 | 5/22 | 4.50 | (2.16–9.39) | 0.00001 |
| 18p− | CTD-2048F17(18p12) | 18p11.21-11.32,12 | 8396.160 | 8 396 803 | 3.51E-06 | 14/38 | 3.24 | (1.84–5.69) | 0.00001 |
| 18q− | RP11-60P1 (18q21.3) | 18q11-12, 21.3-23, tel | 59 072.800 | 59 251 211 | 3.44E-06 | 16/44 | 3.80 | (2.20–6.55) | 0.00001 |
| 20q+ | CTD2238P18 (20q12) | 20q12,13 | 45 712.070 | 45 864 616 | 0.0001 | 17/37 | 2.28 | (1.32–3.94) | 0.003 |
| Chromosome arm | Clone with highest signal | Regions altered | Start (Mb) | End | P-valuea | Stage I, II (%)vs III, IV (%) | ORb | 95% CI | P-value adjb |
|---|---|---|---|---|---|---|---|---|---|
| Stage | |||||||||
| 1p− | RP11-219F4 (36.2–36.3) | 1p36.2-36.3 | 14 774.025 | 14 774 291 | 0.002 | 17/29 | 2.16 | (1.26–3.72) | 0.005 |
| 2p+ | RP11-57F9 | 2p23 | 28 514.930 | 28 515 223 | 0.0056 | 13/23 | 1.89 | (1.06–3.38) | 0.03 |
| 2q+ | CTD-22500B20 (2q22) | 2q22-24.3 | 158 357.236 | 158 357 713 | 0.0034 | 9/20 | 2.94 | (1.52–5.71) | 0.001 |
| 3q+ | RP11-160A13 (3q23-24) | 22-24, 26-29, tel | 144 154.808 | 144 312 333 | 0.0015 | 12/25 | 1.74 | (0.97–3.11) | 0.06 |
| 4p− | RP11-126C7 (4p13) | 11-12,13 | 38 087.290 | 38 242.92 | 0.0066 | 12/26 | 2.24 | (1.32–3.41) | 0.03 |
| 4q− | RP11-101N17 (4q26) | 4q11-12, 26 | 120 563.175 | 120 720 926 | 0.0003 | 14/29 | 2.42 | (1.35–4.43) | 0.003 |
| 6p− | RP11-284E1 (6p12) | 6p12, 24-25 | 53 823.776 | 53 824 135 | 0.0003 | 14/30 | 2.48 | (1.37–4.42) | 0.001 |
| 7q+ | RP11-38P11 (7q32) | 7q26.2-.3, 32,34,36.3 | 129 557.600 | 129 557 976 | 0.0018 | 26/41 | 1.63 | (1.02–2.63) | 0.04 |
| 9p− | RP11-125K10 (9p24) | 9p21-24, tel | 4819.655 | 4 991 841 | 8.63E-0.05 | 28/49 | 2.17 | (1.33–3.53) | 0.002 |
| 9q− | RP11-8D10 (9q21.3) | 9q12-21.3 | 82 120.447 | 82 209 078 | 8.63E-0.05 | 28/46 | 2.28 | (1.41–3.70) | 0.001 |
| 12p+ | RP11-78F16 (12p11.2) | 12p11.2,12.1-13.1 | 31 959.002 | 32 128 568 | 0.0005 | 20/32 | 2.04 | (1.20–3.45) | 0.008 |
| 12q+ | RP11-89E9 (12q23) | 12q23.3 | 97 222.144 | 97 411 481 | 0.0005 | 18/31 | 2.14 | (1.26–3.64) | 0.005 |
| 13q− | RP11-8C15 (13q12.1) | 13q12.1,12.3-14.3,21.1-tel | 20 985.475 | 20 993 099 | 8.63E-0.05 | 15/38 | 3.72 | (2.11–6.57) | <0.00001 |
| 14q− | RP11-206J4 (14q23) | 14q13-24, 31-32, tel | 63 996.230 | 64 080 508 | 0.0003 | 38/62 | 2.36 | (1.48–3.75) | <0.00001 |
| 16p− | CTD-2032H1 | 16p13 | 3232.028 | 3 296 628 | 0.0104 | 14/28 | 2.01 | (1.28–3.33) | 0.01 |
| 17q+ | RP11-86L18 | 17q12-25.3,36 | 153 645.400 | 153 645 775 | 0.0003 | 27/43 | 1.63 | (1.02–2.60) | 0.04 |
| 18p− | RP11-106J7 (18p11.21-.23) | 18p11.2-12 | 3268.728 | 3 443 000 | 0.0002 | 13/35 | 3.15 | (1.81–5.48) | <0.00001 |
| 18q− | RP11-12J12 (18q22) | 18q11-12, 21-23, tel | 55 424.497 | 55 607 583 | 3.14E-0.06 | 27/43 | 2.84 | (1.68–4.88) | <0.00001 |
| 20q+ | LLNL-255K9 | 20q13.2 | 55 338.240 | 55 352 455 | 0.0005 | 15/34 | 2.24 | (1.31–3.82) | 0.003 |
Abbreviations: ccRCC, clear cell renal cell carcinoma; CI, confidence interval; OR, odds Ratio.
a
P-value adjusted for multiple comparisons.
b
OR, 95% CI and P-values from multivariate models(MV) adjusted for age, sex, country stage, grade, smoking status and family history of cancer.