High-resolution delineation of common regions of gain, amplification, and loss in MCL and in other B-NHL subtypes
. | Patients with MCL; n = 68 . | % . | MCL cell lines; n = 9 . | % . | B-NHL cell lines; n = 36 . | % . | Consensus region . | Size, Mb . | Candidate genes . |
|---|---|---|---|---|---|---|---|---|---|
| Gain (amplification*) | |||||||||
| 3q26.3 | 31 (2) | 46 | 2 | 22 | 9 | 25 | GS-115H3-RP11-114M1 | 5.8 | ECT2 |
| 7p21.1-p22.3 | 11 | 16 | 3 | 33 | 17 | 47 | CTC-329F6-RP11-71F18 | 17 | CARD11, ETV1 |
| 8p11.2 | 6 (1) | 9 | 1 | 11 | 5 | 14 | RP11-100B16-RP11-284J3 | 2.5 | FGFR1 |
| 8q24.2 | 13 | 19 | 3 | 33 | 18 (2) | 50 | RP11-65D17-RP11-237F24 | 1.5 | MYC |
| 9p24.1 | 2 (2) | 3 | 1 (1) | 11 | 4 | 11 | RP11-125K10-RP11-165O14 | 1.3 | JAK2 |
| 10p12.2 | 8 (3) | 12 | 1 | 11 | 3 | 8 | RP11-200C22-RP11-75N18 | 2.5 | BMI1, PIP5K2A |
| 11q13.3 | 7 (1) | 9 | 2 (1) | 22 | 3 | 8 | CTB-36F16-RP11-120P20 | 0.8 | BCL1 |
| 12q13.1-q14.1 | 2 | 3 | 4 (1) | 44 | 6 | 17 | RP11-132H4-RP11-276L24 | 6 | CDK4 |
| 13q31.3 | 3 (1) | 5 | 2 (1) | 22 | 16 (6) | 44 | RP11-86C3 | 1 | GPC5, miRNAs |
| 15q22.3-q25.1 | 6 | 9 | — | 0 | 2 (1) | 6 | RP11-60J12-RP11-30M4 | 15 | PML |
| 18q21.33 | 3 | 5 | 3 (3) | 33 | 10 (4) | 28 | RP11-40D15-RP11-75O12 | 2.8 | BCL-2 |
| Xq27.3-q28 | 4 | 6 | 2 (1) | 22 | 4 | 11 | CTD-2060E7-RP11-221G13 | 2 | FMR1, FMR2 |
| Genomic loss | |||||||||
| 1p21.2-p21.3 | 21 | 31 | 3 | 33 | — | 0 | RP11-156M23-RP11-178M11 | 5.6 | CDC14A, miRNA-137 |
| 6q21 | 17 | 25 | 2 | 22 | 6 | 17 | RP11-165E15-RP11-59F18 | 5 | FOXO3A, SESN1 |
| 6q23.2-q24.1 | 18 | 26 | 3 | 33 | 6 | 17 | RP11-177M4-RP11-15H7 | 6.8 | IFNGR1 |
| 8p21.3 | 18 | 26 | 4 | 44 | 9 | 25 | RP11-274M9-RP11-89M8 | 1.5 | DR4, DR5, DcR1, DcR2 |
| 8p23.3 | 20 | 29 | 3 | 33 | 8 | 22 | GS1-77L23-RP11-240A17 | 1.6 | DLGAP2, FBCXO25 |
| 9p21.3 | 12 | 18 | 7 | 78 | 8 | 22 | CTB-65D18-RP11-33O15 | 3 | P16-INK4A |
| 9q21.33-q22.33 | 12 | 18 | 1 | 11 | 2 | 6 | RP11-65C15-RP11-147H22 | 13 | CDC14B, FANCC |
| 10p14 | 12 | 18 | 2 | 22 | 4 | 11 | RP11-5B23-RP11-72C6 | 1.4 | PRKCQ, KIN |
| 11q22.3 | 14 | 21 | 2 | 22 | 1 | 3 | RP11-179B7-RP11-964M3 | 4 | ATM |
| 11q25 | 2 | 5 | 2 | 22 | 8 | 22 | RP11-17M17-RP11-27H17 | 1.5 | OPMCL, THY28 |
| 13q14.2-q14.3 | 17 | 25 | 4 | 44 | 6 | 17 | RP11-52B21-RP11-16F6 | 6 | miRNA15, miRNA16 |
| 13q33.3-q34 | 19 | 28 | 1 | 11 | 6 | 22 | RP11-183A20-RP11-61I17 | 1.4 | ING1, LIG4, TNFSF13B |
| 17p13.1 | 15 | 22 | 3 | 33 | 10 | 28 | RP11-61B20-RP11-9A21 | 1.4 | P53 |
| 17p13.3 | 14 | 21 | 4 | 44 | 8 | 22 | GS1-68F18-RP11-26N16 | 1 | OVCA1, OVCA2, RPA1, CRK |
. | Patients with MCL; n = 68 . | % . | MCL cell lines; n = 9 . | % . | B-NHL cell lines; n = 36 . | % . | Consensus region . | Size, Mb . | Candidate genes . |
|---|---|---|---|---|---|---|---|---|---|
| Gain (amplification*) | |||||||||
| 3q26.3 | 31 (2) | 46 | 2 | 22 | 9 | 25 | GS-115H3-RP11-114M1 | 5.8 | ECT2 |
| 7p21.1-p22.3 | 11 | 16 | 3 | 33 | 17 | 47 | CTC-329F6-RP11-71F18 | 17 | CARD11, ETV1 |
| 8p11.2 | 6 (1) | 9 | 1 | 11 | 5 | 14 | RP11-100B16-RP11-284J3 | 2.5 | FGFR1 |
| 8q24.2 | 13 | 19 | 3 | 33 | 18 (2) | 50 | RP11-65D17-RP11-237F24 | 1.5 | MYC |
| 9p24.1 | 2 (2) | 3 | 1 (1) | 11 | 4 | 11 | RP11-125K10-RP11-165O14 | 1.3 | JAK2 |
| 10p12.2 | 8 (3) | 12 | 1 | 11 | 3 | 8 | RP11-200C22-RP11-75N18 | 2.5 | BMI1, PIP5K2A |
| 11q13.3 | 7 (1) | 9 | 2 (1) | 22 | 3 | 8 | CTB-36F16-RP11-120P20 | 0.8 | BCL1 |
| 12q13.1-q14.1 | 2 | 3 | 4 (1) | 44 | 6 | 17 | RP11-132H4-RP11-276L24 | 6 | CDK4 |
| 13q31.3 | 3 (1) | 5 | 2 (1) | 22 | 16 (6) | 44 | RP11-86C3 | 1 | GPC5, miRNAs |
| 15q22.3-q25.1 | 6 | 9 | — | 0 | 2 (1) | 6 | RP11-60J12-RP11-30M4 | 15 | PML |
| 18q21.33 | 3 | 5 | 3 (3) | 33 | 10 (4) | 28 | RP11-40D15-RP11-75O12 | 2.8 | BCL-2 |
| Xq27.3-q28 | 4 | 6 | 2 (1) | 22 | 4 | 11 | CTD-2060E7-RP11-221G13 | 2 | FMR1, FMR2 |
| Genomic loss | |||||||||
| 1p21.2-p21.3 | 21 | 31 | 3 | 33 | — | 0 | RP11-156M23-RP11-178M11 | 5.6 | CDC14A, miRNA-137 |
| 6q21 | 17 | 25 | 2 | 22 | 6 | 17 | RP11-165E15-RP11-59F18 | 5 | FOXO3A, SESN1 |
| 6q23.2-q24.1 | 18 | 26 | 3 | 33 | 6 | 17 | RP11-177M4-RP11-15H7 | 6.8 | IFNGR1 |
| 8p21.3 | 18 | 26 | 4 | 44 | 9 | 25 | RP11-274M9-RP11-89M8 | 1.5 | DR4, DR5, DcR1, DcR2 |
| 8p23.3 | 20 | 29 | 3 | 33 | 8 | 22 | GS1-77L23-RP11-240A17 | 1.6 | DLGAP2, FBCXO25 |
| 9p21.3 | 12 | 18 | 7 | 78 | 8 | 22 | CTB-65D18-RP11-33O15 | 3 | P16-INK4A |
| 9q21.33-q22.33 | 12 | 18 | 1 | 11 | 2 | 6 | RP11-65C15-RP11-147H22 | 13 | CDC14B, FANCC |
| 10p14 | 12 | 18 | 2 | 22 | 4 | 11 | RP11-5B23-RP11-72C6 | 1.4 | PRKCQ, KIN |
| 11q22.3 | 14 | 21 | 2 | 22 | 1 | 3 | RP11-179B7-RP11-964M3 | 4 | ATM |
| 11q25 | 2 | 5 | 2 | 22 | 8 | 22 | RP11-17M17-RP11-27H17 | 1.5 | OPMCL, THY28 |
| 13q14.2-q14.3 | 17 | 25 | 4 | 44 | 6 | 17 | RP11-52B21-RP11-16F6 | 6 | miRNA15, miRNA16 |
| 13q33.3-q34 | 19 | 28 | 1 | 11 | 6 | 22 | RP11-183A20-RP11-61I17 | 1.4 | ING1, LIG4, TNFSF13B |
| 17p13.1 | 15 | 22 | 3 | 33 | 10 | 28 | RP11-61B20-RP11-9A21 | 1.4 | P53 |
| 17p13.3 | 14 | 21 | 4 | 44 | 8 | 22 | GS1-68F18-RP11-26N16 | 1 | OVCA1, OVCA2, RPA1, CRK |
The number of tumors with amplification