Recurrent high-level DNA amplifications and focal gains in mantle-cell lymphoma
| Cytoband . | Sample . | Start (kb) . | End (kb) . | Size (kb) . | No. of genes . | Overlapping region (no. of genes) . | Overexpressed genes in the overlapping region* . | Putative microRNA in the overlapping region . |
|---|---|---|---|---|---|---|---|---|
| 8q21.11-q24.3 | MCL26 | 74 752.6 | 146 052.2 | 71 299.5 | > 500 | 8q24.21 (2) | CCNE2, E2F5,†EDD1, EIF2C2, BXL6, FBXO43, FZD6,† (MYC),‡NIBP and several zinc finger proteins§ | — |
| 8q24.21 | JEKO1 | 127 321.4 | 128 809.0 | 1 487.5 | 2 | (MYC)‡ | ||
| 9pter-p24.1 | Z138 | 239.4 | 6 759.2 | 6 519.8 | 30 | 9p24.2-p24.1 (14) | AK3, C9orf38,†C9orf46, CDC37L1, JAK2,†PPAPDC2, RANBP6, RCL1, RFX3,†TPD52L3 | hsa mir 101–2 |
| 9p24.2-p24.1 | MCL21 | 2 332.2 | 5 415.1 | 3 082.9 | 14 | ND | ||
| 10p12.33-p12.1 | MCL19 | 19 237.3 | 26 503.1 | 7 265.9 | 15 | 10p12.31-p12.1 (11) | ND | hsa mir 603 |
| 10p12.31-p12.1 | MCL20 | 22 316.8 | 25 365.9 | 3 049.1 | 11 | ND | ||
| 11q13.3-q13.5 | HBL2 | 68 979.0 | 76 176.0 | 7 197.0 | 77 | 11q13.3-q13.5 (77) | ATG16L2, C11orf30, C11orf51, CCND1,†CENTD2, CHCHD8, CLPB, DHCR7,†FADD,†FCHSDs2, INPPL1, LRRC51, MRPL48, NADSYN1,†NUMA1, ORAOV1,†PGM2L1, POLD3, PPFIA1,†PPME1, RAB6A, RNF169, SPCS2, TNFRSF19L, UCP2,†UCP3, PAAF1 | hsa mirs 139/326 |
| 11q13.3-q14.1 | MAVER1 | 69 059.8 | 80 083.5 | 11 023.7 | 101 | |||
| 11q13.1-q14.3‖ | MCL14 | 64 457.5 | 92 492.5 | 28 034.9 | > 200 | CCND1,†DGAT2,†PGM2L1,†PPME1,†PAAF1† | ||
| 11q13.3-q23.3‖ | MCL1 | 69 041.4 | 119 717.6 | 50 441.9 | > 200 | |||
| 11q13.2-q14.1‖ | MCL26 | 68 435.5 | 81 720.1 | 13 284.5 | > 100 | ATG16L2, C11orf30, SLCO2B1 | ||
| 11q13.2-q21‖ | MCL18 | 68 986.2 | 95 676.4 | 26 690.2 | > 150 | ND | ||
| 13q31.1-q31.2 | REC1 | 85 593.0 | 91 208.3 | 5 615.3 | 2 | 13q31.3 (1) | C13orf25† | hsa mirs 17/18a/19a/19b1/20a/92a1/622 |
| 13q31.2-q32.1 | MCL20 | 86 090.6 | 94 386.2 | 8 295.6 | 7 | |||
| 13q31.2-q31.3 | MCL18 | 88 696.3 | 92 595.3 | 3 899.0 | 1 | |||
| 13q31.3 | HBL2 | 89 815.1 | 90 996.6 | 1 181.5 | 1 | |||
| 13q31.3 | JEKO1 | 89 815.1 | 92 166.6 | 2 351.5 | 1 | |||
| 13q31.3 | MCL17 | 90 738.1 | 91 700.9 | 962.8 | 1 | |||
| 18q12.2-q22.1 | MINO | 31 201.2 | 61 451.2 | 30 250.0 | 89 | 18q21.33 (10) | BCL2,†FVT1, PHLPP, VPS4B | hsa mir 122 |
| 18q21.2-q22.2¶ | HBL2 | 49 877.1 | 65 507.0 | 15 629.9 | 57 | |||
| 18q21.31-q22.2 | Z138 | 52 434.9 | 66 564.3 | 14 129.4 | 48 | |||
| 18q21.32-q22.3 | GRANTA519 | 55 604.1 | 69 248.9 | 13 644.8 | 33 | |||
| 18q21.33-q22.1¶ | MCL21 | 57 749.3 | 63 438.4 | 5 689.2 | 21 | |||
| 18q21.33 | MAVER1 | 58 464.6 | 59 544.8 | 1 080.2 | 10 |
| Cytoband . | Sample . | Start (kb) . | End (kb) . | Size (kb) . | No. of genes . | Overlapping region (no. of genes) . | Overexpressed genes in the overlapping region* . | Putative microRNA in the overlapping region . |
|---|---|---|---|---|---|---|---|---|
| 8q21.11-q24.3 | MCL26 | 74 752.6 | 146 052.2 | 71 299.5 | > 500 | 8q24.21 (2) | CCNE2, E2F5,†EDD1, EIF2C2, BXL6, FBXO43, FZD6,† (MYC),‡NIBP and several zinc finger proteins§ | — |
| 8q24.21 | JEKO1 | 127 321.4 | 128 809.0 | 1 487.5 | 2 | (MYC)‡ | ||
| 9pter-p24.1 | Z138 | 239.4 | 6 759.2 | 6 519.8 | 30 | 9p24.2-p24.1 (14) | AK3, C9orf38,†C9orf46, CDC37L1, JAK2,†PPAPDC2, RANBP6, RCL1, RFX3,†TPD52L3 | hsa mir 101–2 |
| 9p24.2-p24.1 | MCL21 | 2 332.2 | 5 415.1 | 3 082.9 | 14 | ND | ||
| 10p12.33-p12.1 | MCL19 | 19 237.3 | 26 503.1 | 7 265.9 | 15 | 10p12.31-p12.1 (11) | ND | hsa mir 603 |
| 10p12.31-p12.1 | MCL20 | 22 316.8 | 25 365.9 | 3 049.1 | 11 | ND | ||
| 11q13.3-q13.5 | HBL2 | 68 979.0 | 76 176.0 | 7 197.0 | 77 | 11q13.3-q13.5 (77) | ATG16L2, C11orf30, C11orf51, CCND1,†CENTD2, CHCHD8, CLPB, DHCR7,†FADD,†FCHSDs2, INPPL1, LRRC51, MRPL48, NADSYN1,†NUMA1, ORAOV1,†PGM2L1, POLD3, PPFIA1,†PPME1, RAB6A, RNF169, SPCS2, TNFRSF19L, UCP2,†UCP3, PAAF1 | hsa mirs 139/326 |
| 11q13.3-q14.1 | MAVER1 | 69 059.8 | 80 083.5 | 11 023.7 | 101 | |||
| 11q13.1-q14.3‖ | MCL14 | 64 457.5 | 92 492.5 | 28 034.9 | > 200 | CCND1,†DGAT2,†PGM2L1,†PPME1,†PAAF1† | ||
| 11q13.3-q23.3‖ | MCL1 | 69 041.4 | 119 717.6 | 50 441.9 | > 200 | |||
| 11q13.2-q14.1‖ | MCL26 | 68 435.5 | 81 720.1 | 13 284.5 | > 100 | ATG16L2, C11orf30, SLCO2B1 | ||
| 11q13.2-q21‖ | MCL18 | 68 986.2 | 95 676.4 | 26 690.2 | > 150 | ND | ||
| 13q31.1-q31.2 | REC1 | 85 593.0 | 91 208.3 | 5 615.3 | 2 | 13q31.3 (1) | C13orf25† | hsa mirs 17/18a/19a/19b1/20a/92a1/622 |
| 13q31.2-q32.1 | MCL20 | 86 090.6 | 94 386.2 | 8 295.6 | 7 | |||
| 13q31.2-q31.3 | MCL18 | 88 696.3 | 92 595.3 | 3 899.0 | 1 | |||
| 13q31.3 | HBL2 | 89 815.1 | 90 996.6 | 1 181.5 | 1 | |||
| 13q31.3 | JEKO1 | 89 815.1 | 92 166.6 | 2 351.5 | 1 | |||
| 13q31.3 | MCL17 | 90 738.1 | 91 700.9 | 962.8 | 1 | |||
| 18q12.2-q22.1 | MINO | 31 201.2 | 61 451.2 | 30 250.0 | 89 | 18q21.33 (10) | BCL2,†FVT1, PHLPP, VPS4B | hsa mir 122 |
| 18q21.2-q22.2¶ | HBL2 | 49 877.1 | 65 507.0 | 15 629.9 | 57 | |||
| 18q21.31-q22.2 | Z138 | 52 434.9 | 66 564.3 | 14 129.4 | 48 | |||
| 18q21.32-q22.3 | GRANTA519 | 55 604.1 | 69 248.9 | 13 644.8 | 33 | |||
| 18q21.33-q22.1¶ | MCL21 | 57 749.3 | 63 438.4 | 5 689.2 | 21 | |||
| 18q21.33 | MAVER1 | 58 464.6 | 59 544.8 | 1 080.2 | 10 |
ND indicates not done; and —, not applicable.
Target overexpressed genes (> 2-fold) are listed in alphabetical order.
Genes overexpressed 4-fold more than the nonamplified samples, C13orf25 was overexpressed 10 times more than the nonamplified samples.
MYC probe sets were not evaluable.
Only a selection of cancer-related genes is shown for the large 8q region.
11q13 focal gain.
18q21.33 amplification in a region of uniparental disomy.