Most frequently gained clones in MCL
Clone name . | Base position, Kb . | Cytogenetic band . | % of cases with copy number gain . | Genes in affected interval . |
|---|---|---|---|---|
| Group A | ||||
| RP11-79f11* | Chr3: 165,285 | 3q26.1 | 83 | SI, BCHE |
| RP11-21j16 | Chr8: 116,016 | 8q23.3 | 77 | TRPS1 |
| RP11-90m7 | Chr3: 164,334 | 3q26.1 | 75 | — |
| RP11-80f24 | Chr8: 78,335 | 8q21.12 | 69 | — |
| RP11-89i16 | Chr8: 114,648 | 8q23.3 | 69 | — |
| RP11-90d3 | Chr4: 43,447 | 4p13 | 64 | — |
| RP11-89e20 | Chr3: 112,456 | 3q13.13 | 64 | PVRL3, CD96, TACTILE |
| RP11-91f9 | Chr3: 119,136 | 3q13.32 | 62 | — |
| RP11-91f17 | Chr3: 167,543 | 3q26.1 | 57 | SI, BCHE |
| Group B | ||||
| RP11-90e13* | Chr4: 171,790 | 4q33 | 85 | — |
| RP11-54818 | Chr12: 55,220 | 12q13.2 | 75 | NEUROD4, HEM1, DCD |
| RP11-75h6 | Chr19: 0,988 | 19p13.3 | 73 | DRIL 1, CNN2, STK11 |
| RP11-91i19 | Chr4: 144,372 | 4q31.21 | 69 | INPP4B, HP43, SNARCA5 |
| RP11-14k17 | Chr11: 39,871 | 11p12 | 69 | — |
| RP11-111p16 | Chr6: 55,523 | 6p12.1 | 69 | BMP5, COL21A1 |
| RP11-91o1 | Chr13: 89,942 | 13q31.3 | 69 | GPC5 |
| RP11-89a6 | Chr15: 54,253 | 15q21.3 | 69 | TCF12, AQP9 |
| RP11-88n10 | Chr12: 88,021 | 12q21.32 | 67 | KITLG |
| CTD-2101j13 | Chr12: 88,824 | 12q21.3 | 64 | DUSP6, TUWD12, KITLG |
| RP11-142f22 | Chr8: 100,581 | 8q22.2 | 64 | COX6, RNF19, SPAG1 |
| RP11-171g12 | Chr4: 181,787 | 4q34.3 | 62 | — |
| RP11-35p16 | Chr16: 4,580 | 16p13.3 | 62 | GLIS2, HMOX2, DNAJA3 |
| RP11-71f18 | Chr7: 19,239 | 7p21.1 | 62 | HDAC9, TWIST1, FERD3L |
| RP11-131k16 | Chr4: 121,820 | 4q27 | 57 | MAD2L1, PRDM5 |
| Group C | ||||
| RP11-91a22 | Chr16: 46,347 | 16q11.2 | 86 | SHCBP1, VPS35, GPT2 |
| RP11-91m10 | Chr11: 85,444 | 11q14.1 | 77 | DLG2 |
| RP11-229a12 | Chr3: 57,333 | 3p14.3 | 75 | DNAH12, SLMAP, ARF 4 |
| RP11-172k14 | Chr5: 74,567 | 5q13.3 | 62 | HEXB, EFG2, POLK, F2R |
Clone name . | Base position, Kb . | Cytogenetic band . | % of cases with copy number gain . | Genes in affected interval . |
|---|---|---|---|---|
| Group A | ||||
| RP11-79f11* | Chr3: 165,285 | 3q26.1 | 83 | SI, BCHE |
| RP11-21j16 | Chr8: 116,016 | 8q23.3 | 77 | TRPS1 |
| RP11-90m7 | Chr3: 164,334 | 3q26.1 | 75 | — |
| RP11-80f24 | Chr8: 78,335 | 8q21.12 | 69 | — |
| RP11-89i16 | Chr8: 114,648 | 8q23.3 | 69 | — |
| RP11-90d3 | Chr4: 43,447 | 4p13 | 64 | — |
| RP11-89e20 | Chr3: 112,456 | 3q13.13 | 64 | PVRL3, CD96, TACTILE |
| RP11-91f9 | Chr3: 119,136 | 3q13.32 | 62 | — |
| RP11-91f17 | Chr3: 167,543 | 3q26.1 | 57 | SI, BCHE |
| Group B | ||||
| RP11-90e13* | Chr4: 171,790 | 4q33 | 85 | — |
| RP11-54818 | Chr12: 55,220 | 12q13.2 | 75 | NEUROD4, HEM1, DCD |
| RP11-75h6 | Chr19: 0,988 | 19p13.3 | 73 | DRIL 1, CNN2, STK11 |
| RP11-91i19 | Chr4: 144,372 | 4q31.21 | 69 | INPP4B, HP43, SNARCA5 |
| RP11-14k17 | Chr11: 39,871 | 11p12 | 69 | — |
| RP11-111p16 | Chr6: 55,523 | 6p12.1 | 69 | BMP5, COL21A1 |
| RP11-91o1 | Chr13: 89,942 | 13q31.3 | 69 | GPC5 |
| RP11-89a6 | Chr15: 54,253 | 15q21.3 | 69 | TCF12, AQP9 |
| RP11-88n10 | Chr12: 88,021 | 12q21.32 | 67 | KITLG |
| CTD-2101j13 | Chr12: 88,824 | 12q21.3 | 64 | DUSP6, TUWD12, KITLG |
| RP11-142f22 | Chr8: 100,581 | 8q22.2 | 64 | COX6, RNF19, SPAG1 |
| RP11-171g12 | Chr4: 181,787 | 4q34.3 | 62 | — |
| RP11-35p16 | Chr16: 4,580 | 16p13.3 | 62 | GLIS2, HMOX2, DNAJA3 |
| RP11-71f18 | Chr7: 19,239 | 7p21.1 | 62 | HDAC9, TWIST1, FERD3L |
| RP11-131k16 | Chr4: 121,820 | 4q27 | 57 | MAD2L1, PRDM5 |
| Group C | ||||
| RP11-91a22 | Chr16: 46,347 | 16q11.2 | 86 | SHCBP1, VPS35, GPT2 |
| RP11-91m10 | Chr11: 85,444 | 11q14.1 | 77 | DLG2 |
| RP11-229a12 | Chr3: 57,333 | 3p14.3 | 75 | DNAH12, SLMAP, ARF 4 |
| RP11-172k14 | Chr5: 74,567 | 5q13.3 | 62 | HEXB, EFG2, POLK, F2R |
In group A, hotspots are present in the smallest regions of overlap. In group B, hotspots are present in consecutive areas. In group C, hotspots are not present in any of the consecutive areas. Mb positions of the clones were determined with USSC genome browser (April 2003 freeze). Hotspots were defined as clones with a ratio >0.3 in 8 or more of the 14 cases. Percentages were calculated by dividing the number of cases with ratio >0.3 with the number of samples that gave a hybridization signal. RP11-79f11 and RP11-91f17, RP11-89i16 and RP11-21j16, RP11-88n10 and CTD-2101j13 are consecutive clones. Genes were identified in the Mb region between the flanking clones of a hotspot.
— indicates that there are no known genes in the interval.
These clones were identified as polymorphisms in the human genome by either Sebat et al27 or lafrate et al.28