Most frequently lost clones in MCL
Clone name . | Base position, Kb . | Cytogenetic band . | % of cases with copy number loss . | Genes in affected interval . |
|---|---|---|---|---|
| Group A | ||||
| RP11-89b24 | Chr1:94,003 | 1p22.1 | 77 | PARG1, TGFBR3, GF11 |
| RP11-122a8 | Chr13:98,597 | 13q32.3 | 67 | ZIZIMIN1, STK24, EBI2 |
| RP11-246o4 | Chr1:82,559 | 1p31.1 | 62 | — |
| RP11-19j14 | Chr13:97,890 | 13q32.2 | 62 | FARP1, STK24, DOCK9 |
| RP11-65f22 | Chr22:31,034 | 22q12.3 | 62 | SLC5A4, LIF, PES1 |
| RP11-40h10 | Chr13:94,399 | 13q32.1 | 57 | — |
| RP11-17i11 | Chr13:42,711 | 13q14.11 | 57 | DNAJD1, MJC |
| Group B | ||||
| RP11-58f7* | Chr7:156,972 | 7q36.3 | 79 | PTPRN2 |
| RP11-3p8 | Chr13:111,893 | 13q34 | 75 | ING1, SOX1 |
| RP11-88j24 | Chr1:36,922 | 1p34.3 | 73 | GRIK3 |
| CTC-200d12* | Chr14:104,922 | 14q32.33 | 71 | IGHM |
| RP11-19o15 | Chr13:112,427 | 13q34 | 69 | TUBGCP3 |
| RP11-58c16 | Chr13:50,175 | 13q14.3 | 67 | NEK3, CKAP2 |
| RP11-278e23 | Chr22:17,193 | 22q11.21 | 64 | DRCR6, ZNF74, HIC2 |
| RP11-2111 | Chr1:14,410 | 1p36.21 | 57 | MGC4342 |
| RP11-2c23 | Chr11:20,127 | 11p15.1 | 57 | NAV2 |
| RP11-79d15 | Chr1:17,016 | 1p36.13 | 57 | PAD12 SDHN, PAX7 |
| Group C | ||||
| RP11-55m23† | Chr1:54,836 | 1p32.3 | 77 | BSND |
| RP11-116m19 | Chr2:236,646 | 2q37.2 | 62 | CENTG2, SH3BP4 |
| RP4-771p4 | Chr7:73,000 | 7q11.23 | 62 | LIMK, RFC21 |
| RP11-14k9 | Chr5:168,448 | 5q35.1 | 62 | SLIT3, RARS, PANK3 |
Clone name . | Base position, Kb . | Cytogenetic band . | % of cases with copy number loss . | Genes in affected interval . |
|---|---|---|---|---|
| Group A | ||||
| RP11-89b24 | Chr1:94,003 | 1p22.1 | 77 | PARG1, TGFBR3, GF11 |
| RP11-122a8 | Chr13:98,597 | 13q32.3 | 67 | ZIZIMIN1, STK24, EBI2 |
| RP11-246o4 | Chr1:82,559 | 1p31.1 | 62 | — |
| RP11-19j14 | Chr13:97,890 | 13q32.2 | 62 | FARP1, STK24, DOCK9 |
| RP11-65f22 | Chr22:31,034 | 22q12.3 | 62 | SLC5A4, LIF, PES1 |
| RP11-40h10 | Chr13:94,399 | 13q32.1 | 57 | — |
| RP11-17i11 | Chr13:42,711 | 13q14.11 | 57 | DNAJD1, MJC |
| Group B | ||||
| RP11-58f7* | Chr7:156,972 | 7q36.3 | 79 | PTPRN2 |
| RP11-3p8 | Chr13:111,893 | 13q34 | 75 | ING1, SOX1 |
| RP11-88j24 | Chr1:36,922 | 1p34.3 | 73 | GRIK3 |
| CTC-200d12* | Chr14:104,922 | 14q32.33 | 71 | IGHM |
| RP11-19o15 | Chr13:112,427 | 13q34 | 69 | TUBGCP3 |
| RP11-58c16 | Chr13:50,175 | 13q14.3 | 67 | NEK3, CKAP2 |
| RP11-278e23 | Chr22:17,193 | 22q11.21 | 64 | DRCR6, ZNF74, HIC2 |
| RP11-2111 | Chr1:14,410 | 1p36.21 | 57 | MGC4342 |
| RP11-2c23 | Chr11:20,127 | 11p15.1 | 57 | NAV2 |
| RP11-79d15 | Chr1:17,016 | 1p36.13 | 57 | PAD12 SDHN, PAX7 |
| Group C | ||||
| RP11-55m23† | Chr1:54,836 | 1p32.3 | 77 | BSND |
| RP11-116m19 | Chr2:236,646 | 2q37.2 | 62 | CENTG2, SH3BP4 |
| RP4-771p4 | Chr7:73,000 | 7q11.23 | 62 | LIMK, RFC21 |
| RP11-14k9 | Chr5:168,448 | 5q35.1 | 62 | SLIT3, RARS, PANK3 |
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 hydridization signal. RP11-19j14 and RP11-122a8, RP11-3p8 and RP11-19o15 are consecutive clones.
— 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
This clone was mapped to different locations using the USSC genome browser; in this table the position in FISH clone track was used for this table. Genes were identified in the Mb region between the flanking clones of a hotspot.