List of BAC/PAC clones showing recurrent high copy number gains and homozygous losses in lymphoma type
Clone name* . | Cytogenetic position . | Gain/loss, no. patients† . | Amplification/homozygous loss, no. patients‡ . | Gene§ . |
|---|---|---|---|---|
| Gain | ||||
| RP3-510D11 | 1p36.22 | 12 | 2 | H6PD, LOC440558 |
| RP5-888M10 | 1p36.21 | 11 | 2 | VPS13D |
| RP5-1177E19 | 1p36.21 | 9 | 2 | PRDM2 |
| RP11-233K4 | 6p25.3 | 18 | 2 | IRF4∥ |
| RP11-498D18 | 7p22.2 | 12 | 2 | CARMA1,∥GNA12 |
| RP5-911H5 | 7q21.2 | 22 | 2 | ANKIB1 |
| RP11-736C20 | 7q21.2 | 23 | 2 | CALCR |
| RP11-148A10 | 7q22.2 | 26 | 2 | LHFPL3 |
| RP11-77E2 | 7q22.3 | 25 | 2 | DLD, LAMB1, LAMB4 |
| RP11-573B16 | 7q31.1 | 25 | 2 | — |
| RP11-9C22 | 7q31.33 | 25 | 2 | SND1 |
| RP11-66F23 | 7q31.33 | 24 | 2 | NYD-SP18, CALU, OPN1SW, DKFZP434G156, FLNC, ATP6V1F, LOC375616 |
| RP11-35B6 | 7q31.33 | 24 | 2 | KIAA0828, FAM40B |
| RP11-233L24 | 7q33 | 21 | 2 | — |
| RP4-659J6 | 7q33 | 24 | 2 | ZC3HDC1, KIAA1718 |
| RP11-188A12 | 7q33 | 20 | 2 | — |
| RP11-796I2 | 7q35 | 17 | 2 | PRKAG2, LOC441301, GALNTL5 |
| RP11-476H24 | 7q36.2 | 18 | 2 | DPP6 |
| RP11-691F21 | 7q36.3 | 18 | 2 | LOC285889 |
| RP11-452C13 | 7q36.3 | 16 | 2 | PTPRN2 |
| RP11-1127D7 | 14q32.2 | 21 | 2 | FLJ25773,¶RPL3P4,¶BCL11B∥¶ |
| Loss | ||||
| RP1-101M23 | 6q21 | 12 | 2 | PRDM1 |
| RP11-149I2 | 9p21.3 | 14 | 2 | MTAP, CDKN2A,∥CDKN2B,∥NSGX |
| RP11-214L15 | 9p21.3 | 7 | 2 | — |
| RP11-468C2 | 9p21.3 | 5 | 2 | — |
| RP11-461N23 | 13q32.1 | 24 | 2 | GPR18, PHGDHL1, EBI2 |
Clone name* . | Cytogenetic position . | Gain/loss, no. patients† . | Amplification/homozygous loss, no. patients‡ . | Gene§ . |
|---|---|---|---|---|
| Gain | ||||
| RP3-510D11 | 1p36.22 | 12 | 2 | H6PD, LOC440558 |
| RP5-888M10 | 1p36.21 | 11 | 2 | VPS13D |
| RP5-1177E19 | 1p36.21 | 9 | 2 | PRDM2 |
| RP11-233K4 | 6p25.3 | 18 | 2 | IRF4∥ |
| RP11-498D18 | 7p22.2 | 12 | 2 | CARMA1,∥GNA12 |
| RP5-911H5 | 7q21.2 | 22 | 2 | ANKIB1 |
| RP11-736C20 | 7q21.2 | 23 | 2 | CALCR |
| RP11-148A10 | 7q22.2 | 26 | 2 | LHFPL3 |
| RP11-77E2 | 7q22.3 | 25 | 2 | DLD, LAMB1, LAMB4 |
| RP11-573B16 | 7q31.1 | 25 | 2 | — |
| RP11-9C22 | 7q31.33 | 25 | 2 | SND1 |
| RP11-66F23 | 7q31.33 | 24 | 2 | NYD-SP18, CALU, OPN1SW, DKFZP434G156, FLNC, ATP6V1F, LOC375616 |
| RP11-35B6 | 7q31.33 | 24 | 2 | KIAA0828, FAM40B |
| RP11-233L24 | 7q33 | 21 | 2 | — |
| RP4-659J6 | 7q33 | 24 | 2 | ZC3HDC1, KIAA1718 |
| RP11-188A12 | 7q33 | 20 | 2 | — |
| RP11-796I2 | 7q35 | 17 | 2 | PRKAG2, LOC441301, GALNTL5 |
| RP11-476H24 | 7q36.2 | 18 | 2 | DPP6 |
| RP11-691F21 | 7q36.3 | 18 | 2 | LOC285889 |
| RP11-452C13 | 7q36.3 | 16 | 2 | PTPRN2 |
| RP11-1127D7 | 14q32.2 | 21 | 2 | FLJ25773,¶RPL3P4,¶BCL11B∥¶ |
| Loss | ||||
| RP1-101M23 | 6q21 | 12 | 2 | PRDM1 |
| RP11-149I2 | 9p21.3 | 14 | 2 | MTAP, CDKN2A,∥CDKN2B,∥NSGX |
| RP11-214L15 | 9p21.3 | 7 | 2 | — |
| RP11-468C2 | 9p21.3 | 5 | 2 | — |
| RP11-461N23 | 13q32.1 | 24 | 2 | GPR18, PHGDHL1, EBI2 |
List of BAC clones from p telomere to q telomere are listed for each chromosome number.
Gain was defined as log2 ratio +0.2 to +1.0, loss as log2 ratio -1.0 to -0.2.
Amplification was defined as log2 ratio greater than +1.0 and homozygous loss as log2 ratio less than -1.0.
All of the genes located on the BAC/PAC clones. If there were any oncogenes in the clone adjacent to the amplified or lost one, they were listed.
The names of genes located in the BAC clones adjacent to RP11-1127D7 are listed. BCL11B is 0.3 Mb telomeric to RP11-1127D7.
These genes have been implicated in lymphoid malignancies.17,21