Molecular delineation of 7 regions of homozygous genomic loss in B-NHL and identification of putative tumor suppressor genes in B-NHL
| Region of chromosome deletion* . | Cell lines . | Deleted BACs . | Size of region of deletion (Mb)*† . | Putative target genes within region of deletion . |
|---|---|---|---|---|
| 1p32.3 | HBL2, UPN1 | — | 0.006-0.690 | INK4c/P18 |
| 2q13 | UPN1‡, SP49, SP53, JEKO1, Z-138, P32 | — | 0.043-0.751 | BIM |
| 3p14.2 | P32 | 11-94D19 | 0.2 | FHIT |
| 4q35.1 | ELIJAH | 11-203L17, RP11-159A22 | 0.25 | ARGBP2, SNX25 |
| 9p21.3-9p21.2§ | REC1, Z-138, OZ, Karpas 353, DOHH2, MD903‖, Granta 452, Granta 380 | B-65D18, RP11-33015, RP11-85J15, RP11-55P9, CTD-2170E19, RP11-235F7 | 0.1-5.6 | INK4/ARF |
| 16p13.13 | K1106 | 11-396B14¶, RP11-49M6, RP11-547D14¶ | 0.6 | SOCSI, LITAF |
| 18q21.32-18q21.33 | ELIJAH | 11-12J12, RP11-40D15, RP11-15C15 | 2.0 | NOXA |
| Region of chromosome deletion* . | Cell lines . | Deleted BACs . | Size of region of deletion (Mb)*† . | Putative target genes within region of deletion . |
|---|---|---|---|---|
| 1p32.3 | HBL2, UPN1 | — | 0.006-0.690 | INK4c/P18 |
| 2q13 | UPN1‡, SP49, SP53, JEKO1, Z-138, P32 | — | 0.043-0.751 | BIM |
| 3p14.2 | P32 | 11-94D19 | 0.2 | FHIT |
| 4q35.1 | ELIJAH | 11-203L17, RP11-159A22 | 0.25 | ARGBP2, SNX25 |
| 9p21.3-9p21.2§ | REC1, Z-138, OZ, Karpas 353, DOHH2, MD903‖, Granta 452, Granta 380 | B-65D18, RP11-33015, RP11-85J15, RP11-55P9, CTD-2170E19, RP11-235F7 | 0.1-5.6 | INK4/ARF |
| 16p13.13 | K1106 | 11-396B14¶, RP11-49M6, RP11-547D14¶ | 0.6 | SOCSI, LITAF |
| 18q21.32-18q21.33 | ELIJAH | 11-12J12, RP11-40D15, RP11-15C15 | 2.0 | NOXA |
— indicates BACs not deleted.
Map positions and cytogenetic locations are based on data available through the UCSC genome browser (May 2004 freeze).
Molecular delineation of regions of homozygous genomic loss was performed using array CGH, FISH, and PCR of genomic DNA. For delineation of homozygous deletion borders, the more open positions of deleted BACs have been used. The homozygous deletions of BIM and CDKN2C were demonstrated only by PCR.
In UPN1 cell line, partial homozygous deletion of BIM locus was demonstrated by PCR of genomic DNA.
REC1, Z138, K353, DOHH2, G452, and 380 cell lines showed only one deleted BAC, CTB-65D18, sized 0.1 Mb (9p21.3). OZ and MD903 cell lines showed a region of deletion of 5.6 Mb (9p21.3-9p21.2), from CTB-65D18 to RP11-235F7.
In MD903 cell line, partial homozygous deletion of CTB-65D18 including the INK4/ARF locus was demonstrated by PCR of genomic DNA.
Homozygous deletion of BACs not included in the array was demonstrated by FISH.