Table 3.
Regions containing a putative homozygous deletion in more than one cell line
| Chromosome | Region (Mb)a,b | CRO (Mb)a,b | Cell lines with homozygous loss | Tumors with hemizygous loss | Genes |
| 8 | 4.8–7.6 | 2.8 | 3 (16.7%) | 19 (40%) | ANGPT2, LPAAT-e, DEFA1, DEFA3, DEFA4, DEFA5, DEFA6, DEFB1, DEFB10, DEFT1, SPAG11, DEFB103, DEFB104, DEFB105, DEFB106, DEFB4, CLDN23 |
| 8 | 10.3–11.7 | 1.4 | 2 (%) | 6 (13%) | UNQ9391, RP1L1, SOX7, PINX1, MTMR9, AMAC, TDH, BLK, GATA4, NEIL2 |
| 8 | 19.9–20.0 | 0.1 | 2 (11.1%) | 15 (32%) | PCM1, NAT1, NAT2, EFA6R, ChGn, LPL, GFRA2, DOK2, XPO7, NPM2, FGF17, EPB49, RAI16 |
| 8 | 23.5–27.5 | 4.0 | 2 (11.1%) | 17 (36%) | TNFRSF10A, EFL, DOCK5, GNRH1, KCTD9, EBF2, PPP2R2A, BNIP3L, PTK2B |
| 9 | 0.6–4.2 | 3.6 | 2 (11.1%) | 9 (19%) | ANKRD15, DMRT1, DMRT2, DMRT3, SMARCA2, VLDLR, KCNV2, RFX3, ZNF515 |
| 9 | 27.6–27.9 | 0.3 | 2 (11.1%) | 14 (30%) | ELAV, PLAA, CCDC2, LRRC19, TEK, MOB3B, IFNK |
| 13 | 72.1–74.0 | 1.9 | 2 (11.1%) | 6 (13%) | KLF12, TBC1D4, UCHL3 |
| 18 | 32.2–37.4 | 5.2 | 2 (11.1%) | 9 (19%) | BRUNOL4 |
| 18 | 38.1–41.8 | 3.7 | 3 (16.7%) | 13 (28%) | RIT2, SYT4, SETBP1 |
| 18 | 46.8–52.8 | 6.0 | 2 (11.1%) | 6 (13%) | MADH4, DCC, MBD2, POLI, STARD6, RAB27B, SE57-1, TCF4, TXNL, WDR7 |
aMap positions and cytogenetic locations containing putative homozygous deletions (intensity ratio <0.5 within a region of hemizygous loss) are based on data available from UCSC genome browser (July 2003 freeze) [35]. bRegion boundaries were determined by the next bacterial artificial chromosome with different copy number. CRO, common region of overlap.