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Table 3 Regions containing a putative homozygous deletion in more than one cell line

From: High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization

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
  1. 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.