Table 3.
Copy number losses recurrently observed in the 23 ATM-associated breast tumours
| Locus | Associated morphology | All ATM tumours (N = 23) | ATM tumours with proven biallelic inactivation of ATM (n = 16) | ATM tumours sequenced by WGS (n = 4) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cytogenetic band | Number of genes | Cancer genesa | Cytogenetic band | Number of genes | Cancer genesa | Cytogenetic band | Number of genes | Cancer genesa | ||
| 6q | 20% of ATM tumours | 6q23.3-q27 | 190 | ARID1B, ECT2L, ESR1, EZR, FGFR10P, QKI, TNFAIP3 | ||||||
| 8p | Breast cancer | 8p21.3 | 6b | – | 8p23.3-p12 | 216 | WRN, NRG1 | 8p21.3 | 6b | – |
| 11q | ATM tumours | 11q22 | 2 | ATM, ZBTB16 | 11q21-q25 | 276 | ATM, ZBTB16, DDX10, POU2AF1, SDHD, ZBTB16, PAFAH1B2, PDCK7, KMT2A, MAML2, DDX6, BCL9L, CBL, ARHGEF12, KCNJ5 | 11q21-q24.2 | 236 | ATM, ZBTB16, DDX10, POU2AF1, SDHD, ZBTB16, PAFAH1B2, PDCK7, KMT2A, MAML2, DDX6, BCL9L, CBL |
| 13q | 70% ATM tumours | 13q14.11-q14.3 | 90 | LCP1, RB1 | 13q13.3-q32.3 | 320 | LHFP, FOXO1, LCP1, RB1 | 13q13.3-q32.3 | 320 | LHFP, FOXO1, LCP1, RB1 |
| 16q | Luminal tumours | 16q13-q24.3 | 364 | HERPUD1, CDH11, CBFB, CTCF, CDH1, ZFHX3, MAF, CBFA2T3, FANCA | 16q22.1 | 1c | – | 16q22.1 | 1c | – |
| 17p | Luminal tumours | 17p13.3 | 46 | YWHAE | – | – | 17p13.3 | 46 | YWHAE | |
| 17p | Luminal tumours | 17p13.2-p12 | 166 | USP6, RABEP1, TP53, GAS7, MAP2K4 | – | – | ||||
| 19p | 40% of ATM tumours | 19p13.3-p13.2 | 256 | FSTL3, GNA11, MAP2K2, MLLT1, SH3GL1, STK11, TCF3 | ||||||
| 21p | 70% of ATM tumours | 21p11.2-p11.1 | 2a | – | 21p11.2-p11.1 | 2d | – | |||
| 22q | Luminal B tumours, 70% ATM tumours | 22q11.23 | 2b | 22q11.23 | 3e | GSTT1 | ||||
| Luminal B tumours, 70% ATM tumours | – | – | – | 22q12.3 | 199 | APOBEC3B, MKL1, EP300 | ||||
aAs reported in the COSMIC database
bThis region contains PPP3CC, SORBS3, PDLIM2, BIN3, BIN3-IT1 and EGR3
cThis region contains WWP2 and the microRNA MIR140
dThis region contains TEKT4P2, TPTE and four miRNAs (MIR3648-1, MIR3648-2, MIR3687-1, MIR3687-2)
eThis region contains the pseudogenes GSTTP1 and GSTTP2