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Table 3 Copy number losses recurrently observed in the 23 ATM-associated breast tumours

From: Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

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    
  1. aAs reported in the COSMIC database
  2. bThis region contains PPP3CC, SORBS3, PDLIM2, BIN3, BIN3-IT1 and EGR3
  3. cThis region contains WWP2 and the microRNA MIR140
  4. dThis region contains TEKT4P2, TPTE and four miRNAs (MIR3648-1, MIR3648-2, MIR3687-1, MIR3687-2)
  5. eThis region contains the pseudogenes GSTTP1 and GSTTP2