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

Breast Cancer Research

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 genes^a	Cytogenetic band	Number of genes	Cancer genes^a	Cytogenetic band	Number of genes	Cancer genes^a
6q	20% of ATM tumours							6q23.3-q27	190	ARID1B, ECT2L, ESR1, EZR, FGFR10P, QKI, TNFAIP3
8p	Breast cancer	8p21.3	6^b	–	8p23.3-p12	216	WRN, NRG1	8p21.3	6^b	–
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	1^c	–	16q22.1	1^c	–
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	2^a	–	21p11.2-p11.1	2^d	–
22q	Luminal B tumours, 70% ATM tumours	22q11.23	2^b		22q11.23	3^e	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

ISSN: 1465-542X