Clonal relationships between lobular carcinoma in situ and other breast malignancies

Begg, Colin B.; Ostrovnaya, Irina; Carniello, Jose V. Scarpa; Sakr, Rita A.; Giri, Dilip; Towers, Russell; Schizas, Michail; De Brot, Marina; Andrade, Victor P.; Mauguen, Audrey; Seshan, Venkatraman E.; King, Tari A.

doi:10.1186/s13058-016-0727-z

Breast Cancer Research

Table 1 Results of all comparisons meeting quality control criteria

From: Clonal relationships between lobular carcinoma in situ and other breast malignancies

Case	Age (years)	Lesion pairs	Same quadrant?	Size of invasive lesion (cm)	Number of mutations (shared/total)^a		Clonality test p values		Diagnosis	Shared mutations^b
Case	Age (years)	Lesion pairs	Same quadrant?	Size of invasive lesion (cm)	Tumor 1	Tumor 2	Mutations^a	Copy number arrays^c	Diagnosis	CDH1	PIK3CA ^d
LCIS-ILC
13	50	LCIS1-ILC	No	1.6	16/3300	16/56	<0.001	0.002	Clonal	–	–
24	57	LCIS1-ILC	Yes	2.1	25/36	25/34	<0.001	<0.001	Clonal	√	√
24	57	LCIS2-ILC	No	2.1	2/29	2/34	<0.001		Clonal	–	–
28	60	LCIS-ILC	Yes	0.12				0.93	Independent
31	69	LCIS-ILC	Yes	1.5				0.31	Independent
33	65	LCIS-ILC	Yes	2.1	66/81	66/1015	<0.001	<0.001	Clonal	–	–
35	72	LCIS-ILC	Yes	4.7				<0.001	Clonal
38	73	LCIS2-ILC	Yes	Missing	23/527	23/615	<0.001	0.54	Clonal	–	–
42	52	LCIS-ILC	Yes	2.3	56/119	56/109	<0.001		Clonal	√	√
42	52	LCIS2-ILC	Yes	2.3				0.01	Equivocal
43	41	LCIS-ILC	Yes	1.9				0.001	Clonal
45	55	LCIS-ILC	Yes	12.2				<0.001	Clonal
46	51	LCIS-ILC	Yes	4.5	0/46	0/15	1.0		Independent
46	51	LCIS3-ILC	No	4.5	0/37	0/15	1.0		Independent
47	51	LCIS1-ILC	No	1.5	7/29	7/25	<0.001	<0.001	Clonal	√	–
47	51	LCIS2-ILC	No	1.5	7/22	7/25	<0.001	0.42	Clonal	√	–
48	37	LCIS1-ILC	Yes	6.0	20/33	20/40	<0.001	<0.001	Clonal	√	–
48	37	LCIS2-ILC	No	6.0	1/22	1/40	0.03	0.10	Equivocal	–	–
52	50	LCIS-ILC	Yes	1.9				0.005	Clonal
52	50	LCIS2-ILC	Yes	1.9				0.05	Independent
55	72	LCIS-ILC	Yes	1.3	6/31	6/36	<0.001	0.002	Clonal	–	√
68	48	LCIS1-ILC	No	1.4	0/44	0/33	1.0	0.58	Independent	–	–
69	56	LCIS-ILC	Yes	3.0	18/56	18/31	<0.001	0.001	Clonal	√	√
73	44	LCIS1-ILC	Yes	0.5	0/26	0/42	1.0		Independent
75	58	LCIS1-ILC	Yes	3.5	15/46	15/39	<0.001		Clonal	√	√
LCIS-IDC
26	54	LCIS-IDC	No	1.8	0/29	0/32	1.0		Independent
47	51	LCIS1-IDC	No	1.0	1/29	1/30	0.02	0.35	Equivocal	–	–
47	51	LCIS2-IDC	No	1.0	1/22	1/30	0.03	0.48	Equivocal	–	–
53	41	LCIS1-IDC	Yes	3.7	2/20	2/23	<0.001	0.40	Clonal	–	–
53	41	LCIS2-IDC	Yes	3.7	1/15	1/23	0.02	0.62	Equivocal	–	–
74	61	LCIS1-IDC	Yes	0.75	0/32	0/34	1.0	0.50	Independent	–	–
		LCIS2-IDC	No		0/37	0/34	1.0	0.73	Independent	–	–
		LCIS3-IDC	No		3/42	3/34	<0.001		Clonal	–	–
75	58	LCIS2-IDC	Yes	1.8	0/22	0/29	1.0		Independent	–	–
LCIS-LCIS
4	44	LCIS1-LCIS2	No	N/A	11/46	11/30	<0.001		Clonal	–	–
5	67	LCIS1-LCIS2	No	N/A				0.85	Independent
8	47	LCIS1-LCIS2	No	N/A	9/34	9/25	<0.001		Clonal	–	–
17	48	LCIS1-LCIS2	No	N/A	13/26	13/27	<0.001		Clonal	√	–
19	43	LCIS1-LCIS2	No	N/A	12/24	12/185	<0.001		Clonal	–	–
24	57	LCIS1-LCIS2	No	N/A	0/36	0/28	1.0		Independent	–	–
38	73	LCIS1-LCIS2	Yes	N/A	23/174	23/527	<0.001		Clonal	–	–
46	51	LCIS-LCIS3	No	N/A	5/46	5/37	<0.001		Clonal	–	–
47	51	LCIS1-LCIS2	Yes	N/A	8/29	8/22	<0.001	0.59	Clonal	√	–
48	37	LCIS1-LCIS2	No	N/A	0/33	0/22	1.0	0.59	Independent	–	–
52	50	LCIS-LCIS2	Yes	N/A	13/28	13/34	<0.001	0.02	Clonal	√	√
53	41	LCIS1-LCIS2	Yes	N/A	6/21	6/17	<0.001	0.005	Clonal	√	–
59	47	LCIS-LCIS2	No	N/A	12/31	12/26	<0.001	0.10	Clonal	√	–
73	44	LCIS3-LCIS4	No	N/A	0/14	0/11	1.0		Independent
74	61	LCIS1-LCIS2	No	N/A	0/32	0/37	1.0	0.02	Independent	–	–
		LCIS1-LCIS3	No	N/A	1/34	1/43	0.03		Equivocal	–	–
		LCIS2-LCIS3	No	N/A	24/37	24/42	<0.001		Clonal	√	–
		LCIS4-LCIS5	No	N/A	14/41	14/47	<0.001		Clonal	–	–
LCIS-DCIS
04	44	LCIS1-DCIS1	Yes	N/A	15/46	15/703	<0.001	<0.001	Clonal	–	–
		LCIS2-DCIS1	No	N/A	10/30	10/703	<0.001		Clonal	–	–
		LCIS1-DCIS2	No	N/A	13/46	13/24	<0.001	<0.001	Clonal	–	–
		LCIS2-DCIS2	Yes	N/A	8/30	8/24	<0.001		Clonal	–	–
06	57	LCIS-DCIS	Yes	N/A	6/50	6/75	<0.001	0.81	Clonal	–	–
16	62	LCIS-DCIS	No	N/A	0/92	0/57	1.0		Independent	–	–
26	54	LCIS-DCIS	No	N/A	0/29	0/34	1.0	0.14	Independent	–	–
47	51	LCIS1-DCIS	Yes	N/A	3/29	3/23	<0.001	0.71	Clonal	–	–
47	51	LCIS2-DCIS	Yes	N/A	0/22	0/23	1.0	0.03	Independent	–	–
59	47	LCIS-DCIS	Yes	N/A	6/31	6/31	<0.001	0.74	Clonal	–	–
59	47	LCIS2-DCIS	No	N/A	2/26	2/31	0.003	0.67	Clonal	–	√
68	48	LCIS1-DCIS	Yes	N/A	8/44	8/33	<0.001	0.03	Clonal	–	–
75	58	LCIS2-DCIS	Yes	N/A	0/22	0/38	1.0		Independent	–	–

^aA blank entry indicates that whole-exome sequencing was not performed
^bIn cases with shared mutations “√” represents the presence of a shared mutation in the designated gene, while a dash represents its absence
^cCopy number comparisons using Agilent comparative genomic hybridization. A blank entry indicates that one or more of the copy number profiles did not meet our quality control criteria (except for case 75, for which copy number profiling was not performed)
^dNote that only seven cases are listed with a PIK3CA match, versus eight in Table 2. The additional match occurred between the two ductal lesions in case 47

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