Clonal relationships between lobular carcinoma in situ and other breast malignancies

Breast Cancer Research

Table 2 Mutation frequencies^a

Gene	Mutations per gene^b (20 cases)					Percent functional mutations^c
Gene	Mutations	Cases^d	Clonal	Private	Percent clonal	Clonal		Private
CDH1	24	16	11	13	54 %	11/11	100 %	13/13	100 %
PIK3CA	13	11	9	4	54 %	9/9^e	100 %	4/4	100 %
SPRR3	10	9	1	9	30 %	1/1	55 %	1/9	70 %
CBFB	10	8	7	3		6/6		3/3
GATA3	9	6	2	7		2/2		6/7
NBPF1	8	8	2	6		2/2		4/6
MUC12	7	5	1	6		0/1		4/6
KMT2C	6	6	1	5		1/1		4/5
MUC4	6	5	2	4		0/2		3/4
TCEAL3	6	4	5	1		0/5		0/1
MAP3K1	6	4	3	3		3/3		3/3
BCLAF1	5	5	0	5		0/5		5/5
HMCN1	5	5	0	5		0/0		3/5
TMPRSS13	5	4	1	4		1/1		4/4
REXO1L1	4	4	0	4	13 %	0/0	75 %	0/4	79 %
TDG	4	4	0	4		0/0		3/4
DDX11	4	4	1	3		1/1		2/3
ABCC5	4	4	0	4		0/0		3/4
MACF1	4	4	0	4		0/0		4/4
AGGF1	4	4	1	3		1/1		3/3
OR13C2	4	2	0	4		0/0		4/4
NASP	4	2	0	4		0/0		4/4
SERPINA3	4	2	0	4		0/0		4/4
28 genes	3	3	14	70		10/14		50/70
159 genes	2	2	69	249	16 %	50/69	72 %	164/249	66 %
1477 genes	1	1	224	1253	16 %	158/224	71 %	854/1253	68 %

^aThis table includes only the 20 cases with exome sequencing results available. Data from five tumors that were hypermutated are excluded: case 4 (DCIS1), case 13 (LCIS), case 33 (ILC), case 38 (LCIS), and case 38 (ILC)
^bIf a mutation was observed in two or more tumors from the case, it was designated a “clonal” mutation. If it was detected in a single tumor from the case, it was designated “private.” Note that the sum of clonal and private mutations can exceed the number of cases, since more than one distinct mutational locus can occur in the same patient or even in the same tumor
^cThe category “functional” excludes synonymous mutations
^dThis represents the number of cases in which one or more tumors possess mutations in the designated gene
^eWe note that two of the nine clonal PIK3CA mutations occurred in pairs of ductal tumors

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