Table 1.

Comparison of IHC, FISH and SNP data

	IHC/FISH		SNP array
Tumor sample number	HER2 IHC	HER2 FISH	HER2 segment copy number	HER2/CEP17 ratio	HER2 copy number status
1	0	n/a	1,98	balance	normal
2	0	n/a	2,35	HER2+	amp*
3	0	1,92	1,81	balance	normal
4	0	n/a	2,06	balance	normal
5	0	n/a	2,04	balance	normal
6	0	n/a	1,72	cent+	del
7	0	n/a	1,67	balance	del
8	0	n/a	1,83	balance	normal
9	0	n/a	1,51	cent+	del
10	0	n/a	2,51	balance	amp*
11	0	n/a	1,78	balance	del
12	0	n/a	1,85	balance	normal
13	1	n/a	1,97	balance	normal
14	1	n/a	2,08	balance	normal
15	1	0,83	2,33	balance	amp*
16	1	0,80	1,70	balance	del
17	1	0,80	1,80	cent+	normal
18	1	0,86	2,49	balance	amp*
19	1	n/a	2,06	balance	normal
20	1	n/a	2,09	balance	normal
21	1	n/a	1,96	balance	normal
22	1	n/a	1,97	balance	normal
23	1	n/a	2,13	balance	normal
24	1	n/a	1,90	balance	normal
25	1	n/a	1,87	balance	normal
26	1	n/a	4,46	balance	amp*
27	1	n/a	2,34	balance	amp*
28	2	1,41	2,45	balance	amp*
29	2	1,54	2,16	balance	normal
30	2	3,05*	2,04	balance	normal
31	2	2,69*	2,48	balance	amp*
32	2	2,42*	1,75	cent+	del
33	2	1,73	1,99	balance	normal
34	2	2,65*	1,92	balance	normal
35	2	1,50	1,91	balance	normal
36	2	1,57	2,00	balance	normal
37	2	1,68	1,79	balance	del
38	2	1,90	1,84	balance	normal
39	2	1,60	2,05	balance	normal
40	2	1,58	1,89	balance	normal
41	2	2,13*	2,73	balance	amp*
42	2	1,54	2,04	balance	normal
43	2	1,82	1,54	balance	del
44	2	1,90	1,77	balance	del
45	2	1,66	2,33	balance	amp*
46	2	1,48	2,04	balance	normal
47	2	1,73	1,98	balance	normal
48	2	1,67	2,36	balance	amp*
49	2/3	0,93/8,8	11,10	HER2+	amp*
50	2	1,81	2,04	balance	normal
51	2	1,58	2,65	HER2+	amp*
52	2	1,60	2,23	balance	amp*
53	2	2,27*	8,03	HER2+	amp*
54	2	1,87	2,91	balance	amp*
55	2	1,24	2,66	balance	amp*
56	2	7,38*	7,01	HER2+	amp*
57	2	1,00	1,88	balance	normal
58	2	8,60*	7,98	HER2+	amp*
59	2	3,24*	3,18	HER2+	amp*
60	3*/1	1,65	2,00	balance	normal
61	3	4,11*	5,28	HER2+	amp*
62	3	7,00*	4,58	HER2+	amp*
63	3*/2	1,50	2,05	balance	normal
64	3*	n/a	3,15	HER2+	amp*
65	3*	1,35	3,75	HER2+	amp*

Asterisk indicates HER2 positive results, while bold indicates samples that have been reanalyzed. Abbreviations: amp amplified CEP17 centromere on chromosome 17, del deletion, FISH fluorescent in situ hybridization, HER2 human epidermal growth factor receptor-2, IHC immunohistochemistry, n/a not analysed.