Table 1 Reference laboratory results from the UK National External Quality Assessment Scheme (NEQAS) pilot HER2 fluorescence in situ hybridisation (FISH) scheme.

	HER2:chromosome 17 ratio			HER2 copy number
	Average	Range	Borderline	Average	Range	Borderline
MDA‐MB‐231
Run 1	1.09 (0.05)	0.87–1.43	0.78–1.57	2.41 (0.12)	1.55–2.85	1.40–3.14
Run 2	1.16 (0.08)	0.88–1.44	0.79–1.58	2.25 (0.25)	1.53–2.80	1.38–3.08
Run 3	1.04 (0.05)	0.71–1.19	0.64–1.31	2.62 (0.22)	1.45–3.65	1.31–4.02
BT20/MDA‐MB‐175*
Run 1	0.93 (0.04)	0.74–1.15	0.67–1.27	3.05 (0.14)	2.50–4.15	2.25–4.57
Run 2	1.19 (0.08)	0.92–1.34	0.83–1.47	2.97 (0.20)	2.60–3.55	2.34–3.91
Run 3	1.21 (0.02)	1.13–1.29	1.02–1.42	3.32 (0.26)	1.70–4.17	1.53–4.59
MDA‐MB‐453
Run 1	2.37 (0.06)	2.12–2.72	1.91–2.99	6.72 (0.24)	5.70–8.20	5.13–9.02
Run 2	2.30 (0.13)	2.08–2.85	1.87–3.14	6.21 (0.18)	5.78–6.90	5.20–7.59
Run 3	2.39 (0.09)	2.10–2.90	1.89–3.19	7.45 (0.42)	5.00–10.0	4.50–11.0
SK‐BR‐3
Run 1	3.52 (0.14)	2.58–4.09	2.32–4.50	14.57 (0.34)	13.3–17.1	12.0–18.8
Run 2	3.53 (0.20)	3.01–4.06	2.71–4.47	13.53 (0.80)	12.1–16.1	10.9–17.7
Run 3	3.88 (0.12)	3.37–4.41	3.03–4.85	16.23 (0.78)	11.7–20.7	10.5–22.8

Mean (SEM) of results from reference laboratories relating to three separate quality assurance “runs” during 2004/05. Results are expressed either as copies of HER2 gene per chromosome 17 (HER2/chromosome 17 ratio) or mean copies of HER2/cell (HER2 copy number). Five separate cell lines were used to represent either non‐amplified or amplified breast carcinomas.

*BT20 was used in run 1 and MDA‐MB‐175 was used for runs 2 and 3.