Table 1.

Thresholds Used to Call Gains and Losses in Array CGH Publications in the Year 2005

Reference number	Thresholds used (log2 ratio values unless otherwise stated)	Reason for selection
13	±0.25	None identified
14, 15, 16	±0.3
17, 18	±0.4
19	±0.5
20, 21, 22	±0.2	±2 SDs from normal hybridizations
23	±0.08	±3 SDs from normal hybridizations
24	±0.13
25	±0.3
26	±0.42
27, 28	±2 SDs of each sample profile	±2 SDs of each sample profile
29	±2.5 SDs of each sample profile	±2.5 SDs of each sample profile
30	±3 SDs of all clones	±3 SDs of all clones
31	±3 SDs of the normal regions of each sample	±3 SDs of the normal regions of each sample
32	Gain 0.39; loss −0.5	None identified
33	± 0.4	Gaussian modeling
34, 35	Loss by comparison with X chromosome controls; gains using arbitrary values	X chromosome controls for losses
36	Gain 1.2; loss 0.69 (absolute ratio values)	FISH validation of true positives
37, 38, 39	Gain 1.2; loss 0.8 (absolute ratio values)	None identified
40	Gain 1.5; loss 0.5 (absolute ratio values)
41	Amplified 1.8; deleted 0.55 (absolute ratio values)

The literature search was done via the National Library of Medicine (NCBI) search engine (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi), using the search term ′array CGH.′ This search resulted in 90 studies (up to the end of December, 2005). The studies were surveyed for their relevance by reading the abstracts, when available. Twenty-nine relevant studies were found, and these were assessed in more detail.