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.