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Table 1: Top focal regions of amplification and deletion
| Cytoband* | q value | Peak region* | Max /Min inferred copy # | # of genes *^ | Known proto-oncogene/ tumor suppressor gene in region *# | New candidate(s) |
| Amplifications | | | | | | |
| 14q13.3 | 2.26E-29 | 35.61-36.09 | 13.7 | 2 | | NKX2-1, MBIP |
| 12q15 | 1.78E-15 | 67.48-68.02 | 9.7 | 3 | MDM2 | |
| 8q24.21 | 9.06E-13 | 129.18-129.34 | 10.3 | 0 | MYC $ | |
| 7p11.2 | 9.97E-11 | 54.65-55.52 | 8.7 | 3 | EGFR | |
| 8q21.13 | 1.13E-07 | 80.66-82.55 | 10.4 | 8 | | |
| 12q14.1 | 1.29E-07 | 56.23-56.54 | 10.4 | 15 | CDK4 | |
| 12p12.1 | 2.83E-07 | 24.99-25.78 | 10.4 | 6 | KRAS | |
| 19q12 | 1.60E-06 | 34.79-35.42 | 6.7 | 5 | CCNE1 | |
| 17q12 | 2.34E-05 | 34.80-35.18 | 16.1 | 12 | ERBB2 | |
| 11q13.3 | 5.17E-05 | 68.52-69.36 | 6.5 | 9 | CCND1 | |
| 5p15.33 | 0.000279 | 0.75-1.62 | 4.2 | 10 | TERT | |
| 22q11.21 | 0.001461 | 19.06-20.13 | 6.6 | 15 | | |
| 5p15.31 | 0.007472 | 8.88-10.51 | 5.6 | 7 | | |
| 1q21.2 | 0.028766 | 143.48-149.41 | 4.6 | 86 | ARNT | |
| 20q13.32 | 0.0445 | 55.52-56.30 | 4.4 | 6 | | |
| 5p14.3 | 0.064673 | 19.72-23.09 | 3.8 | 2 | | |
| 6p21.1 | 0.078061 | 43.76-44.12 | 7.7 | 2 | | VEGFA |
| Deletions | | | | | | |
| 9p21.3 | 3.35E-13 | 21.80-22.19 | 0.7 | 3 | CDKN2A/ CDKN2B | |
| 9p23 | 0.001149 | 9.41-10.40 | 0.4 | 1 | | PTPRD $$ |
| 5q11.2 | 0.005202 | 58.40-59.06 | 0.6 | 1 | | PDE4D |
| 7q11.22 | 0.025552 | 69.50-69.62 | 0.7 | 1 | | AUTS2 |
| 10q23.31 | 0.065006 | 89..67-89.95 | 0.5 | 1 | PTEN | |
* based on hg17 human genome assembly, positions in Mb;
^ RefSeq genes only;
# Known tumor suppressor genes and proto-oncogenes defined as found in either COSMIC, CGP Census or other evidence; if there is more than one known proto-oncogene in the region, only one is listed (priority for listing is, in order: known lung adenocarcinoma mutation, known lung cancer mutation, other known mutation (by COSMIC frequency), listing in CGP Census);
$ MYC is near, but not within the peak region;
$$ Single gene deletions previously seen, this study provides new mutations as well.
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