Copy Number
The putative cancer-causing HAMPs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).
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| HGNC | Ensembl | Overall_Gscore | No. of Cancer Types | ||
| Symbol | Gene ID | Amplification | Deletion | Amplification | Deletion |
| CECR2 | ENSG00000099954 | 0 | 0.13 | 0 | 1 |
| KIAA2026 | ENSG00000183354 | 0.25 | 0.12 | 1 | 1 |
| BRD1 | ENSG00000100425 | 0 | 1.57 | 0 | 7 |
| BRPF3 | ENSG00000096070 | 0 | 0 | 0 | 0 |
| BRPF1 | ENSG00000156983 | 0 | 0.36 | 0 | 2 |
| BRD7 | ENSG00000166164 | 0 | 0.14 | 0 | 1 |
| BRD9 | ENSG00000028310 | 2.81 | 0 | 9 | 0 |
| BAZ2A | ENSG00000076108 | 0 | 0 | 0 | 0 |
| BAZ2B | ENSG00000123636 | 0 | 0 | 0 | 0 |
| ATAD2 | ENSG00000156802 | 1.54 | 0 | 5 | 0 |
| ATAD2B | ENSG00000119778 | 0.17 | 0 | 1 | 0 |
| BRD8 | ENSG00000112983 | 0.28 | 0.12 | 1 | 1 |
| BRWD3 | ENSG00000165288 | 0 | 0 | 0 | 0 |
| BRWD1 | ENSG00000185658 | 0.15 | 0 | 1 | 0 |
| PHIP | ENSG00000146247 | 0 | 0.14 | 0 | 1 |
| HDAC1 | ENSG00000116478 | 0 | 0 | 0 | 0 |
| HDAC2 | ENSG00000196591 | 0 | 0.41 | 0 | 3 |
| HDAC3 | ENSG00000171720 | 0.3 | 0.15 | 1 | 1 |
| HDAC8 | ENSG00000147099 | 0 | 0 | 0 | 0 |
| HDAC11 | ENSG00000163517 | 0 | 0.18 | 0 | 1 |
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