Table 2.
Genes with significant combined burden of somatic CNVs and somatic SNVs.
| Gene | SCNV Type | % of CTCL With SCNV or SSNV | % of CTCL with Deletions | SSNVs | Q-value | Likelihood Ratio | ||
|---|---|---|---|---|---|---|---|---|
| Biallelic | Monoallelic | |||||||
| Focal | Broad | |||||||
| TP53 | Deletion | 92.5 | 2.5 | 7.5 | 80 | NS (3), MS (4) | 5.1 × 10−7 | 1.9 × 106 |
| ZEB1 | Deletion | 65 | 12.5 | 20 | 27.5 | NS (2), MS (1) | 2.8 × 10−19 | 5.9 × 105 |
| ARID1A | Deletion | 62.5 | 0 | 57.5 | 0 | NS (1), FS (1) | 5.7 × 10−24 | 2.4 × 103* |
| DNMT3A | Deletion | 42.5 | 2.5 | 27.5 | 7.5 | NS (1), MS (3) | 2.3 × 10−13 | 2.3 × 105 |
| FAS | Deletion | 42.5 | 2.5 | 10 | 27.5 | MS (3) | 2.2 × 10−3 | 1.3 ×104 |
| CDKN2A | Deletion | 40 | 30 | 7.5 | 2.5 | NS (1) | 3.1 × 10−34 | 6.5 × 105 |
|
| ||||||||
| Gene | SCNV Type | % of CTCL With SCNV or SSNV | % of CTCLs with SCNVs | SSNVs | Q-value | Likelihood Ratio | ||
| Focal | Broad | |||||||
|
| ||||||||
| NFKB2** | C-terminal truncations | 12.5 | 10 | 0 | SS (1) | 5.1 × 10−43 | 5.8 × 1023 | |
NS, nonsense (premature termination) mutation; MS, missense mutation; FS, frameshift mutation; SS, Splice-site mutations. Numbers in parentheses indicate number of CTCLs with SSNVs. Q-value, family-wise error rate for burden of SSNVs and focal SCNVs. Likelihood ratio represents the probability of the total number of somatic mutations in the listed gene occurring by chance divided by the probability of the next most likely gene in the focal SCNV interval.
Likelihood ratio based on number of focal deletions and damaging SSNVs (frameshift, nonsense or splice site mutations).
includes two truncating mutations (one deletion and a splice-site mutation) upstream of exon 17 and three truncating deletions upstream of exon 18.