Table 3.
GATA2 and CEBPA alterations in patients with CEBPA DM
| Patient ID | RNA frequency* | GATA2 ASE† | GATA2 expression, TPM | GATA2 mutations‡ | GATA2 allele expressed§ | CEBPA mutations|| | CEBPA expression, TPM | CEBPA mutation VAF | ||
|---|---|---|---|---|---|---|---|---|---|---|
| n | Type (VAF) | Mut1 | Mut2 | |||||||
| 1316 | 0.233 | Skewed | 106.2 | 0 | — | — | N/C | 483.9 | 0.462 | 0.448 |
| 2192 | 0.023 | Monoallelic | 456.2 | 2 | ZF1 (0.39), ZF2 (0.59) | Mut (indel), mut (0.97) | N/C | 390.3 | 0.526 | 0.486 |
| 2218 | 0.263 | Skewed | 67.8 | 0 | — | — | C/C | 308.9 | 0.923 | HMZ |
| 2234 | 0.144 | Skewed | 28.5 | 2 | ZF1 (0.03) | Mut (0.07) | N/C | 380.5 | 0.498 | 0.475 |
| 2240 | 0.223 | Skewed | 41.0 | 1 | ZF1 (0.02) | Mut (0.03) | N/C | 328.0 | 0.486 | 0.461 |
| 2242 | Unknown | 55.5 | 0 | — | — | N/C | 162.0 | 0.472 | 0.447 | |
| 2253 | 0.269 | Skewed | 106.2 | 1 | ZF1 (0.47), ZF2 (0.07) | Mut (0.71), mut (0.49) | N/C | 168.1 | 0.490 | 0.418 |
| 2273 | 0.0993 | Monoallelic | 61.0 | 1 | ZF1 (0.47) | Mut (0.92) | N/C | 161.4 | 0.488 | 0.423 |
| 2545 | 0.037 | Monoallelic | 106.5 | 1 | ZF2 (0.39) | Mut (0.96) | N/C | 274.7 | 0.497 | 0.484 |
| 2753 | 0.106 | Skewed | 40.9 | 1 | ZF1 (0.45) | Mut (0.93) | N/C | 233.7 | 0.448 | 0.441 |
| 3101¶ | 0.126 | Skewed | 50.9 | 0 | — | — | N/N | 194.4 | NA | NA |
| 3327 | 0.071 | Monoallelic | 94.1 | 0 | — | — | C/C | 86.2 | 0.918 | HMZ |
| 4336 | 0.285 | Skewed | 36.7 | 0 | — | — | N/C | 143.7 | 0.442 | 0.470 |
| 5352 | 0.174 | Skewed | 24.3 | 0 | — | — | N/C | 417.6 | 0.472 | 0.412 |
| 5362 | 0.064 | Monoallelic | 60.2 | 2 | ZF1 (0.03), ZF2 (0.49) | Mut (0.12), mut (0.93) | N/C | 238.8 | 0.497 | 0.464 |
| 5364 | 0.097 | Monoallelic | 113.9 | 0 | — | — | N/N | 427.4 | 0.283 | 0.277 |
| 6376 | 0.024 | Monoallelic | 43.4 | 0 | — | — | C/C | 258.7 | 0.899 | HMZ |
| 7142 | 0.208 | Skewed | 29.7 | 0 | — | — | N/C | 141.2 | 0.482 | 0.473 |
| AML0104 | 0.107 | Monoallelic | 66.6 | 0 | — | — | C/C | 264.1 | 0.422 | HMZ |
| AML0129# | 0.018 | Monoallelic | 10.1 | 0 | — | — | N/N | 169.5 | 0.035 | 0.334 |
| AML0135 | 0.097 | Monoallelic | 60.3 | 2 | ZF1 (0.19), ZF2 (0.37) | Mut (0.46), mut (0.87) | N/C | 125.0 | 0.399 | 0.173 |
| UKR169 | 0.051 | Monoallelic | 13.9 | 1 | ZF1 (0.45) | Mut (0.96) | N/C | 318.8 | 0.847 | HMZ |
HMZ, homozygous; mut, mutated allele; NA, not available; TPM, transcripts per million; ZF, zinc finger.
Indicates the proportion of reads that come from the minor allele for all the single-nucleotide polymorphisms considered in the gene.
Categorized as monoallelic for RNA frequency ≤0.10 or skewed for RNA frequency ≤0.35. The expression of GATA2 and CEBPA is presented in TPM as reported by Salmon.
Contains the no., type (ZF1/2), and VAF of the mutations identified in GATA2.
Includes the VAF of these GATA2 mutations measured in the RNA.
VAF of the 2 CEBPA mutations, based on deep amplicon sequencing, is indicated in N- to C-terminal order.
Amplicon sequencing was not conducted for 3101, and CEBPA VAF was unavailable.
AML0129 had a CEBPA mutation in only 1 allele, but the other allele was not expressed; therefore, it acted like a CEBPA HMZ mutation at the transcriptional level.