Table 1.
Gene Alternation at Diagnosis and Disease Flare
| Gene |
At Diagnosisa |
At Disease Flare |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| RNA-Seq |
RNA-Seq |
WES |
CN Analysis |
||||||||
| Gene Name | Variant Classification | Amino Acid Change | Total Depth | VAF (%) | Total Depth | VAF (%) | Total Depth | VAF (%) | Major CN | Minor CN | Type |
| KIT | In-frame deletion | p.Q575_P577delinsH | 3527 | 96.9 | 854 | 97.7 | 249 | 30.1 | 4 | 0 | AMP-LOH |
| TP53 | Missense mutation | p.Y236C | 1263 | 87.6 | 165 | 58.8 | 136 | 30.9 | 3 | 0 | AMP-LOH |
| KMT2C | Frameshift deletion | p.F2313Wfs∗8 | 670 | 39.7 | 58 | 20.7 | 328 | 21.0 | 3 | 3 | AMP |
| BAP1 | Nonsense mutation | p.W5∗ | 39b | 23.1b | 97 | 52.6 | 331 | 30.5 | 3 | 0 | AMP-LOH |
AMP, amplification; CN, copy number; GATK, Genome Analysis Toolkit; IGV, Integrative Genomics Viewer; LOH, loss of heterozygosity; RNA-seq, RNA sequencing; VAF, variant allele frequency; WES, whole-exome sequencing.
a
We could not carry out whole-exome sequencing because of a lack of DNA quantity.
b
Although the GATK pipeline did not detect this mutation, we observed it using the IGV.