Driver detection in targeted genome sequencing for BCAST and MSK-Impact panels using TCGA breast and lung cancer data.
With the increase in targeted sequencing usage, it is uncertain whether driver detection methods developed for whole-exome are applicable. Here, we highlight an easy to use framework to investigate the applicability of seven driver detection methods when applied to targeted sequencing data. We addressed method applicability by assessing the concordance of matching whole-exome and targeted driver predictions. Whole exome datasets from TCGA MC3 mutation file (v0.2.8) and cancer type labels can be obtained from the TCGA database. Individual matching targeted sequencing datasets were constructed by only keeping mutations overlapping with either the breast-cancer-specific B-CAST panel or the pan-cancer MSK-IMPACT panel.
Felipe Rojas-Rodriguez Netherlands Cancer Institute f.rojas@nki.nl
| Author | Role | Description |
|---|---|---|
| Felipe Rojas-Rodriguez | Author | Development and support |
| Sander Canisius | Author | Development and review |
| Marjanka Schmidt | Author | Review |