SJPedPanel: A pan cancer gene panel for childhood malignancies

Extensive efforts in the past decade have revolutionized our understanding of the genetic underpinnings of childhood malignancies. Many of these genetic alterations define diseases and subtypes and some result in potential targets and vulnerabilities for novel therapeutics. Furthermore, our prior studies indicated that these alterations are excellent biomarkers for disease monitoring via ultra-deep sequencing. For these purposes, the traditional whole genome/exome sequencing approach can be resource prohibitive. Toward this challenge, we have developed a pan-cancer gene panel for childhood malignancies. We validated the effectiveness of this panel using 114 previously established clinical specimens. We demonstrated the power of this panel in detecting cancer cells from specimens with very low tumor content using both cell line-based dilution experiments and clinical specimens collected from AML patients in morphologic remission, establishing its potential for disease monitoring. We also provide cost estimates under state-of-art clinical practices. We expect this gene panel to significantly impact the clinical management of childhood cancers.