Comprehensive genomic profiling
CGP was performed using either FoundationOne® CDx or
FoundationOne® Heme oncopanels (Foundation Medicine,
Inc., Cambridge, MA, USA). Both are clinical-grade Clinical Laboratory
Improvement Amendments (CLIA)-approved next-generation sequencing tests.
FoundationOne® CDx interrogates 324 genes for single
nucleotide variants, copy number alterations, indels, gene arrangements,
tumor mutation burden (TMB), and microsatellite status (Table S1), while
FoundationOne® Heme interrogates 406 genes and
selected introns of 31 genes involved in rearrangements. Additionally,
FoundationOne® Heme interrogates the RNA of 265 genes
commonly rearranged in cancer to better identify known and novel gene
fusions (Table S2). Therefore, FoundationOne® Heme is
a more effective assay for pediatric patients with hematologic
malignancies, sarcoma, and other solid tumors.