Comparative RNA-sequencing analysis benefits a pediatric patient with relapsed cancer.

Clinical detection of sequence and structural variants in known cancer genes points to viable treatment options for a minority of children with cancer.¹ To increase the number of children who benefit from genomic profiling, gene expression information must be considered alongside mutations.^2,3 Although high expression has been used to nominate drug targets for pediatric cancers,^4,5 its utility has not been evaluated in a systematic way.⁶ We describe a child with a rare sarcoma that was profiled with whole-genome and RNA sequencing (RNA-Seq) techniques. Although the tumor did not harbor DNA mutations targetable by available therapies, incorporation of gene expression information derived from RNA-Seq analysis led to a therapy that produced a significant clinical response. We use this case to describe a framework for inclusion of gene expression into the clinical genomic evaluation of pediatric tumors.