Single Test Boosts Childhood Cancer Care

Mutation analysis in oncology is a fast-growing field – but some mutations are trickier than others. Gene fusions present a challenge due to the rarity of individual fusions, the potential for atypical breakpoints, and promiscuous fusion partners. Nonetheless, it’s believed that gene fusions play a role in up to 20 percent of all human cancers (1). In fact, several childhood cancers, including leukemias, lymphomas, and sarcomas, are distinguished by their potential for gene fusions. Accurate detection of these mutations is vital for effective patient care – and that’s why a research team in the Netherlands has employed a method of RNA sequencing using the whole transcriptome in a bid to improve diagnostic accuracy.

The results stem from the Princess Máxima Center for Pediatric Oncology, which has increased its identification of relevant tumor characteristics by almost 40 percent since adopting whole transcriptome RNA sequencing for all of their patients (2). Using the new approach, the researchers were able to identify 83 fusions within 244 patients, 24 of which were missed by traditional methods and seven of which modified the original diagnosis or treatment. And, although standard diagnostics identified many of the same fusion genes, the identification was often just one half of the two-sided fusion, yielding an incomplete picture.

“RNA sequencing was already used before, but only in children who were very ill, and for whom standard treatment had stopped working,” said study co-author Bastiaan Tops (3). “In our research hospital setting at the Princess Máxima Center, we have implemented RNA sequencing into standard diagnostics. Our new study shows that this approach is paying off.”

Whole transcriptome RNA sequencing is not without its disadvantages – most significantly, that the ideal sample size is 300 ng of RNA (with a minimum of at least 50 ng), whereas traditional methods such as RT-PCR require as little as 10 ng. Nonetheless, the study authors encountered insufficient sample volume or quality in only 3 percent of cases, making this a minor issue relative to the clinical benefits offered by whole transcriptome RNA sequencing.