RNA Sequencing Improves Gene Fusion Detection in Childhood Cancers

Nearly 20% of all cancers and metastases result from gene fusions—chromosomal rearrangements that lead to chimeric transcripts. This makes gene fusion detection critical for accurate diagnosis, prognosis, and treatment. Yet, current diagnostic methods such as RT-PCR (reverse transcriptase polymerase chain reaction), FISH (fluorescence in situ hybridization), karyotyping and SNP (single nucleotide polymorphism) arrays are often unable to detect gene fusions.

A new study from scientists at the Princess Máxima Center in the Netherlands demonstrates RNA sequencing can overcome the limitations of traditional diagnostic methods in identifying gene fusions. The researchers conducted RNA sequencing on 24 samples with a known gene fusion event to validate their method and thereafter performed prospective RNA sequencing in 244 patients, in addition to routine diagnostic procedures.

Their findings were published in an article the journal JCO Precision Oncology on January 27, titled “Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing.” The study was funded by NWO, KiKa and the Adessium Foundation.

“We identified a clinically relevant gene fusion in 83 of 244 cases in the prospective cohort,” the authors note. The 244 cases consisted of tissue samples from children with suspected cancer who were referred to the Princess Máxima Center between late 2018 and mid-2019.

The investigators found 60 fusions through both routine diagnostic techniques and RNA sequencing, and one fusion through routine diagnostics alone. However, RNA sequencing was able to detect 24 fusions that could not be detected by routine diagnostics, increasing the diagnostic yield by 38–39%. RNA sequencing had the added benefit of identifying both gene partners involved in the gene fusion, in contrast to most routine techniques.

“RNA sequencing was already used before, but only in children who were very ill, and for whom standard treatment had stopped working. 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,” said Bastiaan Tops, MD, head of the Diagnostic Lab at the Princess Máxima Center for pediatric oncology, and co-leader of the study. “Because we can look at the full genetic landscape of a child’s tumor at diagnosis, we can discuss possible consequences for treatment with the child’s doctor right away. That means we can offer children with cancer the very best opportunities, based on the latest scientific insights.”

For two patients, the new fusion identified through RNA sequencing led doctors to adopt more targeted treatment options. In the case of one girl, the pathologist’s diagnosis was modified to infantile fibrosarcoma, a soft tissue tumor, with an NTRK fusion that led to her receiving a new targeted drug as part of a clinical trial. In another instance, the diagnosis of a one-year-old boy with a brain tumor was changed from glioblastoma to hemispheric glioma, a tumor with a less bad outcome. When standard treatment stopped working, he was given a precision medicine that kept him stable for another year.

“In this study, we show that a single test that searches the entire tumor RNA is almost one and a half times more sensitive to genetic faults in childhood cancer,” said Patrick Kemmeren, MD, group leader and head of the Big Data Core at the Princess Máxima Center for Pediatric Oncology, and a co-author of the study. “In my group, we conduct much broader research into DNA and RNA abnormalities in childhood cancer. If we discover new abnormalities, they can also be immediately included as part of new diagnoses—and even tested retrospectively in children who are already under treatment. In this way, children with cancer benefit as quickly as possible from new findings within fundamental research.”

The authors expect RNA sequencing will replace traditional methods of diagnosing cancer-related genetic abnormalities in the foreseeable future.