Pediatric Cancer Sequencing Expands Relapse Treatment Options

Comprehensive molecular profiling of tumors through high-throughput technologies identifies molecular targets and predictive biomarkers.

Together with improved understanding of tumor biology and development of targeted anticancer agents, these approaches have facilitated therapeutic approaches adapted to cancer molecular profiles. This “cancer precision medicine” approach has now been implemented to guide treatment in patients with advanced malignancy, including in children.

A large team of international scientists working with the Gustave Roussy Cancer Center (Villejuif, France) collected tissue samples from 787 patients in France, Italy, Ireland, and Spain from 2016 to 2020, with a subset of 624 individuals successfully sequenced. A clinical molecular tumor board then reviewed the data for each participant, and classified the findings into two groups, either "ready for routine use," which comprised gene alterations with significant clinical evidence supporting targeted drug efficacy, or "potentially actionable," which meant cases where there was at least some evidence that an approved or investigational drug could target the mutated protein or another member of the affected signaling pathway.

The team used whole-exome sequencing (WES) and sequencing libraries were constructed according to standard procedures from 600 ng of tumor and paired constitutional DNA. Sequencing of subsequent libraries was performed using Illumina sequencers: Next-Seq 500 or HiSeq 2000/2500/4000 (Illumina, San Diego, CA, USA), in 75 bp paired-end mode, aiming for a mean depth of coverage of 100×. For RNA sequencing libraries were prepared with TruSeq Stranded mRNA kit, PolyA mRNA capture with oligo dT beads 1 mg total RNA, fragmentation to approximately 400 bp, cDNA double strand synthesis, and ligation of adaptors, library amplification and sequencing.

The investigators reported that among the 624 sequenced patients, the Gustave Roussy molecular tumor board marked 436 as having potentially actionable alterations, with about 10% of those "ready for routine use." Oncologists went on to treat 107 of these individuals with a matched targeted therapy, either alone, in combination with chemotherapy, or with another targeted drug. For patients who received a matched therapy, the average overall response rate was 17 %, with a 41% disease control rate. For the subset with "ready for routine use" alterations the objective response rate was 38%. Though physicians did not make treatment decisions based on this arm of the study, the group was successful in sequencing whole exomes in ctDNA from 128 patients, identifying 94 potentially actionable mutations, about 76% of those found in tumor tissue. Liquid biopsy also identified 35 targets that had not been detected by the matched tumor WES.

The authors concluded that their study underlines the feasibility of molecular profiling at the time of pediatric cancer recurrence on a multicenter international level. While selected high evidence level alterations should be part of the initial diagnostic workup, cancer complexity justifies the continuous efforts and introduction of high-throughput sequencing and treatment recommendations as a standard of care for high risk cancers. The study was published on March 16, 2022 in the journal Cancer Discovery.

Related Links:
Gustave Roussy Cancer Center 
Illumina