Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine.

BACKGROUND: High tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an anti-PD-1, received FDA-approval for the treatment of unresectable/metastatic tumors with high TMB as determined by the FoundationOne®CDx test. It remains to be determined how TMB can also be calculated using other tests. RESULTS: FFPE/frozen tumor samples from various origins were sequenced in the frame of the Institut Curie (IC) Molecular Tumor Board using an in-house next-generation sequencing (NGS) panel. A TMB calculation method was developed at IC (IC algorithm) and compared to the FoundationOne® (FO) algorithm. Using IC algorithm, an optimal 10% variant allele frequency (VAF) cut-off was established for TMB evaluation on FFPE samples, compared to 5% on frozen samples. The median TMB score for MSS/POLE WT tumors was 8.8 mut/Mb versus 45 mut/Mb for MSI/POLE-mutated tumors. When focusing on MSS/POLE WT tumor samples, the highest median TMB scores were observed in lymphoma, lung, endometrial, and cervical cancers. After biological manual curation of these cases, 21% of them could be reclassified as MSI/POLE tumors and considered as "true TMB high." Higher TMB values were obtained using FO algorithm on FFPE samples compared to IC algorithm (40 mut/Mb [10-3927] versus 8.2 mut/Mb [2.5-897], p < 0.001). CONCLUSIONS: We herein propose a TMB calculation method and a bioinformatics tool that is customizable to different NGS panels and sample types. We were not able to retrieve TMB values from FO algorithm using our own algorithm and NGS panel.

[De novo cancer after solid organ transplantation: Epidemiology, prognosis and management]. / Cancers solides après transplantation d'organe : épidémiologie, pronostic et spécificités de prise en charge.

The risk of cancer after solid organ transplantation is increased by 2.6 compared to overall population. Cancer is currently the third leading cause of death in solid organ transplanted patients, making screening and early management of de novo cancers a major challenge. This increased risk of cancer in this population results from the combination of known environmental risk factors of cancer, comorbidities of transplanted patients, and exposure to chronic immunosuppression. The prognosis of cancer in these patients seems poorer as compared to other cancer patients owing to their comorbidities, the immunosuppression and patient's poorer tolerance to oncologic treatment. Moreover, interactions between immunosuppressive agents and antitumor therapies must be taken into account in the therapeutic strategy. Better knowledge of the specificities of solid organ transplanted patients with de novo cancer is required to improve cancer care in this patient population. This article aims to review the current data available on de novo cancers in solid organ transplanted patients, with a focus on epidemiology, risks factors of de novo cancers, impact of immunosuppressive drugs and oncologic prognosis.