406MO - Sequencing paired tumor DNA and white blood cells (WBCs) increases sensitivity to track plasma circulating tumor DNA (ctDNA) for detecting minimal residual disease (MRD) in localized colon cancer (CC)

Background

Monitoring plasma ctDNA in localized CC detects MRD and patients at higher risk of recurrence. Tumor-only sequencing, without a deep prior knowledge of studied genes, may confounds germline with somatic variants. Consequently, up to 11% of patients cannot be tracked due to the absence of known somatic mutations. We aim at enhancing sensitivity by identifying novel somatic variants sequencing paired tumor DNA and WBCs to monitor CC patients.

Methods

150 patients with localized CC were prospectively recruited from October 2015 to October 2017. A custom 29-gene panel based on the Qiaseq chemistry which includes Unique Molecular Identifier was designed. The panel contains recurrent mutated regions and genes in CC. DNA extracted from matched FFPE and WBCs samples was sequenced on NextSeq platform at 500X and 1500X. Data analysis was performed with an optimized in-house bioinformatics pipeline to reduce background noise in variant calling. Variant allele frequency (VAF) was limited to 5%. Variants were ranked attending to VAF. Known pathogenic variants were determined based on our knowledge somatic variant database. Statistical analysis included log-rank test, Fischer´s exact test and Kaplan-Meier curves.

Results

All patients presented at least one cancer somatic mutation (CSM) trackable by ctDNA analysis. Known pathogenic mutations were found in only 134 (89.3%). The mean number of CSM versus pathogenic mutations were 14 and 2, respectively. We identified 12 recurrently mutated genes which did not concur when we considered both known and unknown CSM. In patients harboring only one pathogenic variant (29.3%), 34% of times did not coincide with the somatic variant with the highest VAF. In those with 2 pathogenic variants (60%), just 12.2% coincided with the highest CSM. After a median follow-up of 35.8 months, 19 patients recurred.

Conclusions

In localized CC, when only known pathogenic mutations were studied, almost 11% of cases could not be tracked. In contrast, targeted sequencing of matched tumor and WBCs samples revealed novel cancer CMS and increased the sensitivity to universally track MRD in plasma.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

Andrés Cervantes.

Funding

Instituto de Salud Carlos III (PI15/02180 and PI18/01909).

Disclosure

A. Cervantes: Advisory/Consultancy, Speaker Bureau/Expert testimony, Research grant/Funding (institution): Merck Serono; Advisory/Consultancy, Speaker Bureau/Expert testimony, Research grant/Funding (institution): Roche; Advisory/Consultancy, Research grant/Funding (institution): Takeda; Advisory/Consultancy, Research grant/Funding (institution): Beigene; Advisory/Consultancy, Speaker Bureau/Expert testimony, Research grant/Funding (institution): Bayer; Advisory/Consultancy, Speaker Bureau/Expert testimony, Research grant/Funding (institution): Servier; Advisory/Consultancy, Research grant/Funding (institution): Lilly; Advisory/Consultancy, Research grant/Funding (institution): Novartis; Advisory/Consultancy, Research grant/Funding (institution): Astelas; Research grant/Funding (institution): Genentech; Speaker Bureau/Expert testimony: Amgen; Speaker Bureau/Expert testimony: Foundation Medicine; Research grant/Funding (institution): Pierre Fabre; Research grant/Funding (institution): Fibrogen; Research grant/Funding (institution): Amcure; Research grant/Funding (institution): Sierra Oncology; Research grant/Funding (institution): Astra Zeneca; Research grant/Funding (institution): Medimmune; Research grant/Funding (institution): BMS; Research grant/Funding (institution): MSD; Officer/Board of Directors: Executive Board member of ESMO; Officer/Board of Directors: INCLIVA General and Scientific Director. All other authors have declared no conflicts of interest.