Mutational profiling of tumour tissue and sequential plasma illustrates emergent clones during treatment in late stage small cell lung cancer (SCLC)

Background SCLC is an aggressive disease with poor prognosis. Despite initial response to chemotherapy and radiotherapy, relapse occurs in most cases. To characterize genomic changes in SCLC over the course of therapy, we explored tracking tumor mutations in cell-free DNA (cfDNA) across post-treatment blood draws and comparing them to pre-treatment plasma and tissue profiles. Methods We retrospectively evaluated 235 samples collected from 24 subjects with late stage SCLC treated with first-line chemotherapy or chemoradiation in a prospective observational study. Tumor tissue samples were analyzed with the AVENIO Tumor Tissue Surveillance Kit (For Research Use Only, not for use in diagnostic procedures), a 198-kb next-generation sequencing panel covering 197 cancer genes. Matched peripheral blood mononuclear cells (PBMC), pre-treatment plasma, and multiple plasma from post-treatment timepoints were analyzed with the same panel using the AVENIO ctDNA Surveillance Kit (For Research Use Only, not for use in diagnostic procedures). A median input amount of 29 ng cfDNA, 129 ng tumor tissue DNA, and 50 ng PBMC DNA were sequenced to median deduplicated depths of 4491, 1315, and 6512, respectively. Somatic single nucleotide variants (SNVs) in tissue and plasma were identified by removing PBMC-matched germline or clonal hematopoietic mutations. Results We detected a median of 4 SNVs in tissue samples and a median of 100% (range 66 - 100%) of tissue SNVs in matched pre-treatment plasma. 96% (23/24) of subjects had at least one shared SNV between tissue and plasma, most commonly a TP53 mutation. A median of 7 SNVs were detected in pre-treatment plasma, whereas across all available post-treatment plasma (range 2 - 20 time points per subject), a median of 4 SNVs were detected. 53% of these mutations were not present in pre-treatment plasma or tissue. Conclusions Somatic mutations found in pre-treatment plasma were concordant with matched tissue, consistent with the highly metastatic nature of SCLC. ctDNA sequencing can provide additional molecular insights; in particular, detecting emergent mutations in ctDNA during treatment could advance our knowledge of SCLC. Legal entity responsible for the study Roche Sequencing Solutions, Inc. Funding Roche Sequencing Solutions, Inc. Disclosure S. Yaung: Full / Part-time employment: Roche. C. Woestmann: Full / Part-time employment: Roche. L. Xi: Full / Part-time employment: Roche. C. Ju: Full / Part-time employment: Roche. B. Hinzmann: Shareholder / Stockholder / Stock options, Full / Part-time employment: Roche. M. Thomas: Honoraria (institution), Advisory / Consultancy, Research grant / Funding (institution), Travel / Accommodation / Expenses: Roche. F. Lasitschka: Research grant / Funding (institution): Roche. M. Meister: Research grant / Funding (institution): Roche. M. Schneider: Research grant / Funding (institution): Roche. F.J.F. Herth: Honoraria (institution): Roche. T. Muley: Research grant / Funding (institution), Licensing / Royalties: Roche. B. Wehnl: Full / Part-time employment: Roche. J. Palma: Shareholder / Stockholder / Stock options, Full / Part-time employment: Roche. X.M. Ma: Shareholder / Stockholder / Stock options, Licensing / Royalties, Full / Part-time employment: Roche.