Abstract A048: Whole exome sequencing of circulating free DNA reveals concordance with matched metastatic tumors and predicts survival in small cell lung cancer patients
Authors: Rajapakse Vinodh N. , Takahashi Nobuyuki , Pongor Lorinc , Kim Sehyun , Thomas Anish 
Published: March 2020

Abstract
Small cell lung cancer (SCLC) remains one of the most aggressive malignancies, with 5-year overall survival under 10%. Limited opportunities for surgical resection restrict the tumor tissue available for study of resistance mechanisms. We applied the ichorCNA methodology to quantify tumor content in circulating free DNA from 20 relapsed SCLC patients, using 0.1x coverage whole-genome sequencing data. Samples from 13 patients with sufficient circulating tumor DNA (ctDNA fraction [ctDNAfx] &gt; 10%) were subject to whole exome sequencing (WES), allowing matched tumor concordance analyses. Among 20 patients, the median (interquartile range) ctDNAfx at baseline was 38.3% (16.2%–48.4%). Using the threshold of median ctDNAfx, we divided the patients into low (n=10) or high (n=10) ctDNAfx groups. No significant differences were found in age, gender, smoking status, stage at diagnosis, and platinum-sensitivity between the two groups. Progression free survival (PFS) and overall survival (OS) durations were significantly longer in patients with low-ctDNAfx than those with high-ctDNAfx (63 [54–335] days vs. 29 [22–56] days, p=0.009; 7.5 [4.4–27.2] months vs. 3.5 [2.2–4.4] months, p=0.01, respectively). After adjusting for covariates (age, sex, stage, platinum-sensitivity) using a multivariate Cox proportional hazards model, ctDNAfx at baseline independently contributed to OS (adjusted hazard ratio [95% CI]: 20.1 [1.6–249.2], p=0.02). Consistently, PFS and OS durations were significantly correlated with the level of ctDNAfx at baseline (R2 = 0.22, p=0.035; R2 = 0.24, p=0.03; respectively). For 13 patients with ctDNAfx &gt; 10%, we compared baseline tumor and ctDNA-derived somatic mutations and subclonal architecture using WES data. A median of 62% of tumor-associated mutations were detected in patient-matched ctDNA samples (range: 33%-74%), while a median of 64% of ctDNA-associated mutations were found in matched tumor samples (range: 30%-81%). We used PyClone to group mutations in tumor and ctDNA samples by inferred cancer cell fraction (CCF). Overall, the ctDNA samples yielded more mutation clusters than corresponding tumor samples (median 36 per ctDNA sample, 8 clusters per tumor sample, p = 0.00024, Wilcoxon matched pairs signed rank test). Together, our results show that ichorCNA-based estimates of baseline ctDNA fraction are independently predictive of SCLC patient survival. Moreover, they allow efficient selection of patient samples for WES. Tumor vs. ctDNA comparisons show concordance with respect to somatic mutations; ctDNA-specific mutations and subclonal structure are suggestive of additionally recovered features of baseline intra/inter-tumor heterogeneity.
Citation Format: Vinodh N. Rajapakse, Nobuyuki Takahashi, Lorinc Pongor, Sehyun Kim, Anish Thomas. Whole exome sequencing of circulating free DNA reveals concordance with matched metastatic tumors and predicts survival in small cell lung cancer patients [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A048. doi:10.1158/1535-7163.TARG-19-A048