Abstract 5395: Genomic variations in plasma cell free DNA from small cell lung cancer
Authors: Du Meijun , Fisher Hannah , Zhang Peng , Zhang Huijuan , Wang Liang 
Published: July 2017

Abstract
Background Small cell lung cancer (SCLC) is a highly aggressive malignancy with rapid development of chemo resistance and a high rate of recurrence. Although tumor tissues-based studies have shown characteristic genomic changes in SCLC, it is little known about tumor-derived genomic variations in cell free DNA (cfDNA), a promising source of genetic materials for monitoring disease progression, evaluating treatment efficacy and predicting clinical outcomes.
Methods We collected plasma from 26 SCLC patients and extracted cfDNAs from 250μl of plasma. We prepared DNA libraries and analyzed sequencing data using a various bioinformatic tools. We binned read counts from the mapped sequence files into 60kb windows and performed log2 ratio-based copy number analysis using segmentation-based approach. We compared copy number changes detected in cfDNA to previously reported genomic regions from tumor tissues-based studies.
Results The whole genome sequencing generated approximately 9.4 million mappable sequence reads per subject and 175 read counts per 60kb genomic region. Copy number analysis using log2 ratios between cfDNA and matched gDNA showed significant genomic abnormalities in 17 of 26 plasma samples. Overall, we observed the most frequent deletion of 3p, 13q,17p,10p and amplification of 3q, 5p, 8q,1p, which were consistent with previous reports from tumor tissues-based studies. To further define the copy number changes, we performed a detailed analysis at chromosomal regions showing frequent aberrations in SCLC. Among these, deletion of gene RASSF1 at 3p21.3 was most frequently observed (12 deletions in 26 samples). Another common deletion was RB1 at 13q14 (5/26), TP53 at 17p13 (4/26). The most common amplification was involved in MYC gene at 8q24(18/26). Other common amplifications included SOX2 at 3q26 (17/26), MYCL at 1p34.2 (9/26) and FGF10 at 5p13 (9/26). We also observed low frequent genomic alterations at other genomic regions such as PTEN loss at 10q23(1/26) and FHIT loss at 3p14 (1/26). Interestingly, we observed contradictory genomic changes at MAD1L1 locus. Among the 26 cfDNA samples, we detected ten patients with MAD1L1 loss and three patients with MAD1L1 gain. Past studies have shown that the MAD1L1 locus at 7p22 is frequently ampliated in SCLC patients. We are currently analyzing if these genomic variations are associated with disease progression and overall survival.
Conclusions This study provides a comprehensive analysis of genomic alterations in plasma cfDNAs from SCLC. We identified multiple candidate genes whose genomic aberrations may be used as biomarkers for accessing treatment efficacy and predicting prognosis. Our result supports blood plasma as an alternative sample source for tumor-associated genomic analysis in SCLC patients. Further targeted sequencing and clinical association analyses is needed to fully validate the potential clinical utilities of cfDNA-based liquid biopsy for clinical management of this deadly disease.
Citation Format: Meijun Du, Hannah Fisher, Peng Zhang, Huijuan Zhang, Liang Wang. Genomic variations in plasma cell free DNA from small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5395. doi:10.1158/1538-7445.AM2017-5395