Abstract 2739: Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA

Circulating tumor DNA (ctDNA) is released from necrotic/apoptotic tumor cells into the bloodstream. Recent studies have demonstrated the value of using ctDNA as biomarkers in cancer diagnosis, prognosis, and drug resistance. Unlike local tissue biopsy, ctDNA collection and analysis is non-invasive, allows continuous monitoring of clonal evolution, and provides an overview of tumor heterogeneity. Copy number variations (CNVs) play an important role in cancer biology. However, traditional CNV analyses of ctDNA using droplet digital PCR (ddPCR) and SNP arrays can only assess a small number of genes due to the low abundance of ctDNA in the majority of patient samples. Next generation sequencing (NGS) offers a more efficient and high-throughput way to study CNVs in ctDNA. Here, we evaluated the use of low-pass whole genome sequencing (WGS) in determining CNVs in ctDNA. In this work, cell-free DNA was isolated from 1-5 ml of plasma from phase II clinical trial patients with metastatic breast cancer and non-small cell lung cancer (NSCLC) using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). DNA yield was determined by ddPCR, with a range from 2-4000 ng. Sequencing libraries were prepared using 2-10 ng DNA by the ThruPLEX Plasma-Seq Kit (Rubicon Genomics). WGS at 0.1x, 0.25x, 0.5x, and 1x coverage was performed on Illumina NextSeq, and data was analyzed using Nexus Copy Number software (BioDiscovery). As a reference, we sequenced DNA from peripheral blood mononuclear cells (PBMCs) of 20 healthy donors at the same coverage. Low-pass WGS was also performed on a subset of matched tumor tissue samples as comparisons. Our results showed that WGS of ctDNA at 0.5x coverage was efficient to identify CNVs. CNVs were detected in ctDNA from about half of the patients analyzed, and in general CNVs identified in ctDNA matched the ones found in tumor tissue from the same patient. We also found that CNV patterns from different time points of the same patients clustered together. With this promising system, we will present CNV analysis in ctDNA from breast cancer and NSCLC patients enrolled in phase II clinical trials of the PI3K inhibitor pictilisib. We will evaluate the ability of the method to classify patients into different subgroups, monitor tumor progression, and identify drug resistance mechanisms. Citation Format: Xiaoji Chen, Jill M. Spoerke, Kathryn Yoh, Walter C. Darbonne, Ling-Yuh Huw, Steven Gendreau, Shih-Min A. Huang, Mark R. Lackner. Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA [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 2739. doi:10.1158/1538-7445.AM2017-2739