Low-Pass Whole-Genome Sequencing of Circulating Cell-Free DNA Demonstrates Dynamic Changes in Genomic Copy Number in a Squamous Lung Cancer Clinical Cohort

Purpose: We developed a method to monitor copy number variations (CNVs) in plasma cell-free DNA (cfDNA) from metastatic squamous non-small-cell lung cancer (NSCLC) patients. We aimed to explore the association between tumor-derived cfDNA and clinical outcomes, and sought CNVs that may suggest potential resistance mechanisms. Experimental Design: Sensitivity and specificity of low-pass whole-genome sequencing (LP-WGS) were first determined using cell line DNA and cfDNA. LP-WGS was performed on baseline and longitudinal cfDNA of 152 squamous NSCLC patients treated with chemotherapy, or in combination with pictilisib, a pan-PI3K inhibitor. cfDNA tumor fraction and detected CNVs were analyzed in association with clinical outcomes. Results: LP-WGS successfully detected CNVs in cfDNA with tumor fraction ≥ 10%, which represented approximately 30% of the first-line NSCLC patients in this study. The most frequent CNVs were gains in chromosome 3q, which harbors the PIK3CA and SOX2 oncogenes. The CNV landscape in cfDNA with a high tumor fraction generally matched that of corresponding tumor tissue. Tumor fraction in cfDNA was dynamic during treatment and increases in tumor fraction and corresponding CNVs could be detected before radiographic progression in 7 out of 12 patients. Recurrent CNVs, such as MYC amplification, were enriched in cfDNA from post-treatment samples compared to the baseline, suggesting a potential resistance mechanism to pictilisib. Conclusion: LP-WGS offers an unbiased and high-throughput way to investigate CNVs and tumor fraction in cfDNA of cancer patients. It may also be valuable for monitoring treatment response, detecting disease progression early, and identifying emergent clones associated with therapeutic resistance.

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