Low-pass Whole-genome Sequencing of Circulating Cell-free DNA Demonstrates Dynamic Changes in Genomic Copy Number in a Squamous Lung Cancer Clinical Cohort

Abstract

Purpose: We developed a method to monitor copy number variations (CNV) in plasma cell-free DNA (cfDNA) from patients with metastatic squamous non-small cell lung cancer (NSCLC). 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 patients with squamous NSCLC 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 of 12 patients. Recurrent CNVs, such as MYC amplification, were enriched in cfDNA from posttreatment samples compared with the baseline, suggesting a potential resistance mechanism to pictilisib. Conclusions: LP-WGS offers an unbiased and highthroughput way to investigate CNVs and tumor fraction in cfDNA of patients with cancer. It may also be valuable for monitoring treatment response, detecting disease progression early, and identifying emergent clones associated with therapeutic resistance.

Targeting the PI3K/Akt/mTOR pathway in non‐small cell lung cancer (NSCLC)

“…This led to the phase II FIGARO study of pictilisib in combination with first-line chemotherapy; however, preliminary data did not reveal any significant progressionfree survival (PFS) or overall survival (OS) benefit. 84 Similar findings have been reported in a phase IA/IB trial in a Japanese cohort of patients. 85 PX-866 has been evaluated in combination with docetaxel chemotherapy in a randomized phase II trial of advanced, refractory NSCLC patients.…”

“…Of 66 patients, 29 (43.9%) had partial response and 20 (30.9%) had stable disease. This led to the phase II FIGARO study of pictilisib in combination with first‐line chemotherapy; however, preliminary data did not reveal any significant progression‐free survival (PFS) or overall survival (OS) benefit . Similar findings have been reported in a phase IA/IB trial in a Japanese cohort of patients .…”

Genome‐wide profiling of circulating tumor DNA depicts landscape of copy number alterations in pancreatic cancer with liver metastasis

“…Shallow genome-wide sequencing provides a way for estimation of tumor burden [20]. Several studies adopted this approach in breast cancer, lung cancer, prostate carcinoma, and neuroblastoma and found the estimated tumor fractions are clinically relevant [33][34][35][36][37][38]. We found that TFx was remarkably higher in the metastatic setting than localized tumor.…”

Interest of circulating tumor DNA as a biomarker for canine cancers: illustration in histiocytic sarcoma, oral malignant melanoma and multicentric lymphoma

“…Detecting CNAs in cfDNA is challenging, and depends also on the level of amplification of the gene in the tumor which in turns, involves deeper sequencing 56 . In humans, more reliable methods are used to detect CNA in cfDNA like low-pass whole genome sequencing 57 . Beck et al used whole genome sequencing on tumor and plasma samples of 2 dogs with mammary carcinoma and found a good concordance of tumor and cfDNA copy number profiles for the regions with high-level amplifications 50 .…”