A feasibility study of colorectal cancer diagnosis via circulating tumor DNA derived CNV detection

<div><p>Circulating tumor DNA (ctDNA) has shown great promise as a biomarker for early detection of cancer. However, due to the low abundance of ctDNA, especially at early stages, it is hard to detect at high accuracies while keeping sequencing costs low. Here we present a pilot stage study to detect large scale somatic copy numbers variations (CNVs), which contribute more molecules to ctDNA signal compared to point mutations, via cell free DNA sequencing. We show that it is possible to detect somatic CNVs in early stage colorectal cancer (CRC) patients and subsequently discriminate them from normal patients. With 25 normal and 24 CRC samples, we achieve 100% specificity (lower bound confidence interval: 86%) and ~79% sensitivity (95% confidence interval: 63% - 95%,), though the performance should be considered with caution given the limited sample size. We report a lack of concordance between the CNVs detected via cfDNA sequencing and CNVs identified in parent tissue samples. However, recent findings suggest that a lack of concordance is expected for CNVs in CRC because of their sub-clonal nature. Finally, the CNVs we detect very likely contribute to cancer progression as they lie in functionally important regions, and have been shown to be associated with CRC specifically. This study paves the path for a larger scale exploration of the potential of CNV detection for both diagnoses and prognoses of cancer.</p></div

Cell free DNA CNV detection.

<p>A) Distribution of normalized 10Kb bin values in cfDNA in each cancer and normal blood sample. B) Heatmap of the genome broken down in large chromosomal segments colored based on their median normalized bin value. A value of 1 represents a normal diploid segment, values less than one are potential deletions, and values higher than one are potential amplifications. C) Distribution of the number of potential CNVs detected in normal vs colorectal cancer cfDNA samples.</p

Colorectal cancer prediction results.

<p>Colorectal cancer prediction results.</p

Comparison of cfDNA CNVs and tumor tissue CNVs.

<p>A) Distribution of direct correlation between CNVs detected via cfDNA samples and CNVs identified in parent tumor tissue (Red); darker color represents higher stage (1–4). Distribution of highest correlation between CNVs detected via a cfDNA sample when compared to all tumor tissue samples (Green); darker color represents higher stage (1–4). B) Heatmap of potential CNVs detected via cfDNA sequencing along with CNVs identified in parent tumor tissue scaled separately. A value of 1 represents a normal diploid segment, values less than one are potential deletions, and values higher than one are potential amplifications.</p

Colorectal cancer samples staging, size, and metastasis.

<p>Colorectal cancer samples staging, size, and metastasis.</p