Skip to main content
. 2017 Sep 22;8(52):89848–89866. doi: 10.18632/oncotarget.21163

Figure 1. Leveraging tumor-derived cfDNA distribution in advanced cancer to develop a pan-cancer, rapid, inexpensive, ultra-low pass whole genome next generation sequencing (NGS) cfDNA precision oncology workflow (PRINCe).

Figure 1

(A) Theoretical cfDNA tumor content distributions and typical next-generation sequencing (NGS) coverage requirements for mutation profiling are presented for early detection (left) and precision oncology in advanced disease (right) applications. In early detection context, the majority of cfDNA samples are expected to have a low proportion of tumor-derived cfDNA fragments (e.g., < 5%), whereas advanced cancers have an elevated proportion of tumor-derived cfDNA. Tumor content requiring ultra-deep, extreme-fidelity (e.g. 10,000x coverage) targeted sequencing are shaded red, while those amenable to targeted sequencing on larger panels or whole-exome/whole-genome (WES/WGS) are shaded blue and green, respectively. (B) Copy number alterations (CNAs) are frequent across human cancers. The fraction of the genome altered (FGA, see Methods) by CNAs in 11,576 The Cancer Genome Atlas (TCGA) samples from 32 solid tumor types is shown across multiple thresholds (overall cohort on left, individual tumor types on right). Increased FGA in a cohort of 129 advanced/metastatic cancers (prostate, kidney, lung and breast cancers) subjected to exome sequencing in the MI-ONCOSEQ program (plotted on the right panel) is seen in comparison to the TCGA cohort, consistent with increasing frequency of CNAs in advanced/metastatic cancers. (C) Schematic for pan-cancer, rapid, inexpensive, ultra-low pass NGS cfDNA workflow (PRINCe). Segmented copy-number calls from ultra-low-pass cfDNA whole-genome sequencing are generated, followed by CNA-clustering based tumor content approximation to inform on precision oncology management. In patients with sufficient tumor content by PRINCe (e.g. > 5–10%), CNA profiles may directly guide treatment (if focal targSupplementary Table alterations are identified), enable routine panel, WGS, or WES based cfDNA NGS tuned to tumor content, as well as establish pre-treatment (tx) CNA profiles for disease (dx) monitoring post-therapy. More costly ultra-deep, extreme fidelity cfDNA and tissue based profiling can thus be reserved for patients with low cfDNA tumor content.