New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis

CfDNA fragments shorter than 100？nt are accessible for sequencing following single-strand library preparation (SSP). Comparison of the size profiles of cancer patient cfDNA obtained from DSP-S (dotted lines) as compared to SSP-S (full lines) DSP-S was performed on plasma from lung cancer (IC58 and IC61), while SSP-S was performed on four lung (IC10, IC32, IC15, and IC20), two colorectal (IC33 and IC37), two breast (IC34 and IC35), and one liver (IC17) cancers. In order to differentiate SSP-S derived size profile curves, two sets of data are presented (IC15, IC17, IC20, IC35, IC37, a; and IC10, IC32, IC33, IC34, b) each containing one of the two cfDNA size profile as determined by DSP-S. The nine cfDNA extracts from cancer patients analyzed by SSP-S were examined in the blinded study comparing SSP-S with Q-PCR size profile analysis. c presents the proportion of three size ranges we set based on the previous cfDNA sizing biological paradigm: MF, corresponding to the length of the DNA sequence compacted in a mononucleosome (145–249nt); WF, corresponding to weakly fragmented cfDNA (？249nt); and HF, corresponding to highly fragmented cfDNA (<145nt). d presents the percent value of the three size ranges obtained from each patients either by SSP-S or DSP-S. ****, p < 0.000