FIG 1.
Capture and detection of short cfDNA fragments in urine using sequence-specific purification and short-target PCR. (A) Overview of sequence-specific purification and short-target PCR (40 bp) protocol for TB cfDNA. (B) Schematic illustrating details of capture probe design targeting the MTB complex-specific insertion element IS6110. (C) Near-complete recovery of short TB-specific DNA spiked into urine using sequence-specific purification. A positive control (103 copies of 50-bp double-stranded DNA in 10 ml pooled urine) was included throughout each experiment alongside clinical samples. The recovery of the positive control was calculated as a percentage of the input (mean ± standard deviation [SD], n = 15). Key design features, assay optimization, and additional analytical characterization of our sequence-specific purification method for cfDNA are reported in reference 24.