Extended Data Fig. 1: Comparison of duplex sequencing to phased variant sequencing.

a, A schema comparing error-suppressed sequencing by duplex sequencing vs. recovery of phased variants. In duplex sequencing, recovery of a single SNV observed on both strands of an original DNA double-helix (that is, in trans) is required. This requires independent recovery of two molecules by sequencing as the plus and minus strands of the original DNA molecule go through library preparation and PCR independently. In contrast, recovery of PVs requires multiple SNVs observed on the same single strand of DNA (that is, in cis). Thus, recovery of only the plus or the minus strand (rather than both) is sufficient for identification of PVs. b, A model showing the two possible reasons for limited sensitivity for ctDNA MRD assays. An assay can be limited by either having i) an insufficient number of cfDNA fragments evaluable for tumor content, or ii) an inadequate error-profile. This plot demonstrates the analytical sensitivity as the number of evaluable cfDNA fragments increase with either the amount of plasma input or the number of mutations tracked, until eventually becoming limited by the background signal (grey). Separate plots shown for single-stranded and double-stranded SNV based methods, assuming 8.92 ng cfDNA/mL plasma; 50% efficiency of library preparation, and 20% efficiency of duplex sequencing.