SySDAACOS Raw Data

The detection of rare variants in cell-free DNA from liquid biopsies is difficult because of low variant allele frequencies (VAFs). Here we developed a generalized method named SySDAACOS (Systematic selective depletion of abundant alleles using Cas9- and optimal single-guide RNAs (sgRNAs)) for enriching rare variants, by Cas9-midiated selective depletion of abundant wild-type sequences in vitro. For this selective depletion, we developed high-throughput methods for assessing Cas9 cleavage efficiencies with divergent sgRNAs with mismatches, RNA bulges, or DNA bulges in vitro and, generated and utilized deep-learning models predicting sgRNA selectivity. SySDAACOS enriched VAFs for 76% and 86% of 2,612 cancer-related mutations by at least ten-fold when SpCas9-HF1 and SpCas9-NRRH-HF1, respectively, were used. This advancement significantly improves the detection of rare variants, potentially aiding in cancer monitoring and diagnosis.