Extended Data Fig. 9: HIV reverse transcriptase mutation detection and future directions for CARMEN–Cas13.
From: Massively multiplexed nucleic acid detection with Cas13
a, Distributions of droplet fluorescence for each HIV reverse transcriptase crRNA–target pair after 30 min in most cases; 3 h time point for V106M and M184V. SNP indices in Fig. 4b are calculated from the medians of these distributions. b, Comparison of prior expectation based on Sanger sequencing from the patient sample provider (Sanger), CARMEN testing (CARMEN), and NGS of RNA from each sample (NGS) for 22 patient samples infected with wild-type HIV (No DRMs) or HIV bearing known drug resistance mutations (known DRMs). In some cases, NGS revealed a high number of mismatches (MM) between the HIV sequence in the sample and the crRNA sequence used in the CARMEN HIV reverse transcriptase DRM panel. Summary tables at the right quantify concordance between CARMEN and Sanger sequencing or CARMEN and NGS. c, Quantitative CARMEN–Cas13 schematic showing amplification primers containing T7 or T3 promoters, leading to increased signal for the majority (T7) product after Cas13 detection. d, Increased dynamic range of detection using quantitative CARMEN–Cas13. Dynamic range is indicated using coloured bars above the graph. Error bars indicate s.e.m. Replicates (n) for T7 and T3 data are noted in colour-coded text beneath the plot.
