Sequencing the previously unsequenceable using amplification-free targeted enrichment powered by CRISPR/Cas9
Genomic regions with extreme base composition bias and repetitive sequences have long proven challenging for targeted enrichment methods, as they rely upon some form of amplification. Similarly, most DNA sequencing technologies struggle to faithfully sequence regions of low complexity. This has especially been true for repeat expansion disorders such as Fragile X syndrome, Huntington’s disease and various Ataxias, where the repetitive elements range from several hundreds of bases to tens of kilobases. We have developed a robust, amplification-free targeted enrichment technique, called No-Amp Targeted Sequencing, that employs the CRISPR/Cas9 system. In conjunction with Single Molecule, Real-Time (SMRT) Sequencing, which delivers long reads spanning the entire repeat expansion, high consensus accuracy, and uniform coverage, these previously inaccessible regions are now accessible. This method is completely amplification-free, therefore removing any PCR errors and biases from the experiment. Furthermore, this technique also preserves native DNA molecules, allowing for direct detection and characterization of epigenetic signatures. The No-Amp method is a two-day protocol, compatible with multiplexing of multiple targets and samples in a single reaction, using as little as 1 µg of genomic DNA input per sample. We have successfully targeted a number of repeat expansion disorder loci (HTT, FMR1, ATXN10, C9orf72) with alleles as long as >2700 repeat unites (>13 kb). Using the No-Amp method we have isolated hundreds of individual on-target molecules, allowing for reliable repeat size estimation, mosaicism detection and identification of interruption sequences – all aspects of repeat expansion disorders which are important for better understanding the underlying disease mechanisms.