Alternatively, deep sequencing is suitable for sampling a large number of samples or target sites. NGS primers are designed for shorter amplicons, typically in the 100–200-bp size range. For the detection of NHEJ mutations, it is important to design primers situated at least 50 bp from the Cas9 target site to allow for the detection of longer indels. For larger deletions mediated by multiple sgRNAs, priming sites should be designed outside the deleted region. We provide guidelines for a two-step PCR fusion method to attach bar-coded sequencing adaptors for multiplex deep sequencing. We recommend the Illumina platform for its generally low levels of false positive indel detection. By comparison, Ion Torrent is less suitable for indel analysis owing to high sequencing error rate with homo-polymers60. Detailed descriptions of NGS optimization and troubleshooting can be found in the Illumina user manual. Off-target indel analysis (Box 1) can then be performed through read-alignment programs such as ClustalW, Geneious or simple custom sequence analysis scripts.
