Fragment analysis is a capillary electrophoresis (CE) based method. CE-based assays have a simple two-step protocol (PCR followed by CE) independent of enzymatic cleavage.
CE methods have been proven to be sensitive, high-throughput and high-resolution approaches for nucleic acid analysis. It has been reported that CE methods have sensitivity and resolution that are comparable to NGS with an indel detection sensitivity of about 0.1% (Lonowski et al., 2017). Hence, they can be used in both basic research and more challenging genome editing applications such as therapeutic indel profiling.
Recently multiple CE-based assays such as IDAA, Fluorescent PCR and CRISPR-STAT have been developed in CRISPR/Cas9 genome editing studies. These are reported to be fast, sensitive, precise and cost-effective methods for mutation detection.
Lonowski, Lindsey A., Yoshiki Narimatsu, Anjum Riaz, Catherine E. Delay, Zhang Yang, Francesco Niola, Katarzyna Duda, Elke A. Ober, Henrik Clausen, Hans H. Wandall, Steen H. Hansen, Eric P. Bennett, and Morten Frödin. "Genome Editing Using FACS Enrichment of Nuclease-expressing Cells and Indel Detection by Amplicon Analysis." Nature Protocols 12, no. 3 (2017): 581-603. doi:10.1038/nprot.2016.165.