Table 1.

Summary of long-read DNA enrichment methods

Method	Typical read length	Typical coverage	Example of percent reads on-target	Example of number of targets	Platform	Advantages	Disadvantages
PCR	7 kb	50–1,000×	>96%141	19 amplicons31	ONT, PacBio	Simple design High enrichment Low hands-on time Easy to multiplex samples Easy to multiplex targets Sensitive Low input	Erases native DNA modifications Limited fragment length Lengthy optimization may be required Introduction of PCR errors Multiple reactions often needed
Hybridization capture	5 kb	200–1,000×	66.3%42	4,800 genes34	ONT, PacBio	Simple design High enrichment Easy to multiplex targets Easy to multiplex samples High scalability Single reaction needed	Erases native DNA modifications Limited fragment length Laborious protocols with high hands-on time Includes multiple PCR steps
Cas-mediated enrichment	Up to 100 kb	50–1,000×	4.6%55	10 genes55	ONT, PacBio	Preserves DNA modifications Long read lengths No PCR	High DNA input Less ability to multiplex
Adaptive sampling	10–20 kb	15–40×	~5%68	717 genes68	ONT	Simple design Preserves DNA modifications Long read lengths No PCR No additional molecular biology steps besides library prep	Low enrichment Limited to ONT nanopore sequencing Multiple sequencing runs to obtain maximum output Computationally intensive

ONT, Oxford Nanopore Technologies; PacBio, Pacific Biosciences.