Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approachesopen access
- Authors
- Kwon, Jeonghun; Kim, Minyoung; Hwang, Woochang; Jo, Anna; Hwang, Gue-Ho; Jung, Minhee; Kim, Un Gi; Cui, Gang; Kim, Heonseok; Eom, Joon-Ho; Hur, Junho K.; Lee, Junwon; Kim, Youngho; Kim, Jin-soo; Bae, Sangsu; Lee, Jungjoon K.
- Issue Date
- Jan-2023
- Publisher
- BMC
- Keywords
- CRISPR; Genome-wide; Off-target; Cell-based; In vitro
- Citation
- GENOME BIOLOGY, v.24, no.1, pp.1 - 20
- Indexed
- SCIE
SCOPUS
- Journal Title
- GENOME BIOLOGY
- Volume
- 24
- Number
- 1
- Start Page
- 1
- End Page
- 20
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/182356
- DOI
- 10.1186/s13059-022-02842-4
- ISSN
- 1474-760X
- Abstract
- We present a novel genome-wide off-target prediction method named Extru-seq and compare it with cell-based (GUIDE-seq), in vitro (Digenome-seq), and in silico methods using promiscuous guide RNAs with large numbers of valid off-target sites. Extru-seq demonstrates a high validation rate and retention of information about the intracellular environment, both beneficial characteristics of cell-based methods. Extru-seq also shows a low miss rate and could easily be performed in clinically relevant cell types with little optimization, which are major positive features of the in vitro methods. In summary, Extru-seq shows beneficial features of cell-based and in vitro methods.
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