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DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes

Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result...

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Autores principales: Kuno, Akihiro, Ikeda, Yoshihisa, Ayabe, Shinya, Kato, Kanako, Sakamoto, Kotaro, Suzuki, Sayaka R., Morimoto, Kento, Wakimoto, Arata, Mikami, Natsuki, Ishida, Miyuki, Iki, Natsumi, Hamada, Yuko, Takemura, Megumi, Daitoku, Yoko, Tanimoto, Yoko, Dinh, Tra Thi Huong, Murata, Kazuya, Hamada, Michito, Muratani, Masafumi, Yoshiki, Atsushi, Sugiyama, Fumihiro, Takahashi, Satoru, Mizuno, Seiya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8765641/
https://www.ncbi.nlm.nih.gov/pubmed/35041655
http://dx.doi.org/10.1371/journal.pbio.3001507
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author Kuno, Akihiro
Ikeda, Yoshihisa
Ayabe, Shinya
Kato, Kanako
Sakamoto, Kotaro
Suzuki, Sayaka R.
Morimoto, Kento
Wakimoto, Arata
Mikami, Natsuki
Ishida, Miyuki
Iki, Natsumi
Hamada, Yuko
Takemura, Megumi
Daitoku, Yoko
Tanimoto, Yoko
Dinh, Tra Thi Huong
Murata, Kazuya
Hamada, Michito
Muratani, Masafumi
Yoshiki, Atsushi
Sugiyama, Fumihiro
Takahashi, Satoru
Mizuno, Seiya
author_facet Kuno, Akihiro
Ikeda, Yoshihisa
Ayabe, Shinya
Kato, Kanako
Sakamoto, Kotaro
Suzuki, Sayaka R.
Morimoto, Kento
Wakimoto, Arata
Mikami, Natsuki
Ishida, Miyuki
Iki, Natsumi
Hamada, Yuko
Takemura, Megumi
Daitoku, Yoko
Tanimoto, Yoko
Dinh, Tra Thi Huong
Murata, Kazuya
Hamada, Michito
Muratani, Masafumi
Yoshiki, Atsushi
Sugiyama, Fumihiro
Takahashi, Satoru
Mizuno, Seiya
author_sort Kuno, Akihiro
collection PubMed
description Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
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spelling pubmed-87656412022-01-19 DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes Kuno, Akihiro Ikeda, Yoshihisa Ayabe, Shinya Kato, Kanako Sakamoto, Kotaro Suzuki, Sayaka R. Morimoto, Kento Wakimoto, Arata Mikami, Natsuki Ishida, Miyuki Iki, Natsumi Hamada, Yuko Takemura, Megumi Daitoku, Yoko Tanimoto, Yoko Dinh, Tra Thi Huong Murata, Kazuya Hamada, Michito Muratani, Masafumi Yoshiki, Atsushi Sugiyama, Fumihiro Takahashi, Satoru Mizuno, Seiya PLoS Biol Methods and Resources Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes. Public Library of Science 2022-01-18 /pmc/articles/PMC8765641/ /pubmed/35041655 http://dx.doi.org/10.1371/journal.pbio.3001507 Text en © 2022 Kuno et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Methods and Resources
Kuno, Akihiro
Ikeda, Yoshihisa
Ayabe, Shinya
Kato, Kanako
Sakamoto, Kotaro
Suzuki, Sayaka R.
Morimoto, Kento
Wakimoto, Arata
Mikami, Natsuki
Ishida, Miyuki
Iki, Natsumi
Hamada, Yuko
Takemura, Megumi
Daitoku, Yoko
Tanimoto, Yoko
Dinh, Tra Thi Huong
Murata, Kazuya
Hamada, Michito
Muratani, Masafumi
Yoshiki, Atsushi
Sugiyama, Fumihiro
Takahashi, Satoru
Mizuno, Seiya
DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
title DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
title_full DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
title_fullStr DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
title_full_unstemmed DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
title_short DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
title_sort dajin enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes
topic Methods and Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8765641/
https://www.ncbi.nlm.nih.gov/pubmed/35041655
http://dx.doi.org/10.1371/journal.pbio.3001507
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