Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Kuno A

PROVIDER: S-EPMC8765641 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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

Kuno Akihiro A Ikeda Yoshihisa Y Ayabe Shinya S Kato Kanako K Sakamoto Kotaro K Suzuki Sayaka R SR Morimoto Kento K Wakimoto Arata A Mikami Natsuki N Ishida Miyuki M Iki Natsumi N Hamada Yuko Y Takemura Megumi M Daitoku Yoko Y Tanimoto Yoko Y Dinh Tra Thi Huong TTH Murata Kazuya K Hamada Michito M Muratani Masafumi M Yoshiki Atsushi A Sugiyama Fumihiro F Takahashi Satoru S Mizuno Seiya S

PLoS biology 20220118 1

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 dive ...[more]

PMID: 35041655

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Project description:BACKGROUND:The majority of patients desire all available prognostic information, but some physicians hesitate to discuss prognosis. The objective of the current study was to examine outcomes of prognostic disclosure among the parents of children with cancer. METHODS:The authors surveyed 353 parents of children with newly diagnosed cancer at 2 tertiary cancer centers, and each child's oncologist. Using multivariable logistic regression, the authors assessed associations between parental report of elements of prognosis discussions with the oncologist (quality of information/communication and prognostic disclosure) and potential consequences of these discussions (trust, hope, peace of mind, prognostic understanding, depression, and anxiety). Analyses were stratified by oncologist-reported prognosis. RESULTS:Prognostic disclosure was not found to be associated with increased parental anxiety, depression, or decreased hope. Among the parents of children with less favorable prognoses (<75% chance of cure), the receipt of high-quality information from the oncologist was associated with greater peace of mind (odds ratio [OR], 5.23; 95% confidence interval [95% CI], 1.81-15.16) and communication-related hope (OR, 2.54; 95% CI, 1.00-6.40). High-quality oncologist communication style was associated with greater trust in the physician (OR, 2.45; 95% CI, 1.09-5.48) and hope (OR, 3.01; 95% CI, 1.26-7.19). Accurate prognostic understanding was less common among the parents of children with less favorable prognoses (OR, 0.39; 95% CI, 0.17-0.88). Receipt of high-quality information, high-quality communication, and prognostic disclosure were not found to be significantly associated with more accurate prognostic understanding. CONCLUSIONS:The results of the current study demonstrate no evidence that disclosure is associated with anxiety, depression, or decreased hope. Communication processes may increase peace of mind, trust, and hope. It remains unclear how best to enhance prognostic understanding. Cancer 2018;124:1232-41. © 2017 American Cancer Society.

Dataset Information

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

Publications

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

Similar Datasets

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