Accurate Detection of Rare Mutant Alleles by Target Base-Specific Cleavage with the CRISPR/Cas9 System

Dongin Lee; Ji Hyun Lee; Duhee Bang

doi:10.1021/acssynbio.1c00056

Accurate Detection of Rare Mutant Alleles by Target Base-Specific Cleavage with the CRISPR/Cas9 System

Dongin Lee, Ji Hyun Lee, Duhee Bang

Department of Chemistry

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

The detection of low-frequency somatic mutations enables early diagnosis of disease; however, base-substitution errors that arise during genomic library preparation and high-throughput sequencing can lead to false diagnostic information. To discriminate true genomic alterations from technical errors, we developed spCas9-assisted true variant labeling sequencing (CARVE-seq), which detects low-frequency mutant alleles with high accuracy. CARVE-seq utilizes single-base discrimination during spCas9 cleavage reactions to exclude technical errors. Ten single nucleotide variants that recurrently occur in tumors were assayed by CARVE-seq using 20 ng reference samples, and 100% positive predictive value and specificity was observed, which proved the highly accurate performance of CARVE-seq.

Original language	English
Pages (from-to)	1451-1464
Number of pages	14
Journal	ACS Synthetic Biology
Volume	10
Issue number	6
DOIs	https://doi.org/10.1021/acssynbio.1c00056
Publication status	Published - 2021 Jun 18

Bibliographical note

Funding Information:
This work was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT; 2016M3A9B6948494); the Midcareer Researcher Program of the National Research Foundation (NRF) funded by the Korean government (MSIT; 2018R1A2A1A05079172); the National Research Foundation (NRF) funded by the Korean government (MSIT; 2021R1A2C2008490); the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (HI18C2282, HI14C1277).

Publisher Copyright:
© 2021 American Chemical Society.

All Science Journal Classification (ASJC) codes

Biomedical Engineering
Biochemistry, Genetics and Molecular Biology (miscellaneous)

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10.1021/acssynbio.1c00056

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title = "Accurate Detection of Rare Mutant Alleles by Target Base-Specific Cleavage with the CRISPR/Cas9 System",

abstract = "The detection of low-frequency somatic mutations enables early diagnosis of disease; however, base-substitution errors that arise during genomic library preparation and high-throughput sequencing can lead to false diagnostic information. To discriminate true genomic alterations from technical errors, we developed spCas9-assisted true variant labeling sequencing (CARVE-seq), which detects low-frequency mutant alleles with high accuracy. CARVE-seq utilizes single-base discrimination during spCas9 cleavage reactions to exclude technical errors. Ten single nucleotide variants that recurrently occur in tumors were assayed by CARVE-seq using 20 ng reference samples, and 100% positive predictive value and specificity was observed, which proved the highly accurate performance of CARVE-seq.",

author = "Dongin Lee and Lee, {Ji Hyun} and Duhee Bang",

note = "Funding Information: This work was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT; 2016M3A9B6948494); the Midcareer Researcher Program of the National Research Foundation (NRF) funded by the Korean government (MSIT; 2018R1A2A1A05079172); the National Research Foundation (NRF) funded by the Korean government (MSIT; 2021R1A2C2008490); the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (HI18C2282, HI14C1277). Publisher Copyright: {\textcopyright} 2021 American Chemical Society.",

year = "2021",

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doi = "10.1021/acssynbio.1c00056",

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N2 - The detection of low-frequency somatic mutations enables early diagnosis of disease; however, base-substitution errors that arise during genomic library preparation and high-throughput sequencing can lead to false diagnostic information. To discriminate true genomic alterations from technical errors, we developed spCas9-assisted true variant labeling sequencing (CARVE-seq), which detects low-frequency mutant alleles with high accuracy. CARVE-seq utilizes single-base discrimination during spCas9 cleavage reactions to exclude technical errors. Ten single nucleotide variants that recurrently occur in tumors were assayed by CARVE-seq using 20 ng reference samples, and 100% positive predictive value and specificity was observed, which proved the highly accurate performance of CARVE-seq.

AB - The detection of low-frequency somatic mutations enables early diagnosis of disease; however, base-substitution errors that arise during genomic library preparation and high-throughput sequencing can lead to false diagnostic information. To discriminate true genomic alterations from technical errors, we developed spCas9-assisted true variant labeling sequencing (CARVE-seq), which detects low-frequency mutant alleles with high accuracy. CARVE-seq utilizes single-base discrimination during spCas9 cleavage reactions to exclude technical errors. Ten single nucleotide variants that recurrently occur in tumors were assayed by CARVE-seq using 20 ng reference samples, and 100% positive predictive value and specificity was observed, which proved the highly accurate performance of CARVE-seq.

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Accurate Detection of Rare Mutant Alleles by Target Base-Specific Cleavage with the CRISPR/Cas9 System

Abstract

Bibliographical note

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