TY - JOUR
T1 - CUT-PCR
T2 - CRISPR-mediated, ultrasensitive detection of target DNA using PCR
AU - Lee, S. H.
AU - Yu, J.
AU - Hwang, G. H.
AU - Kim, S.
AU - Kim, H. S.
AU - Ye, S.
AU - Kim, K.
AU - Park, J.
AU - Park, D. Y.
AU - Cho, Y. K.
AU - Kim, J. S.
AU - Bae, S.
N1 - Funding Information:
We express our gratitude to all of the patients and healthy volunteers who contributed blood samples for this study. The biological specimens for this study were provided by the Pusan National University hospital, a member of the National Biobank of Korea, which is supported by the Ministry of Health and Welfare. All samples were obtained with informed consent according to the institutional review board-approved protocols. The deep-sequencing data are available at the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRX1970116. This work was supported by a grant from the Korea Healthcare technology R&D Project, Ministry for Health and Welfare Affairs (HI16C1012) to SB, (HI12C1845) to JP, DP and YC and Institute for Basic Science (IBS-R021-D1) to J-SK.
Publisher Copyright:
© The Author(s) 2017.
Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.
PY - 2017/8/28
Y1 - 2017/8/28
N2 - Circulating tumor DNA (ctDNA) has emerged as a tumor-specific biomarker for the early detection of various cancers. To date, several techniques have been devised to enrich the extremely small amounts of ctDNA present in plasma, but they are still insufficient for cancer diagnosis, especially at the early stage. Here, we developed a novel method, CUT (CRISPR-mediated, Ultrasensitive detection of Target DNA)-PCR, which uses CRISPR endonucleases to enrich and detect the extremely small amounts of tumor DNA fragments among the much more abundant wild-type DNA fragments by specifically eliminating the wild-type sequences. We computed that by using various orthologonal CRISPR endonucleases such as SpCas9 and FnCpf1, the CUT-PCR method would be applicable to 80% of known cancer-linked substitution mutations registered in the COSMIC database. We further verified that CUT-PCR together with targeted deep sequencing enables detection of a broad range of oncogenes with high sensitivity (< 0.01%) and accuracy, which is superior to conventional targeted deep sequencing. In the end, we successfully applied CUT-PCR to detect sequences with oncogenic mutations in the ctDNA of colorectal cancer patients’ blood, suggesting that our technique could be adopted for diagnosing various types of cancer at early stages.
AB - Circulating tumor DNA (ctDNA) has emerged as a tumor-specific biomarker for the early detection of various cancers. To date, several techniques have been devised to enrich the extremely small amounts of ctDNA present in plasma, but they are still insufficient for cancer diagnosis, especially at the early stage. Here, we developed a novel method, CUT (CRISPR-mediated, Ultrasensitive detection of Target DNA)-PCR, which uses CRISPR endonucleases to enrich and detect the extremely small amounts of tumor DNA fragments among the much more abundant wild-type DNA fragments by specifically eliminating the wild-type sequences. We computed that by using various orthologonal CRISPR endonucleases such as SpCas9 and FnCpf1, the CUT-PCR method would be applicable to 80% of known cancer-linked substitution mutations registered in the COSMIC database. We further verified that CUT-PCR together with targeted deep sequencing enables detection of a broad range of oncogenes with high sensitivity (< 0.01%) and accuracy, which is superior to conventional targeted deep sequencing. In the end, we successfully applied CUT-PCR to detect sequences with oncogenic mutations in the ctDNA of colorectal cancer patients’ blood, suggesting that our technique could be adopted for diagnosing various types of cancer at early stages.
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U2 - 10.1038/onc.2017.281
DO - 10.1038/onc.2017.281
M3 - Article
C2 - 28846115
AN - SCOPUS:85038392617
VL - 36
SP - 6823
EP - 6829
JO - Oncogene
JF - Oncogene
SN - 0950-9232
IS - 49
ER -