CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR

S. H. Lee, J. Yu, G. H. Hwang, S. Kim, H. S. Kim, S. Ye, Kyoungmi Kim, J. Park, D. Y. Park, Y. K. Cho, J. S. Kim, S. Bae

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)6823-6829
Number of pages7
JournalOncogene
Volume36
Issue number49
DOIs
Publication statusPublished - 2017 Aug 28
Externally publishedYes

Fingerprint

Clustered Regularly Interspaced Short Palindromic Repeats
Polymerase Chain Reaction
DNA
Neoplasms
High-Throughput Nucleotide Sequencing
Endonucleases
Mutation
Tumor Biomarkers
Oncogenes
Early Detection of Cancer
Colorectal Neoplasms
Databases

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Cancer Research

Cite this

Lee, S. H., Yu, J., Hwang, G. H., Kim, S., Kim, H. S., Ye, S., ... Bae, S. (2017). CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR. Oncogene, 36(49), 6823-6829. https://doi.org/10.1038/onc.2017.281

CUT-PCR : CRISPR-mediated, ultrasensitive detection of target DNA using PCR. / Lee, S. H.; Yu, J.; Hwang, G. H.; Kim, S.; Kim, H. S.; Ye, S.; Kim, Kyoungmi; Park, J.; Park, D. Y.; Cho, Y. K.; Kim, J. S.; Bae, S.

In: Oncogene, Vol. 36, No. 49, 28.08.2017, p. 6823-6829.

Research output: Contribution to journalArticle

Lee, SH, Yu, J, Hwang, GH, Kim, S, Kim, HS, Ye, S, Kim, K, Park, J, Park, DY, Cho, YK, Kim, JS & Bae, S 2017, 'CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR', Oncogene, vol. 36, no. 49, pp. 6823-6829. https://doi.org/10.1038/onc.2017.281
Lee SH, Yu J, Hwang GH, Kim S, Kim HS, Ye S et al. CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR. Oncogene. 2017 Aug 28;36(49):6823-6829. https://doi.org/10.1038/onc.2017.281
Lee, S. H. ; Yu, J. ; Hwang, G. H. ; Kim, S. ; Kim, H. S. ; Ye, S. ; Kim, Kyoungmi ; Park, J. ; Park, D. Y. ; Cho, Y. K. ; Kim, J. S. ; Bae, S. / CUT-PCR : CRISPR-mediated, ultrasensitive detection of target DNA using PCR. In: Oncogene. 2017 ; Vol. 36, No. 49. pp. 6823-6829.
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