CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system

Jeewon Lee, Hyeonseob Lim, Hoon Jang, Byungjin Hwang, Joon Ho Lee, Junhyuk Cho, Ji Hyun Lee, Duhee Bang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81% and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1%. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.

Original languageEnglish
Article numbere1
JournalNucleic acids research
Volume47
Issue number1
DOIs
Publication statusPublished - 2019 Jan 10

Fingerprint

Clustered Regularly Interspaced Short Palindromic Repeats
DNA
Molecular Probes
Gene Dosage
Human Genome
Gene Frequency
Genes
Escherichia coli
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Lee, Jeewon ; Lim, Hyeonseob ; Jang, Hoon ; Hwang, Byungjin ; Lee, Joon Ho ; Cho, Junhyuk ; Lee, Ji Hyun ; Bang, Duhee. / CRISPR-Cap : multiplexed double-stranded DNA enrichment based on the CRISPR system. In: Nucleic acids research. 2019 ; Vol. 47, No. 1.
@article{e6d057c08bac449a8b817590e7055931,
title = "CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system",
abstract = "Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81{\%} and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1{\%}. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.",
author = "Jeewon Lee and Hyeonseob Lim and Hoon Jang and Byungjin Hwang and Lee, {Joon Ho} and Junhyuk Cho and Lee, {Ji Hyun} and Duhee Bang",
year = "2019",
month = "1",
day = "10",
doi = "10.1093/nar/gky820",
language = "English",
volume = "47",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "1",

}

CRISPR-Cap : multiplexed double-stranded DNA enrichment based on the CRISPR system. / Lee, Jeewon; Lim, Hyeonseob; Jang, Hoon; Hwang, Byungjin; Lee, Joon Ho; Cho, Junhyuk; Lee, Ji Hyun; Bang, Duhee.

In: Nucleic acids research, Vol. 47, No. 1, e1, 10.01.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - CRISPR-Cap

T2 - multiplexed double-stranded DNA enrichment based on the CRISPR system

AU - Lee, Jeewon

AU - Lim, Hyeonseob

AU - Jang, Hoon

AU - Hwang, Byungjin

AU - Lee, Joon Ho

AU - Cho, Junhyuk

AU - Lee, Ji Hyun

AU - Bang, Duhee

PY - 2019/1/10

Y1 - 2019/1/10

N2 - Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81% and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1%. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.

AB - Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81% and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1%. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.

UR - http://www.scopus.com/inward/record.url?scp=85059796278&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85059796278&partnerID=8YFLogxK

U2 - 10.1093/nar/gky820

DO - 10.1093/nar/gky820

M3 - Article

C2 - 30215766

AN - SCOPUS:85059796278

VL - 47

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 1

M1 - e1

ER -