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 metho...
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| Veröffentlicht in: | Nucleic acids research 2019-01, Vol.47 (1), p.e1-e1 |
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| container_title | Nucleic acids research |
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| creator | Lee, Jeewon Lim, Hyeonseob Jang, Hoon Hwang, Byungjin Lee, Joon Ho Cho, Junhyuk Lee, Ji Hyun Bang, Duhee |
| description | 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. |
| doi_str_mv | 10.1093/nar/gky820 |
| format | Article |
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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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky820</identifier><identifier>PMID: 30215766</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Alleles ; CRISPR-Cas Systems - genetics ; DNA - genetics ; Escherichia coli - genetics ; Genome, Bacterial - genetics ; Genome, Human - genetics ; Humans ; Methods Online ; Sequence Analysis, DNA</subject><ispartof>Nucleic acids research, 2019-01, Vol.47 (1), p.e1-e1</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000-0001-8775-9877</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326800/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326800/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30215766$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Jeewon</creatorcontrib><creatorcontrib>Lim, Hyeonseob</creatorcontrib><creatorcontrib>Jang, Hoon</creatorcontrib><creatorcontrib>Hwang, Byungjin</creatorcontrib><creatorcontrib>Lee, Joon Ho</creatorcontrib><creatorcontrib>Cho, Junhyuk</creatorcontrib><creatorcontrib>Lee, Ji Hyun</creatorcontrib><creatorcontrib>Bang, Duhee</creatorcontrib><title>CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>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.</description><subject>Alleles</subject><subject>CRISPR-Cas Systems - genetics</subject><subject>DNA - genetics</subject><subject>Escherichia coli - genetics</subject><subject>Genome, Bacterial - genetics</subject><subject>Genome, Human - genetics</subject><subject>Humans</subject><subject>Methods Online</subject><subject>Sequence Analysis, DNA</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNpVkElPwzAQhS0EoqVw4QegXDiGztix63BAqsJWqWIpcLbsxGkD2ZQFkX9PqkAFp9HMe_Pp6RFyinCB4LNprqvp-qOTFPbIGJmgrucLuk_GwIC7CJ4ckaO6fgdAD7l3SEYMKPKZEGPyHKwWL08rN9DlpZO1aZOUqf2ykRMVrUmtWzeVzqN-v36YOzavknCT2bxxjK77Y5E7zcY6A8Opu7qx2TE5iHVa25OfOSFvtzevwb27fLxbBPOlW6DPGtcC5WabJ9SMx1oYyn2ksQQpPTGjKHwTIcfYUjrjJjIQiliAjFEyH60QbEKuBm7ZmsxGYZ-q0qkqqyTTVacKnaj_Sp5s1Lr4VIJRIQF6wNlfwO7zt5zecD4YirbcqQhqW7rqS1dD6ewbOyhydQ</recordid><startdate>20190110</startdate><enddate>20190110</enddate><creator>Lee, Jeewon</creator><creator>Lim, Hyeonseob</creator><creator>Jang, Hoon</creator><creator>Hwang, Byungjin</creator><creator>Lee, Joon Ho</creator><creator>Cho, Junhyuk</creator><creator>Lee, Ji Hyun</creator><creator>Bang, Duhee</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-8775-9877</orcidid></search><sort><creationdate>20190110</creationdate><title>CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system</title><author>Lee, Jeewon ; Lim, Hyeonseob ; Jang, Hoon ; Hwang, Byungjin ; Lee, Joon Ho ; Cho, Junhyuk ; Lee, Ji Hyun ; Bang, Duhee</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-o193t-e025b1415ca35fa6b25912f80884672169bd151fe2275bdb0c6f608f18391e663</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Alleles</topic><topic>CRISPR-Cas Systems - genetics</topic><topic>DNA - genetics</topic><topic>Escherichia coli - genetics</topic><topic>Genome, Bacterial - genetics</topic><topic>Genome, Human - genetics</topic><topic>Humans</topic><topic>Methods Online</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, Jeewon</creatorcontrib><creatorcontrib>Lim, Hyeonseob</creatorcontrib><creatorcontrib>Jang, Hoon</creatorcontrib><creatorcontrib>Hwang, Byungjin</creatorcontrib><creatorcontrib>Lee, Joon Ho</creatorcontrib><creatorcontrib>Cho, Junhyuk</creatorcontrib><creatorcontrib>Lee, Ji Hyun</creatorcontrib><creatorcontrib>Bang, Duhee</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, Jeewon</au><au>Lim, Hyeonseob</au><au>Jang, Hoon</au><au>Hwang, Byungjin</au><au>Lee, Joon Ho</au><au>Cho, Junhyuk</au><au>Lee, Ji Hyun</au><au>Bang, Duhee</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2019-01-10</date><risdate>2019</risdate><volume>47</volume><issue>1</issue><spage>e1</spage><epage>e1</epage><pages>e1-e1</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>30215766</pmid><doi>10.1093/nar/gky820</doi><orcidid>https://orcid.org/0000-0001-8775-9877</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Alleles CRISPR-Cas Systems - genetics DNA - genetics Escherichia coli - genetics Genome, Bacterial - genetics Genome, Human - genetics Humans Methods Online Sequence Analysis, DNA |
| title | CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system |
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