{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T11:37:17Z","timestamp":1761824237008,"version":"3.37.3"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T00:00:00Z","timestamp":1606176000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HG005946"],"award-info":[{"award-number":["HG005946"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR\u2013Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR\u2013Cas9 DNA labeling. We first design a CRISPR\u2013Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR\u2013Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR\u2013Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1088","type":"journal-article","created":{"date-parts":[[2020,10,28]],"date-time":"2020-10-28T12:11:42Z","timestamp":1603887102000},"page":"e8-e8","source":"Crossref","is-referenced-by-count":16,"title":["Customized optical mapping by CRISPR\u2013Cas9 mediated DNA labeling with multiple sgRNAs"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4587-8269","authenticated-orcid":false,"given":"Heba Z","family":"Abid","sequence":"first","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5393-530X","authenticated-orcid":false,"given":"Eleanor","family":"Young","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer","family":"McCaffrey","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaitlin","family":"Raseley","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3631-092X","authenticated-orcid":false,"given":"Dharma","family":"Varapula","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hung-Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danielle","family":"Piazza","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"},{"name":"Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA"},{"name":"Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua","family":"Mell","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA"},{"name":"Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3215-3752","authenticated-orcid":false,"given":"Ming","family":"Xiao","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA"},{"name":"Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,24]]},"reference":[{"key":"2021012319510809800_B1","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nbt.2303","article-title":"Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly","volume":"30","author":"Lam","year":"2012","journal-title":"Nat. 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