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The\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">N. gonorrhoeae<\/jats:named-content>\n            chromosome contains one expression locus (\n            <jats:italic>pilE<\/jats:italic>\n            ) and many promoterless, partial-coding silent copies (\n            <jats:italic>pilS<\/jats:italic>\n            ) that act as reservoirs for variant pilin information. Pilin Av occurs by high-frequency gene conversion reactions, which transfer\n            <jats:italic>pilS<\/jats:italic>\n            sequences into the\n            <jats:italic>pilE<\/jats:italic>\n            locus. We have developed a 454 sequencing-based assay to analyze the frequency and characteristics of pilin Av that allows a more robust analysis of pilin Av than previous assays. We used this assay to analyze mutations and conditions previously shown to affect pilin Av, confirming many but not all of the previously reported phenotypes. We show that mutations or conditions that cause growth defects can result in Av phenotypes when analyzed by phase variation-based assays. Adapting the 454 sequencing to analyze pilin Av demonstrates the utility of this technology to analyze any diversity generation system that uses recombination to develop biological diversity.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Measuring and analyzing complex recombination-based systems constitute a major barrier to understanding the mechanisms used to generate diversity. We have analyzed the contributions of many gonococcal mutations or conditions to the process of pilin antigenic variation.\n          <\/jats:p>","DOI":"10.1128\/jb.00330-16","type":"journal-article","created":{"date-parts":[[2016,7,6]],"date-time":"2016-07-06T02:38:37Z","timestamp":1467772717000},"page":"2470-2482","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":20,"title":["Analyzing Neisseria gonorrhoeae Pilin Antigenic Variation Using 454 Sequencing Technology"],"prefix":"10.1128","volume":"198","author":[{"given":"Ella","family":"Rotman","sequence":"first","affiliation":[{"name":"Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Webber","sequence":"additional","affiliation":[{"name":"Scanalytics Inc., Milwaukee, Wisconsin, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8651-0375","authenticated-orcid":false,"given":"H. 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