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These methods allow for the sequence capture of a specific locus or small genetic region all the way up to the entire six billion base pairs of the diploid human genome.<\/jats:p><jats:p>Rheumatic diseases are a huge burden on the US population, affecting more than 46 million Americans. Those afflicted suffer from one or more of the more than 100 diseases characterized by inflammation and loss of function, mainly of the joints, tendons, ligaments, bones, and muscles. While genetics studies of many of these diseases (for example, systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease) have had major successes in defining their genetic architecture, causal alleles and rare variants have still been elusive. This review describes the current high-throughput DNA sequencing methodologies commercially available and their application to rheumatic diseases in both case\u2013control as well as family-based studies.<\/jats:p>","DOI":"10.1186\/s13075-014-0490-4","type":"journal-article","created":{"date-parts":[[2014,11,21]],"date-time":"2014-11-21T17:20:19Z","timestamp":1416590419000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease"],"prefix":"10.1186","volume":"16","author":[{"given":"Graham B","family":"Wiley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer A","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick M","family":"Gaffney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,11,22]]},"reference":[{"key":"490_CR1","doi-asserted-by":"publisher","first-page":"1498","DOI":"10.1101\/gr.123638.111","volume":"21","author":"SS Ajay","year":"2011","unstructured":"Ajay SS, Parker SCJ, Abaan HO, Fajardo KVF, Margulies EH: Accurate and comprehensive sequencing of personal genomes. 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