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Using 347 mice in 98 full\u2010sibships, destabilization of medial meniscus (DMM) was performed to induce joint injury. We found that joint destabilization instigated ectopic calcifications as detected and quantified by micro\u2010CT. We performed quantitative trait locus (QTL) analysis to map ectopic calcification phenotypes to discrete genomic locations. To validate the functional significance of the selected QTL candidate genes, we compared mRNA expression between parental LG\/J and SM\/J inbred strains. Overall, we detected 20 QTLs affecting synovial and meniscus calcification phenotypes with 11 QTLs linked to synovial calcification. Functional and bioinformatic analyses of single nucleotide polymorphism (SNP) identified functional classifications relevant to angiogenesis (<jats:italic>Myo1e, Kif26b, Nprl3, Stab2, Fam105b)<\/jats:italic>, bone metabolism\/calcification (<jats:italic>Tle3, Tgfb2, Lipc, Nfe2l1, Ank, Fam105b<\/jats:italic>), arthritis (<jats:italic>Stab2, Tbx21, Map4k4, Hoxb9, Larp6, Col1a2, Adam10, Timp3, Nfe2l1, Trpm3<\/jats:italic>), and ankylosing\u2010spondylitis (<jats:italic>Ank, Pon1, Il1r2, Tbkbp1<\/jats:italic>) indicating that ectopic calcification involves multiple mechanisms. Furthermore, the expression of 11 out of 78 candidate genes was significantly different between LG\/J and SM\/J. Correlation analysis showed that <jats:italic>Aff3<\/jats:italic>, <jats:italic>Fam81a<\/jats:italic>, <jats:italic>Syn3<\/jats:italic>, and <jats:italic>Ank<\/jats:italic> were correlated with synovial calcification. Taken together, our findings of multiple genetic loci suggest the involvement of multiple genes contributing to ectopic calcification. \u00a9 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:1412\u20131423, 2015.<\/jats:p><\/jats:sec>","DOI":"10.1002\/jor.22944","type":"journal-article","created":{"date-parts":[[2015,5,18]],"date-time":"2015-05-18T09:34:23Z","timestamp":1431941663000},"page":"1412-1423","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Genetic loci that regulate ectopic calcification in response to knee trauma in LG\/J by SM\/J advanced intercross mice"],"prefix":"10.1002","volume":"33","author":[{"given":"Muhammad Farooq","family":"Rai","sequence":"first","affiliation":[{"name":"Department of Orthopaedic Surgery, Musculoskeletal Research Center Washington University School of Medicine at Barnes\u2010Jewish Hospital 425 S. 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Sheridan Road Chicago Illinois 60660"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda J.","family":"Sandell","sequence":"additional","affiliation":[{"name":"Department of Orthopaedic Surgery, Musculoskeletal Research Center Washington University School of Medicine at Barnes\u2010Jewish Hospital 425 S. Euclid Avenue MS 8233 St. Louis Missouri 63110"},{"name":"Department of Biomedical Engineering Washington University in St. Louis at Engineering and Applied Sciences Whitaker Hall, MS 1097 St. Louis MO 63130"},{"name":"Department of Cell Biology and Physiology Washington University School of Medicine at Barnes\u2010Jewish Hospital 425 S. 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