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Results were compared to observed means and to longitudinal trends estimated from shared parameter models, assuming that data were missing not at random. Longitudinal trends for SSc intrinsic molecular subsets defined by baseline gene expression signatures (normal\u2010like, inflammatory, and fibroproliferative signatures) were also studied.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Available observed means for pulmonary function tests appeared to improve over time in both arms. However, after accounting for participant loss, forced vital capacity in HSCT recipients increased by 0.77 percentage points\/year but worsened by \u20133.70\/year for CYC (<jats:italic>P<\/jats:italic>\u00a0=\u00a00.004). Similar results were found for diffusing capacity for carbon monoxide and quality of life indicators. Results for both analytic models were consistent. HSCT recipients in the inflammatory (n\u00a0=\u00a020) and fibroproliferative (n\u00a0=\u00a020) subsets had superior long\u2010term trends compared to CYC for pulmonary and quality of life measures. HSCT was also superior for modified Rodnan skin thickness scores in the fibroproliferative subset. For the normal\u2010like subset (n\u00a0=\u00a022), superiority of HSCT was less apparent.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Longitudinal trends estimated from 2 statistical models affirm the efficacy of HSCT over CYC in severe SSc. Failure to account for early loss of participants may distort estimated clinical trends over the long term.<\/jats:p><\/jats:sec>","DOI":"10.1002\/acr.24785","type":"journal-article","created":{"date-parts":[[2021,9,17]],"date-time":"2021-09-17T06:47:22Z","timestamp":1631861242000},"page":"307-316","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Clinical and Molecular Findings After Autologous Stem Cell Transplantation or Cyclophosphamide for Scleroderma: Handling Missing Longitudinal Data"],"prefix":"10.1002","volume":"75","author":[{"given":"Lynette","family":"Keyes\u2010Elstein","sequence":"first","affiliation":[{"name":"Rho Federal Systems Division  Durham North Carolina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Pinckney","sequence":"additional","affiliation":[{"name":"Rho Federal Systems Division  Durham North Carolina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen","family":"Goldmuntz","sequence":"additional","affiliation":[{"name":"National Institute of Allergy and Infectious Diseases  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beverly","family":"Welch","sequence":"additional","affiliation":[{"name":"National Institute of Allergy and Infectious Diseases  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer M.","family":"Franks","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine at Dartmouth  Hanover New Hampshire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktor","family":"Martyanov","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine at Dartmouth  Hanover New Hampshire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tammara A.","family":"Wood","sequence":"additional","affiliation":[{"name":"Geisel School of Medicine at Dartmouth  Hanover New Hampshire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leslie","family":"Crofford","sequence":"additional","affiliation":[{"name":"Vanderbilt University School of Medicine  Nashville Tennessee"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5070-2535","authenticated-orcid":false,"given":"Maureen","family":"Mayes","sequence":"additional","affiliation":[{"name":"University of Texas McGovern Medical School  Houston"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"McSweeney","sequence":"additional","affiliation":[{"name":"Colorado Blood Cancer Institute  Denver"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Nash","sequence":"additional","affiliation":[{"name":"Colorado Blood Cancer Institute  Denver"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Georges","sequence":"additional","affiliation":[{"name":"Fred Hutchinson Cancer Research Center  Seattle Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. 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