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Our previous linkage and genome\u2010wide association studies (<jats:styled-content style=\"fixed-case\">GWAS<\/jats:styled-content>) generated strong evidence for aetiological contributions from inherited genetic variants at different population frequencies, including both rare mutations and common polymorphisms. Additionally, we conducted gene expression (<jats:styled-content style=\"fixed-case\">GE<\/jats:styled-content>) studies on scalp biopsies of 96 patients and controls\u00a0to establish signatures of active disease. In this study, we performed an integrative analysis on these two datasets to test the hypothesis that rare <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s in patients with <jats:styled-content style=\"fixed-case\">AA<\/jats:styled-content> could be leveraged to identify drivers of disease in our <jats:styled-content style=\"fixed-case\">AA GE<\/jats:styled-content> signatures. We analysed copy number variants (<jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s) in a case\u2010control cohort of 673\u00a0patients with <jats:styled-content style=\"fixed-case\">AA<\/jats:styled-content> and 16 311\u00a0controls independent of the case\u2010control cohort of 96 research participants used in our <jats:styled-content style=\"fixed-case\">GE<\/jats:styled-content> study. Using an integrative computational analysis, we identified 14 genes whose expression levels were altered by <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s in a consistent direction of effect, corresponding to gene expression changes in lesional skin of patients. Four of these genes were affected by <jats:styled-content style=\"fixed-case\">CNV<\/jats:styled-content>s in three or more unrelated patients with <jats:styled-content style=\"fixed-case\">AA<\/jats:styled-content>, including <jats:styled-content style=\"fixed-case\">ATG<\/jats:styled-content>4B and <jats:styled-content style=\"fixed-case\">SMARCA<\/jats:styled-content>2, which are involved in autophagy and chromatin remodelling, respectively. Our findings identified new classes of genes with potential contributions to <jats:styled-content style=\"fixed-case\">AA<\/jats:styled-content> pathogenesis.<\/jats:p>","DOI":"10.1111\/exd.13986","type":"journal-article","created":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T13:58:42Z","timestamp":1559829522000},"page":"243-253","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Integrative analysis of rare copy number variants and gene expression data in alopecia areata implicates an aetiological role for autophagy"],"prefix":"10.1111","volume":"29","author":[{"given":"Lynn","family":"Petukhova","sequence":"first","affiliation":[{"name":"Department of Dermatology College of Physicians and Surgeons Columbia University New York New York"},{"name":"Department of Epidemiology Mailman School of Public Health Columbia University New York New 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