{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T12:56:08Z","timestamp":1762606568236,"version":"3.37.3"},"reference-count":22,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2015,7,21]],"date-time":"2015-07-21T00:00:00Z","timestamp":1437436800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100001130","name":"Gerber Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100001130","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Harvard Digestive Disease Grant","award":["P30 DK034854."],"award-info":[{"award-number":["P30 DK034854."]}]},{"name":"NIH","award":["K24DK82792"],"award-info":[{"award-number":["K24DK82792"]}]},{"name":"NIH","award":["R01AI075037"],"award-info":[{"award-number":["R01AI075037"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Clin Experimental Allergy"],"published-print":{"date-parts":[[2015,8]]},"abstract":"<jats:title>Summary<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Quantification of tissue eosinophils remains the golden standard in diagnosing eosinophilic oesophagitis (EoE), but this approach suffers from poor specificity. It has been recognized that histopathological changes that occur in patients with EoE are associated with a disease\u2010specific tissue transcriptome.<\/jats:p><\/jats:sec><jats:sec><jats:title>Objective<\/jats:title><jats:p>We hypothesized that digital <jats:styled-content style=\"fixed-case\">mRNA<\/jats:styled-content> profiling targeted at a set of EoE\u2010specific and Th2 inflammatory genes in oesophageal biopsies could help differentiate patients with EoE from those with reflux oesophagitis (<jats:styled-content style=\"fixed-case\">RE<\/jats:styled-content>) or normal tissue histology (<jats:styled-content style=\"fixed-case\">NH<\/jats:styled-content>).<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The <jats:styled-content style=\"fixed-case\">mRNA<\/jats:styled-content> expression levels of 79 target genes were defined in both proximal and distal biopsies of 196 patients with <jats:styled-content style=\"fixed-case\">nC<\/jats:styled-content>ounter\u00ae (Nanostring) technology. According to clinicopathological diagnosis, these patients were grouped in a training set (35 EoE, 30 <jats:styled-content style=\"fixed-case\">RE<\/jats:styled-content>, 30 <jats:styled-content style=\"fixed-case\">NH<\/jats:styled-content>) for building of a three\u2010class prediction model using the random forest method, and a blinded predictive set (<jats:italic>n<\/jats:italic>\u00a0=\u00a047) for model validation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A diagnostic model built on ten differentially expressed genes was able to differentiate with 100% sensitivity and specificity between conditions in the training set. In a blinded predictive set, this model was able to correctly predict EoE in 14 of 18 patients in distal (sensitivity 78%, 95% <jats:styled-content style=\"fixed-case\">CI<\/jats:styled-content> 52\u201393%) and 16 of 18 patients in proximal biopsies (sensitivity 89%, 95% <jats:styled-content style=\"fixed-case\">CI<\/jats:styled-content> 64\u201398%), without false\u2010positive diagnosis of EoE in <jats:styled-content style=\"fixed-case\">RE<\/jats:styled-content> or <jats:styled-content style=\"fixed-case\">NH<\/jats:styled-content> patients (specificity 100%, 95% <jats:styled-content style=\"fixed-case\">CI<\/jats:styled-content> 85\u2013100%). Sensitivity was increased to 94% (95% <jats:styled-content style=\"fixed-case\">CI<\/jats:styled-content> 71\u2013100%) when either the best predictive distal or proximal biopsy was used.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion and Clinical Relevance<\/jats:title><jats:p>We conclude that <jats:styled-content style=\"fixed-case\">mRNA<\/jats:styled-content> profiling of oesophageal tissue is an accurate diagnostic strategy in detecting EoE.<\/jats:p><\/jats:sec>","DOI":"10.1111\/cea.12523","type":"journal-article","created":{"date-parts":[[2015,2,26]],"date-time":"2015-02-26T08:14:37Z","timestamp":1424938477000},"page":"1317-1327","source":"Crossref","is-referenced-by-count":9,"title":["Accuracy of digital <scp>mRNA<\/scp> profiling of oesophageal biopsies as a novel diagnostic approach to eosinophilic oesophagitis"],"prefix":"10.1111","volume":"45","author":[{"given":"W. S.","family":"Lexmond","sequence":"first","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L.","family":"Hu","sequence":"additional","affiliation":[{"name":"Center for Cancer Computational Biology Department of Biostatistics and Computational Biology Dana\u2010Farber Cancer Institute Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Pardo","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N.","family":"Heinz","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K.","family":"Rooney","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"LaRosa","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.","family":"Dehlink","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.","family":"Fiebiger","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders Eosinophilic Gastrointestinal Disease Center Boston Children's Hospital Harvard Medical School Boston MA USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Nurko","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Nutrition Center for Motility and Functional Gastrointestinal Disorders 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