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Dr. Halloran held a Canada Research Chair in Transplant Immunology until 2008 and currently holds the Muttart Chair in Clinical Immunology."}],"content-domain":{"domain":["portlandpress.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,6,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>There is a major unmet need for improved accuracy and precision in the assessment of transplant rejection and tissue injury. Diagnoses relying on histologic and visual assessments demonstrate significant variation between expert observers (as represented by low kappa values) and have limited ability to assess many biological processes that produce little histologic changes, for example, acute injury. Consensus rules and guidelines for histologic diagnosis are useful but may have errors. Risks of over- or under-treatment can be serious: many therapies for transplant rejection or primary diseases are expensive and carry risk for significant adverse effects. Improved diagnostic methods could alleviate healthcare costs by reducing treatment errors, increase treatment efficacy, and serve as useful endpoints for clinical trials of new agents that can improve outcomes. Molecular diagnostic assessments using microarrays combined with machine learning algorithms for interpretation have shown promise for increasing diagnostic precision via probabilistic assessments, recalibrating standard of care diagnostic methods, clarifying ambiguous cases, and identifying potentially missed cases of rejection. This review describes the development and application of the Molecular Microscope\u00ae Diagnostic System (MMDx), and discusses the history and reasoning behind many common methods, statistical practices, and computational decisions employed to ensure that MMDx scores are as accurate and precise as possible. MMDx provides insights on disease processes and highly reproducible results from a comparatively small amount of tissue and constitutes a general approach that is useful in many areas of medicine, including kidney, heart, lung, and liver transplants, with the possibility of extrapolating lessons for understanding native organ disease states.<\/jats:p>","DOI":"10.1042\/cs20220530","type":"journal-article","created":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T08:56:23Z","timestamp":1717145783000},"page":"663-685","update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope\u00ae Diagnostic System (MMDx)"],"prefix":"10.1042","volume":"138","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2781-6934","authenticated-orcid":false,"given":"Katelynn\u00a0S.","family":"Madill-Thomsen","sequence":"first","affiliation":[{"name":"1Department of Medicine, University of Alberta, Edmonton, AB, Canada"},{"name":"2Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip\u00a0F.","family":"Halloran","sequence":"additional","affiliation":[{"name":"1Department of Medicine, University of Alberta, Edmonton, AB, Canada"},{"name":"2Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"288","published-online":{"date-parts":[[2024,5,31]]},"reference":[{"key":"2024053112553137200_B1","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1097\/TP.0000000000004624","article-title":"The molecular phenotype of kidney transplants: insights from the MMDx Project","volume":"108","author":"Halloran","year":"2024","journal-title":"Transplantation"},{"key":"2024053112553137200_B2","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1097\/TP.0000000000004323","article-title":"The molecular microscope diagnostic system: assessment of rejection and injury in heart transplant biopsies","volume":"107","author":"Halloran","year":"2023","journal-title":"Transplantation"},{"key":"2024053112553137200_B3","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1097\/TP.0000000000004396","article-title":"Relating molecular T cell-mediated rejection activity in kidney transplant biopsies to time and to histologic tubulitis and atrophy-fibrosis","volume":"107","author":"Madill-Thomsen","year":"2023","journal-title":"Transplantation"},{"key":"2024053112553137200_B4","first-page":"S371","article-title":"The spectrum of molecular rejection in the prevalent kidney transplant population: a new analysis of 5087 biopsies","volume":"23","author":"Halloran","year":"2023","journal-title":"Am. 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