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Med."],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Chronic Kidney Disease (CKD) represents a slowly progressive disorder that is typically silent until late stages, but early intervention can significantly delay its progression. We designed a portable and scalable electronic CKD phenotype to facilitate early disease recognition and empower large-scale observational and genetic studies of kidney traits. The algorithm uses a combination of rule-based and machine-learning methods to automatically place patients on the staging grid of albuminuria by glomerular filtration rate (\u201cA-by-G\u201d grid). We manually validated the algorithm by 451 chart reviews across three medical systems, demonstrating overall positive predictive value of 95% for CKD cases and 97% for healthy controls. Independent case-control validation using 2350 patient records demonstrated diagnostic specificity of 97% and sensitivity of 87%. Application of the phenotype to 1.3 million patients demonstrated that over 80% of CKD cases are undetected using ICD codes alone. We also demonstrated several large-scale applications of the phenotype, including identifying stage-specific kidney disease comorbidities, in silico estimation of kidney trait heritability in thousands of pedigrees reconstructed from medical records, and biobank-based multicenter genome-wide and phenome-wide association studies.<\/jats:p>","DOI":"10.1038\/s41746-021-00428-1","type":"journal-article","created":{"date-parts":[[2021,4,13]],"date-time":"2021-04-13T10:05:57Z","timestamp":1618308357000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":68,"title":["Medical records-based chronic kidney disease phenotype for clinical care and \u201cbig data\u201d observational and genetic studies"],"prefix":"10.1038","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7040-5204","authenticated-orcid":false,"given":"Ning","family":"Shang","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6651-2725","authenticated-orcid":false,"given":"Atlas","family":"Khan","sequence":"additional","affiliation":[]},{"given":"Fernanda","family":"Polubriaginof","sequence":"additional","affiliation":[]},{"given":"Francesca","family":"Zanoni","sequence":"additional","affiliation":[]},{"given":"Karla","family":"Mehl","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0815-2370","authenticated-orcid":false,"given":"David","family":"Fasel","sequence":"additional","affiliation":[]},{"given":"Paul E.","family":"Drawz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3802-8183","authenticated-orcid":false,"given":"Robert J.","family":"Carrol","sequence":"additional","affiliation":[]},{"given":"Joshua C.","family":"Denny","sequence":"additional","affiliation":[]},{"given":"Matthew A.","family":"Hathcock","sequence":"additional","affiliation":[]},{"given":"Adelaide M.","family":"Arruda-Olson","sequence":"additional","affiliation":[]},{"given":"Peggy L.","family":"Peissig","sequence":"additional","affiliation":[]},{"given":"Richard A.","family":"Dart","sequence":"additional","affiliation":[]},{"given":"Murray H.","family":"Brilliant","sequence":"additional","affiliation":[]},{"given":"Eric B.","family":"Larson","sequence":"additional","affiliation":[]},{"given":"David S.","family":"Carrell","sequence":"additional","affiliation":[]},{"given":"Sarah","family":"Pendergrass","sequence":"additional","affiliation":[]},{"given":"Shefali Setia","family":"Verma","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1208-1720","authenticated-orcid":false,"given":"Marylyn D.","family":"Ritchie","sequence":"additional","affiliation":[]},{"given":"Barbara","family":"Benoit","sequence":"additional","affiliation":[]},{"given":"Vivian S.","family":"Gainer","sequence":"additional","affiliation":[]},{"given":"Elizabeth W.","family":"Karlson","sequence":"additional","affiliation":[]},{"given":"Adam S.","family":"Gordon","sequence":"additional","affiliation":[]},{"given":"Gail P.","family":"Jarvik","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0783-0918","authenticated-orcid":false,"given":"Ian B.","family":"Stanaway","sequence":"additional","affiliation":[]},{"given":"David R.","family":"Crosslin","sequence":"additional","affiliation":[]},{"given":"Sumit","family":"Mohan","sequence":"additional","affiliation":[]},{"given":"Iuliana","family":"Ionita-Laza","sequence":"additional","affiliation":[]},{"given":"Nicholas P.","family":"Tatonetti","sequence":"additional","affiliation":[]},{"given":"Ali G.","family":"Gharavi","sequence":"additional","affiliation":[]},{"given":"George","family":"Hripcsak","sequence":"additional","affiliation":[]},{"given":"Chunhua","family":"Weng","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5047-6715","authenticated-orcid":false,"given":"Krzysztof","family":"Kiryluk","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,4,13]]},"reference":[{"key":"428_CR1","unstructured":"Centers for Disease Control and Prevention. 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