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Accordingly, we aimed to develop a method that incorporates patients with mild cognitive impairment and unknown cognitive status in GWAS using a machine learning-based AD prediction model.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Simulation analyses showed that weighting imputed phenotypes method increased the statistical power compared to ordinary logistic regression using only AD cases and controls. Applied to real-world data, the penalized logistic method had the highest AUC (0.96) for AD prediction and weighting imputed phenotypes method performed well in terms of power. We identified an association (P&amp;lt;5.0\u00d710-8) of AD with several variants in the APOE region and rs143625563 in LMX1A. Our method, which allows the inclusion of individuals with mild cognitive impairment, improves the statistical power of GWAS for AD. We discovered a novel association with LMX1A.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Simulation codes can be accessed at https:\/\/github.com\/Junkkkk\/wGEE_GWAS.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad534","type":"journal-article","created":{"date-parts":[[2023,9,4]],"date-time":"2023-09-04T18:06:53Z","timestamp":1693850813000},"source":"Crossref","is-referenced-by-count":0,"title":["Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9098-2858","authenticated-orcid":false,"given":"Jun Young","family":"Park","sequence":"first","affiliation":[{"name":"Department of Public Health Sciences, Graduate School of Public Health, Seoul National University , Seoul 08826, Korea"},{"name":"Neurozen Inc. , Seoul 06168, Korea"},{"name":"Gwangju Alzheimer\u2019s & 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