{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T05:25:17Z","timestamp":1787289917361,"version":"build-2736575974"},"reference-count":44,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,9,28]],"date-time":"2021-09-28T00:00:00Z","timestamp":1632787200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Genes"],"abstract":"<jats:p>Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide in 2020. Colonoscopy and the fecal immunochemical test (FIT) are commonly used as CRC screening tests, but both types of tests possess different limitations. Recently, liquid biopsy-based DNA methylation test has become a powerful tool for cancer screening, and the detection of abnormal DNA methylation in stool specimens is considered as an effective approach for CRC screening. The aim of this study was to develop a novel approach in biomarker selection based on integrating primary biomarkers from genome-wide methylation profiles and secondary biomarkers from CRC comorbidity analytics. A total of 125 differential methylated probes (DMPs) were identified as primary biomarkers from 352 genome-wide methylation profiles. Among them, 51 biomarkers, including 48 hypermethylated DMPs and 3 hypomethylated DMPs, were considered as suitable DMP candidates for CRC screening tests. After comparing with commercial kits, three genes (ADHFE1, SDC2, and PPP2R5C) were selected as candidate epigenetic biomarkers for CRC screening tests. Methylation levels of these three biomarkers were significantly higher for patients with CRC than normal subjects. The sensitivity and specificity of integrating methylated ADHFE1, SDC2, and PPP2R5C for CRC detection achieved 84.6% and 92.3%, respectively. Through an integrated approach using genome-wide DNA methylation profiles and electronic medical records, we could design a biomarker panel that allows for early and accurate noninvasive detection of CRC using stool samples.<\/jats:p>","DOI":"10.3390\/genes12101539","type":"journal-article","created":{"date-parts":[[2021,9,28]],"date-time":"2021-09-28T21:38:09Z","timestamp":1632865089000},"page":"1539","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["RETRACTED: Using Comorbidity Pattern Analysis to Detect Reliable Methylated Genes in Colorectal Cancer Verified by Stool DNA Test"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8317-1339","authenticated-orcid":false,"given":"Yi-Chiao","family":"Cheng","sequence":"first","affiliation":[{"name":"Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Po-Hsien","family":"Wu","sequence":"additional","affiliation":[{"name":"Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yen-Ju","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei 10608, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cing-Han","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jhen-Li","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4823-6541","authenticated-orcid":false,"given":"Yu-Ching","family":"Chou","sequence":"additional","affiliation":[{"name":"School of Public Health, National Defense Medical Center, Taipei 11490, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pi-Kai","family":"Chang","sequence":"additional","affiliation":[{"name":"Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chia-Cheng","family":"Wen","sequence":"additional","affiliation":[{"name":"Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu-Wen","family":"Jao","sequence":"additional","affiliation":[{"name":"Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsin-Hui","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Cell Biology, School of Medicine, Taipei Medical University, Taipei 11042, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Hsuan","family":"Tsai","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei 10608, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2869-4169","authenticated-orcid":false,"given":"Tun-Wen","family":"Pai","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei 10608, Taiwan"},{"name":"Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,28]]},"reference":[{"key":"ref_1","first-page":"209","article-title":"Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J. 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