title: Algorithm Optimization in Methylation Detection with Multiple RT-qPCR.
abstract: Epigenetic markers based on differential methylation of DNA sequences are used in cancer screening and diagnostics. Detection of abnormal methylation at specific loci by real-time quantitative polymerase chain reaction (RT-qPCR) has been developed to enable high-throughput cancer screening. For tests that combine the results of multiple PCR replicates into a single reportable result, both individual PCR cutoff and weighting of the individual PCR result are essential to test outcome. In this opportunistic screening study, we tested samples from 1133 patients using the triplicate Epi proColon assay with various algorithms and compared it with the newly developed single replicate SensiColon assay that measures methylation status of the same SEPT9 gene sequence. The Epi proColon test approved by the US FDA (1/3 algorithm) showed the highest sensitivity (82.4%) at a lower specificity (82.0%) compared with the Epi proColon 2.0 CE version with 2/3 algorithm (75.1% sensitivity, 97.1% specificity) or 1/1 algorithm (71.3% sensitivity, 92.7% specificity). No significant difference in performance was found between the Epi proColon 2.0 CE and the SensiColon assays. The choice of algorithm must depend on specific test usage, including screening and early detection. These considerations allow one to choose the optimal algorithm to maximize the test performance. We hope this study can help to optimize the methylation detection in cancer screening and early detection.
authors.affiliation: The Chinese PLA 309th hospital, Beijing, People's Republic of China.
authors.forename: Lele
authors.initials: L
authors.lastname: Song
authors.affiliation: The Chinese PLA 309th hospital, Beijing, People's Republic of China.
authors.forename: Yuemin
authors.initials: Y
authors.lastname: Li
authors.affiliation: The Chinese PLA 309th hospital, Beijing, People's Republic of China.
authors.forename: Jia
authors.initials: J
authors.lastname: Jia
authors.affiliation: BioChain (Beijing) Science and Technology, Inc, Beijing, People's Republic of China.
authors.forename: Guangpeng
authors.initials: G
authors.lastname: Zhou
authors.affiliation: BioChain (Beijing) Science and Technology, Inc, Beijing, People's Republic of China.
authors.forename: Jianming
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Gastroenterology, The Army General Hospital, Beijing, People's Republic of China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Kang
authors.affiliation: Department of Gastroenterology, The Army General Hospital, Beijing, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Jin
authors.affiliation: Department of Gastroenterology, The Army General Hospital, Beijing, People's Republic of China.
authors.forename: Jianqiu
authors.initials: J
authors.lastname: Sheng
authors.affiliation: Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.
authors.forename: Guoxiang
authors.initials: G
authors.lastname: Cai
authors.affiliation: Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.
authors.forename: Sanjun
authors.initials: S
authors.lastname: Cai
authors.affiliation: BioChain (Beijing) Science and Technology, Inc, Beijing, People's Republic of China.
authors.forename: Xiaoliang
authors.initials: X
authors.lastname: Han
mesh_terms: D000368:Aged; D000465:Algorithms; D015179:Colorectal Neoplasms / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D005767:Gastrointestinal Diseases / Q000235:genetics; D023281:Genomics; D006801:Humans; D008297:Male; D008875:Middle Aged; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D058112:Septins / Q000235:genetics
chemical_list: C474315:SEPTIN9 protein, human; D058112:Septins