title: Evaluating the clinical feasibility: The direct bisulfite genomic sequencing for examination of methylated status of protocadherin10 (PCDH10) promoter to predict the prognosis of gastric cancer.
abstract: OBJECTIVE
  To elucidate the clinical significance of the methylated status of CpG site count of PCDH10 promoter in the survival prediction in gastric cancer (GC).
  
  
  METHODS
  In the previous study, we demonstrated that the methylated CpG site count was significantly associated with the overall survival (OS) of GC patients by using the bisulfite genomic sequencing (BGS) with no less than five clones per sample. It was so complex and expensive for patients to undergo the BGS clones. In this study, we detected the different CpG site counts (hypermethylated and hypomethylated) of PCDH10 DNA promoter in GC samples of 471 patients by directly bisulfite genomic sequencing (D-BGS) without any clone. Furthermore, we evaluated the relationships between the methylated status of PCDH10 promoter and OS.
  
  
  RESULTS
  Two hundred and fifty-seven of 471 (54.6%) GC patients were identified to present with PCDH10 promoter methylation by D-BGS. Patients who presented with 5 or more methylated CpG site counts of PCDH10 promoter had significantly poorer prognosis than patients who with less than 5 methylated CpG site counts of PCDH10 promoter (p= 0.039). With the multivariate survival analysis, we demonstrated that T stage, N stage and the hypermethylated CpG site counts of PCDH10 DNA promoter were the independent predictors of OS of GC patients. In addition, the hypermethylated CpG site counts of PCDH10 DNA promoter had smaller Akaike information criterion (AIC) and Bayesian information criterion (BIC) values than the other two independent predictors of the OS, indicating the hypermethylated CpG site counts of PCDH10 DNA promoter as the best prognostic predictor of GC.
  
  
  CONCLUSIONS
  Our present findings suggested that the hypermethylated CpG site counts of PCDH10 DNA promoter for evaluating the prognosis of GC was reasonable by using the D-BGS.
authors.forename: Ya-Chao
authors.initials: YC
authors.lastname: Hou
authors.forename: Jing-Yu
authors.initials: JY
authors.lastname: Deng
authors.forename: Ru-Peng
authors.initials: RP
authors.lastname: Zhang
authors.forename: Xing-Ming
authors.initials: XM
authors.lastname: Xie
authors.forename: Jing-Li
authors.initials: JL
authors.lastname: Cui
authors.forename: Wei-Peng
authors.initials: WP
authors.lastname: Wu
authors.forename: Xi-Shan
authors.initials: XS
authors.lastname: Hao
authors.forename: Han
authors.initials: H
authors.lastname: Liang
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D015820:Cadherins / Q000096:biosynthesis / Q000235:genetics*; D002874:Chromosome Mapping; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D011379:Prognosis; D011401:Promoter Regions, Genetic / Q000235:genetics; D000091363:Protocadherins; D013274:Stomach Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D015820:Cadherins; C438603:PCDH10 protein, human; D000091363:Protocadherins
keywords: PCDH10; direct bisulfite genomic sequencing; gastric cancer; methylation; prognosis