title: A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors.
abstract: BACKGROUND
  DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples.
  
  
  RESULTS
  For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups. Greater than 84% of the top 100 loci previously shown to differentiate ER+ and ER- tumors in FF tissues were also FFPE DML. Weighted Correlation Gene Network Analyses (WCGNA) grouped the DML loci into 16 modules in FF tissue, with ~85% of the module membership preserved across tissue types.
  
  
  METHODS
  Restored FFPE and matched FF samples were profiled using the Illumina Infinium HumanMethylation450K platform. Methylation levels (β-values) across all loci and the top 100 loci previously shown to differentiate tumors by estrogen receptor status (ER+ or ER-) in a larger FF study, were compared between matched FF and FFPE samples using Pearson's correlation, hierarchical clustering and WCGNA. Positive predictive values and sensitivity levels for detecting differentially methylated loci (DML) in FF samples were calculated in an independent FFPE cohort.
  
  
  CONCLUSIONS
  FFPE breast tumors samples show lower overall detection of DMLs versus FF, however FFPE and FF DMLs compare favorably. These results support the emerging consensus that the 450K platform can be employed to investigate epigenetics in large sets of archival FFPE tissues.
authors.affiliation: Department of Molecular and Cell Biology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Allyson C
authors.initials: AC
authors.lastname: Espinal
authors.affiliation: Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.affiliation: Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Yan
authors.affiliation: Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Song
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Tang
authors.affiliation: Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Carl D
authors.initials: CD
authors.lastname: Morrison
authors.affiliation: Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Christine B
authors.initials: CB
authors.lastname: Ambrosone
authors.affiliation: Department of Molecular and Cell Biology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Higgins
authors.affiliation: College of Pharmacy, The Ohio State University, Columbus, OH, USA.|Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
authors.forename: Lara E
authors.initials: LE
authors.lastname: Sucheston-Campbell
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D016022:Case-Control Studies; D019175:DNA Methylation; D057890:Epigenomics; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016612:Paraffin Embedding / Q000379:methods*; D016707:Tissue Fixation
chemical_list: D014408:Biomarkers, Tumor
keywords: DNA methylation/epigenetics; breast cancer; estrogen receptor negative