title: Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas.
abstract: BACKGROUND
  DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 109 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. Data pre-processing, quality control and analysis were performed using R packages. Probes mapping to SNPs, sex chromosomes and unreliable probes were accounted for prior to downstream analyses. The relationship between methylation and patient survival was examined using both agnostic approaches and feature selection. The cohort was enlarged by incorporation of 331 The Cancer Genome Atlas (TCGA) HNSCC samples, which included 91 TCGA OTSCC samples with HM450K and survival data available.
  
  
  RESULTS
  Given the use of FFPE-derived DNA, we defined different cohorts for separate analyses. Overall, similar results were found between cohorts. With an unsupervised approach, no distinct hypermethylated group of samples was identified and nor was a prognostic methylation profile identified. The use of multiple downstream feature selection approaches, including a linear models for microarray data (LIMMA), centroid feature selection (CFS), and recursive feature elimination (RFE) support vector machines, similarly failed to identify a significant methylation signature informative for patient prognosis or any clinicopathological data available. Furthermore, we were unable to confirm the prognostic methylation profiles or specific prognostic loci reported within the literature for HNSCC.
  
  
  CONCLUSIONS
  With genome-scale assessment of DNA methylation using HM450K in one of the largest OTSCC cohorts to date, we were unable to identify a hypermethylated group of tumours or a prognostic methylation signature. This suggests that either DNA methylation in isolation is not likely to be of prognostic value or larger cohorts are required to identify such a biomarker for OTSCC.
authors.affiliation: Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Ave, Nedlands, Western Australia 6009 Australia.|The University of Western Australia, Perth, Australia.
authors.forename: Annette M
authors.initials: AM
authors.lastname: Lim
authors.affiliation: Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010 Australia.
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Wong
authors.affiliation: Epigenetics Research Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010 Australia.
authors.forename: Ruth
authors.initials: R
authors.lastname: Pidsley
authors.affiliation: Epigenetics Research Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010 Australia.
authors.forename: Elena
authors.initials: E
authors.lastname: Zotenko
authors.affiliation: Department of Radiation Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia.
authors.forename: June
authors.initials: J
authors.lastname: Corry
authors.affiliation: The University of Melbourne, Melbourne, Australia.|Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, 145 Studley Rd, Heidelberg, Victoria 3084 Australia.|Department of Cancer Biology, La Trobe University, Bundoora, Victoria 3084 Australia.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobrovic
authors.affiliation: Epigenetics Research Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010 Australia.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Clark
authors.affiliation: Department of Medical Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia.
authors.forename: Danny
authors.initials: D
authors.lastname: Rischin
authors.affiliation: Department of Medical Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Solomon
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology*; D015331:Cohort Studies; D019175:DNA Methylation; D005260:Female; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009062:Mouth Neoplasms / Q000235:genetics* / Q000473:pathology*; D011379:Prognosis; D016019:Survival Analysis; D055815:Young Adult
keywords: DNA methylation; Epigenetics; HM450K; Oral carcinoma; Profiling; Survival; Tongue