Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

AM Lim; NC Wong; R Pidsley; E Zotenko; J Corry; A Dobrovic; SJ Clark; D Rischin; B Solomon

Journal article

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

AM Lim, NC Wong, R Pidsley, E Zotenko, J Corry, A Dobrovic, SJ Clark, D Rischin, B Solomon

Clinical Epigenetics | BMC | Published : 2016

DOI: 10.1186/s13148-016-0235-0

Download PDF

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 pr..

View full abstract

University of Melbourne Researchers

Annette Lim Author

Danny Rischin Author

Benjamin Solomon Author

Grants

Funding Acknowledgements

AML was supported during this project by the Cancer Council of Victoria postgraduate scholarship, RP by a Cancer Institute NSW Fellowship, and SJC by a National Health and Medical Research Fellowship. The authors would like to thank the Peter MacCallum Foundation and donors for their support of our research, and Dr Justin Bedo, IBM Research, Australia for providing Genome toolbox (GTB).