Genetic and epigenetic somatic alterations in head and neck squamous cell carcinomas are globally coordinated but not locally targeted.

In our analysis to define the local relationships between copy number and methylation, we observed only one gene (where promoter-associated CpG alterations were averaged), HOXA11 , with a marginally significant correlation between methylation and copy number alteration, although a number of individual CpG loci reached significance, including sites within potentially oncogenic GRB10, IHH, and HOXA11 .

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Using genomic-level measurements, we observed a highly significant association between copy number and DNA methylation profiles, definitively showing that these modes of gene regulation are linked in HNSCC.

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