BACKGROUND: Non-small cell lung carcinoma (NSCLC) is a complex malignancy that 
owing to its heterogeneity and poor prognosis poses many challenges to 
diagnosis, prognosis and patient treatment. DNA methylation is an important 
mechanism of epigenetic regulation involved in normal development and cancer. It 
is a very stable and specific modification and therefore in principle a very 
suitable marker for epigenetic phenotyping of tumors. Here we present a 
genome-wide DNA methylation analysis of NSCLC samples and paired lung tissues, 
where we combine MethylCap and next generation sequencing (MethylCap-seq) to 
provide comprehensive DNA methylation maps of the tumor and paired lung samples. 
The MethylCap-seq data were validated by bisulfite sequencing and 
methyl-specific polymerase chain reaction of selected regions.
RESULTS: Analysis of the MethylCap-seq data revealed a strong positive 
correlation between replicate experiments and between paired tumor/lung samples. 
We identified 57 differentially methylated regions (DMRs) present in all NSCLC 
tumors analyzed by MethylCap-seq. While hypomethylated DMRs did not correlate to 
any particular functional category of genes, the hypermethylated DMRs were 
strongly associated with genes encoding transcriptional regulators. Furthermore, 
subtelomeric regions and satellite repeats were hypomethylated in the NSCLC 
samples. We also identified DMRs that were specific to two of the major subtypes 
of NSCLC, adenocarcinomas and squamous cell carcinomas.
CONCLUSIONS: Collectively, we provide a resource containing genome-wide DNA 
methylation maps of NSCLC and their paired lung tissues, and comprehensive lists 
of known and novel DMRs and associated genes in NSCLC.