Extended Data Fig. 5: Identification of candidate DNA methylation cancer genes using MethSig.
From: DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution
a) Application of CAMDAC principles to PDR. Bulk PDR (PDRb) can be described as a combination of the tumor PDR (PDRt) and normal PDR (PDRn) weighted by the copy number and purity. b and c) Normal and CAMDAC PDRs correlated with PDRs estimated from WT (WT-LOH PDR) and mutated reads (SNV-LOH PDR) respectively in regions with loss of heterozygosity (LOH) phased to SNVs. d) Correlation between PDR estimated from purified diploid cell populations from five tumor samples experimentally separated using FACS (Methods) vs. matched normal adjacent tissue (NAT). e) Plots showing the median PDR per tumor for bulk (PDRb), CAMDAC tumor (PDRt) and normal (PDRn) data. In concordance with CAMDAC principles, CAMDAC PDR (PDRt) levels are usually higher than the PDRb when the PDRn from adjacent tissue is lower than the PDRb. f) and g) Q-Q plot showing top significant MethSig cancer genes in LUAD and LUSC respectively. h and i) Top enriched Reactome pathways in LUAD and LUSC respectively.
