Overall leukocyte content in 10,814 TCGA tumor aliquots was assessed by identifying DNA methylation probes with the greatest differences between pure leukocyte cells and normal tissue, then estimating leukocyte content using a mixture model. From Illumina Infinium DNA methylation platform arrays HumanMethylation450, 2000 loci were identified (200 for HumanMethylation27) that were the most differentially methylated between leukocyte and normal tissues, 1000 in each direction. For each locus i, assuming two populations (j), for each sample we have the following equation:
Using the tumor with the least evidence of leukocyte methylation as a surrogate for the beta value (β) for each locus in the pure tumor, 2000 estimates were made, solving for π. We took the mode of 200 estimates to avoid loci that violate the assumptions. Using the estimated π and the measured β for tumor and leukocyte, with the same linear model, we solved for β (deconvoluted value) extracting the leukocyte fraction (LF).
Stromal fraction (SF) was defined as the total non-tumor cellular component, obtained by subtracting tumor purity from unity. Tumor purity was generated using ABSOLUTE (Carter et al., 2012 (link)) as detailed in Taylor et al., 2018 .
Using the tumor with the least evidence of leukocyte methylation as a surrogate for the beta value (β) for each locus in the pure tumor, 2000 estimates were made, solving for π. We took the mode of 200 estimates to avoid loci that violate the assumptions. Using the estimated π and the measured β for tumor and leukocyte, with the same linear model, we solved for β (deconvoluted value) extracting the leukocyte fraction (LF).
Stromal fraction (SF) was defined as the total non-tumor cellular component, obtained by subtracting tumor purity from unity. Tumor purity was generated using ABSOLUTE (Carter et al., 2012 (link)) as detailed in Taylor et al., 2018 .