Comparing variants related to chronic diseases from genome-wide association study (GWAS) and the cancer genome atlas (TCGA)

Table 1 Descriptions of TCGA dataset

	TCGA-COAD	TCGA-STAD	TCGA-UCEC	TCGA-SKCM
RNA-seq
Total genes	56,457	56,457	56,457	56,457
RNA-seq, no variant group	429	364	504	101
RNA-seq, variant group	21	9	33	2
Total RNA-seq samples	450	373	537	103
Threshold	PV < 0.01 & \|FC\| > 0.2	PV < 10⁻¹⁰ & \|FC\| > 0.3	PV < 0.01 & \|FC\| > 0.2	(No analysis)
Methylation 450 k
Total CpG sites	118,342	373,352	379,215	380,110
Met450, no variant group	269	384	398	103
Met450, variant group	20	9	27	2
Total Met450 samples	289	393	425	103
Threshold	PV < 10⁻¹² & \|FC\| > 0.2	PV < 10⁻¹² & \|FC\| > 0.2	PV < 10⁻¹² & \|FC\| > 0.2	(No analysis)

ISSN: 1755-8794