Table 1 Data sets used for analysis

Data Set	DNA origin	Description	Platform	Public Availability	N
Non-cancer liver samples					*341*
1	Liver	Non-HCC-Diseases	450 K	GSE61258	79
2	Liver	Liver Cirrhosis	450 K	GSE157973	130
3	Liver	Healthy liver tissue	450 K	GSE69852	6
4	Liver	Healthy liver tissue	450 K	GSE76269	10
5	Liver	Adjacent non-tumor tissues	450 K	TCGA	50
6	Liver	Adjacent non-tumor tissues	450 K	GSE54503	66
Non-cancer non-liver samples					*909*
7	Various tissues	Adjacent non-tumor tissues	450 K	TCGA	677
8	Lung	Normal	450 K	GSE63704	26
9	Ovaries	Normal	450 K	GSE65821	6
10	Stomach	Normal	450 K	GSE85464	19
11	Airway epithelial cells	Normal	450 K	GSE85566	115
12	Breast tissue	Mamoplastic reduction	450 K	GSE60185	15
13	Pancreas	Normal	450 K	GSE53051	12
14	Kidney, prostate, bladder	Normal	450 K	GSE52955	16
15	Colon	Normal	450 K	GSE42752	19
16	17 somatic tissues	Normal	450 K	GSE50192	4
BLOOD					*968*
17	Blood	Healthy	450 K	GSE40279	656
18	Blood	Healthy	450 K	GSE61496	312
Liver Cancer samples					*739*
19	Liver	Liver Cancer	450 K	TCGA	380
20	Liver	Liver Cancer	450 K	GSE76269	227
21	Liver	Liver Cancer	450 K	GSE75041	66
22	Liver	Liver Cancer	450 K	GSE54503	66
Non-liver Cancer samples					*8961*
23	Nonliver cancer tissues	31 types of non-HCC Cancers	450 K	TCGA	8961
Plasma samples					737
24	Plasma	cfDNA	MCTA-Seq	GSE63775	183
25	Plasma	cfDNA	MiSeq	This study	554

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