Table 1. High-throughput methylation analysis of CpG sites per amplicon for the 10 candidate genes.

Genes	Amplicon size (bp)	Total No. of CpG sites in the amplicon	No. of analyzed CpG sites in the amplicon	No. of analyzed CpG sites per amplicons
				Single	Composite
BMP6	397	37	30	11	19
BRCA1	413	30	15	10	5
CST6	445	49	27	15	12
CDKN2A	580	62	36	13	23
CDKN1A	419	30	19	10	9
TIMP3	441	51	44	11	33

The in silico digestion was performed for T-cleavage assay. The percentage of total CpG sites in the amplicon is divided into single sites (single CpG sites) and composite sites (two or more adjacent CpG sites fall within one fragment, or when fragment masses are overlapping).