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Table 2 High-throughput methylation analysis of CpG sites per amplicon for the 12 candidate genes

From: Methylation signature of lymph node metastases in breast cancer patients

Genes Amplicon size (bp) Total No. of CpG sites in amplicon No. of analyzed CpG sites in amplicon No. of analyzed CpG sites per amplicons
Single sites Composite sites
APC 420 26 11 9 2
BIN1 330 32 12 3 9
BMP6 397 37 26 9 17
BRCA1 413 30 15 10 5
CST6 445 49 19 11 8
ESR-b (ER beta) 374 30 13 6 7
GSTP1 381 23 16 11 5
P14 425 36 22 5 17
P16 (CDKN2A) 580 62 38 12 26
P21 (CDKN1A) 419 30 9 8 1
PTEN 451 34 29 10 19
TIMP3v 441 51 40 12 38
  1. The in silico digestion was performed for the 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).