DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer

Clinical Epigenetics

Table 3 Enrichment of genomic features among 641 progression-related loci

A
Polycomb Group Target Genes (PCGT)	PCGT Target	NonPCGT Target
All array CpGs	49,054 (12.3 %)	348,546 (87.7 %)
Progression-related CpGs	123 (19.2 %)	518 (80.8 %)	*P value = 7.3E-07
B
Enhancer Regions	Enhancer	Nonenhancer
All array CpGs	72,289 (18.2 %)	325,311 (81.8 %)
Progression-related CpGs	176 (33.5 %)	465 (66.5 %)	*P value = 1.8E-22
C
CpG Island Status	CpG Island	NonCpG Island
All array CpGs	145,618 (36.6 %)	251,982 (63.4 %)
Progression-related CpGs	176 (33.5 %)	465 (66.5 %)	*P value = 9.8E-07
D
Open Sea	Open Sea	Nonopen Sea
All array CpGs	125,650 (31.6 %)	271,950 (68.4 %)
Progression-related CpGs	248 (38.7 %)	393 (61.3 %)	*P value = 1.5E-04
E
CpG Island Shore	CpG Island Shore	NonCpG Island Shore
All array CpGs	92,703 (23.3 %)	363971 (76.7 %)
Progression-related CpGs	170 (26.5 %)	471 (73.5 %)	*P value = 6.1E-02
F
CpG Island Shelf	CpG Island Shelf	NonCpG Island Shelf
All array CpGs	33,629 (8.5 %)	363,971 (91.5 %)
Progression-related CpGs	176 (7.3 %)	594 (92.7 %)	*P value = 0.35
G
TFBSany	TFBS	NonTFBS
All array CpGs	127 688 (32.2 %)	269 912 (67.8 %)
Progression-related CpGs	204 (31.8 %)	437 (68.2 %)	*P value = 0.89

CpGs among the 641 progression-related loci in DCIS are enriched for localization to A Polycomb group target genes (PCGTs), B informatically predicted enhancer regions, C depleted for localization to CpG Islands, and D enriched at Open Sea probes. Progression-related loci did not exhibit enrichment of E CpG Island shores, F CpG Island shores, or G any transcription factor binding site (TFBS)
*Fisher’s exact test

ISSN: 1868-7083