Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Table 3 Large blocks of aberrant methylation identified in normal versus hyperplastic, adenoma, or cancer samples

	Blocks (n)	Total Mb inside blocks	Intersection with colon blocks (%)	25%length quartile (Mb)	50%length quartile (Mb)	75%length quartile (Mb)	Median diff value	Hypo-meth. (%)
Breast (Cancer-normal)	150	42.87	92	0.15	0.2	0.36	−0.097	83
Breast (DCIS-normal)	349	77.94	91	0.11	0.17	0.28	−0.078	79
Colon (Cancer-normal)	1889	746.93	100	0.16	0.28	0.53	−0.11	100
Colon (Adenoma-normal)	1917	576.63	79	0.13	0.22	0.38	−0.068	100
Lung (Cancer-normal)	702	217.72	87	0.14	0.23	0.38	−0.088	98
Pancreas (ACA-normal)	1114	183	53	0.087	0.14	0.2	−0.061	52
Pancreas (IPMN-normal)	1349	274.09	55	0.099	0.16	0.26	−0.09	99
Pancreas (NET-normal)	683	136.9	69	0.0955	0.16	0.25	−0.16	98
Thyroid (Cancer-normal)	351	63.25	82	0.091	0.15	0.235	−0.054	78
Thyroid (Adenoma-normal)	266	49.9	90	0.09275	0.15	0.24	−0.049	77

The `Blocks (n) column reports the total number of regions classified as blocks by our algorithm. `Total Mb inside blocks' is the total number of megabases contained by these blocks. The `Intersection with colon blocks (%) represents a comparison of the hypomethylated blocks for the comparison represented by the row, to the hypomethylated blocks identified between colon normal and cancer samples; note that 100% of colon blocks are inside colon blocks. We tested if overlaps this extreme can be due to chance and found P values <0.001 (0 occurrences in 1,000 permutations). The next three columns are the 25th, 50th, and 75th percentiles of block region sizes. The `Median diff value2019; is the median of the average difference between cases and controls are all regions defined as blocks. The `Hypo-meth. (%) column shows the percent of blocks that are hypomethylated.

ISSN: 1756-994X