Fig. 2.

Methylation. a Frequency of probes on the HM27 methylation array that have high (value > 0.75), intermediate (0.25-0.75) and low (<0.25) methylation associated with LOH in a sample, comparing all autosomes (no difference between LOH and no LOH) and chromosome X (more low methylation probes in LOH regions). b Considering only probes that were significantly different between LOH and no LOH, the frequency of significant probes where the mean methylation ratio (LOH/no LOH) was increased (>1.5, higher in LOH) or decreased (<0.75, higher in no LOH). c Percentage of significant methylation probes that are located in regions where the majority (>2/3) of LOH is either copy number loss, neutral or neither. Only regions with at least 20 % LOH were included