Table 2.

Overlap of integration breakpoints with keratinocyte-specific enhancers.

Dataset	Integration subgroups	Breakpoints or loci per subgroup (n)	Overlap with enhancers (n)	%	p-Value
CESC	All breakpoints	1,299	495	38.1	0.0001
	Single breakpoints	28	67	26.0	0.0001
	Clustered breakpoints	1041	428	41.1	0.0001
	Condensed clustered breakpoints	326	162	49.7	0.0001
	Combined single and condensed breakpoints	584	229	39.2	0.0001
HNSCCa	All breakpoints	118	43	36.4	0.0001
	Single breakpoints	27	9	33.3	0.0052
	Clustered breakpoints	91	34	37.4	0.0001
	Condensed clustered breakpoints	30	13	43.3	0.0011
	Combined single and condensed breakpoints	57	22	38.6	0.0003

CESC and HNSCC integration breakpoints (±50 Kb flank regions) were grouped by the number of breakpoints per integration locus; single indicates one breakpoint and clustered indicates two or more breakpoints. Integration breakpoints from each subgroup were intersected with cellular enhancers and the frequency of overlap calculated. For the “All breakpoints,” “Single breakpoints (not clustered),” and “Clustered breakpoints” subgroups, each breakpoint was tested independently for its overlap with enhancer regions, regardless of whether it was part of a cluster or not. For the “Condensed clustered breakpoints” subgroup, the region spanning the most 5′- and 3′-breakpoints of an integration locus was used to test for the overlap with enhancer regions. For the “Combined single and condensed breakpoints” subgroup, the “Single breakpoints (not clustered)” and “Condensed clustered breakpoints” subgroups were combined for overlap analysis. The data were permutated 10,000 times to create an expected distribution of overlap. Bold font indicates significant p-values.

^aA single integration breakpoint on chromosome Y was excluded from this analysis.