. 2015 Dec 9;37(2):188–196. doi: 10.1093/carcin/bgv171

Table 2.

Genomic characterization of HPV DNA integration locations

ID	Pathology	Cytoband	Nucleotide position^a	Assay to determine integration locus	Genes^b	Fragile sites^c	% CpG islands^b	Repeat element class (number of events)^b	Number of recombination hotspots^b	Number of peaks of open chromatin^d
ID	Pathology	Cytoband	Nucleotide position^a	Assay to determine integration locus	Genes^b	Fragile sites^c	% CpG islands^b	Repeat element class (number of events)^b	Number of recombination hotspots^b	FAIRE	DNaseI
Subject 1	CIN3	1p36.22	9 819 841	Sequencing	CLSTN1, CTNNBIP1	FRA1A	19.2	LINE (18), SINE (73), LTR (5), other (15)	0	5	3
Subject 1	CIN3	3p11.2	88 525 362	Sequencing	—	—	0	LINE (19), SINE (14), LTR (15), other (26)	0	0	0
Subject 1	CIN3	9q33.3	126 313 825	Sequencing	NR5A1, NR6A1	—	17.2	LINE (26), SINE (31), LTR (9), other (17)	0	2	2
Subject 1	CIN3	10q24.2	99 428 623	Sequencing	PI4K2A, AVPI1	—	19.6	LINE (30), SINE (35), LTR (42), other (28)	0	7	15
Subject 5	CIN3	15q24.2	74 295 689	APOT	ETFA	—	20.1	LINE (16), SINE (61), LTR (11), other (5)	0	4	8
Subject 6	CIN3	1q32.2	207 609 939	Sequencing	—	—	0	LINE (21), SINE (34), LTR (12), other (22)	0	3	5
Subject 8	CIN3	3q28	191 025 132	Sequencing	TP63, MIR944	—	0	LINE (26), SINE (25), LTR (7), other (25)	0	1	7
Subject 9	CIN3	15q24.2	74 297 043	Sequencing	ETFA		0	LINE (16), SINE (60), LTR (13), other (6)	0	4	8
Subject 12	CIN3	4q21.23	85 671 277	Sequencing	-	—	0	LINE (22), SINE (33), LTR (13), other (15)	1	1	2
Subject 15	CIN3	22q11.23	22 060 494	APOT	CES5AP1, ZDHHC8P1	—	17.3	LINE (10), SINE (31), LTR (9), other (33)	0	1	2
Subject 16	CIN3	20q13.13	48 435 994	APOT	-	—	0	LINE (44), SINE (84), LTR (7), other (24)	0	4	12
Subject 18	Cancer	7q11.23	74 757 074	Sequencing	PMS2P5, SPDYE8P	FRA7J	0	LINE (40), SINE (65), LTR (8), other (27)	0	0	0
Subject 18	Cancer	15q23	70 231 187	Sequencing	MY09A, SENP8, GRAMD2	—	0	LINE (31), SINE (54), LTR (9), other (8)	0	3	2
Subject 20	Cancer	3p26.2	4 804 305	Sequencing	ITPR1	—	0	LINE (22), SINE (14), LTR (25), other (8)	0	3	1
Subject 21	Cancer	13q22.1	72 885 297	APOT	-	—	0	LINE (40), SINE (36), LTR (5), other (8)	0	3	10
Subject 23	Cancer	14q32.2	98 775 862	Sequencing	BCL11B	—	16.7	LINE (32), SINE (17), LTR (5), other (11)	0	0	0
Subject 24	Cancer	8q22.1	96 153 569	Sequencing	NDUFAF6, MIR3150A, MIR3150B	FRA8B	20.5	LINE (26), SINE (24), LTR (33), other (23)	0	10	8
Subject 25	Cancer	15q25.3	83 735 261	Sequencing	AKAP13	—	23.2	LINE (40), SINE (57), LTR (6), other (13)	0	6	13
Subject 26	Cancer	21q22.3	42 078 171	Sequencing	RIPK4, PRDM15	—	16.6	LINE (19), SINE (35), LTR (11), other (16)	0	7	8
Subject 27	Cancer	6p25.2	2 847 972	Sequencing	SERPINB9	—	18.9	LINE (9), SINE (18), LTR (3), other (45)	0	3	4
Subject 29	Cancer	8q24.21	128 844 999	Sequencing	MYC	—	13.6	LINE (50), SINE (39), LTR (24), other (35)	0	6	14
Subject 30	Cancer	9p24.2	3 364 982	Sequencing	RFX3	—	0	LINE (30), SINE (30), LTR (27), other (24)	0	0	1
Subject 31	Cancer	10p14	8 648 393	Sequencing	—	—	0	LINE (24), SINE (47), LTR (2), other (23)	1	0	0
Subject 33	Cancer	1p34.2	43 770 932	Sequencing	PTPRF	-	17.7	LINE (35), SINE (33), LTR (10), other (15)	0	2	7
Subject 35	Cancer	9q34.3	138 625 713	APOT	—	—	12.6	LINE (19), SINE (34), LTR (3), other (10)	0	7	7
Subject 37	Cancer	19q13.2	45 789 652	Sequencing	SPTBN4, SHKBP1, LTBP4	FRA19A	18.1	LINE (26), SINE (46), LTR (13), other (11)	0	16	21
Subject 38	Cancer	11q13.1	66 165 789	Sequencing	RBM14, RBM4, RBM4B	FRA11H	18.4	LINE (38), SINE (36), LTR (11), other (14)	0	2	6

^aNucleotide position within corresponding chromosome based on reference genome NCBI Build 36/hg18.

^bWithin a window of 50Kb around the integration site. Information from the ENCODE database.

^cWithin a window of 50Kb around the integration site.

^dWithin a window of 50Kb around the integration site. Information from the ENCODE database. Based on the HeLa cell line. For different open chromatin assays see Ref. (35).