TABLE 2.
The summary of identified integration sites by all three datasets (Nanopore/Illumina/Liu et al.) after reads number filtration.
| Breakpoint* | Reads number (N/I/Liu) | HPV16 gene | Chromosome | Func_refGene | Gene_refGene | GeneDetail_refGene (bp) | Map | Sanger Verified |
| HPV16:2804,chr20:32516985 | 406/1439/940 | E1/E2 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 74812; 63309 | 20q11.22 | |
| HPV16:3327,chr6:7328094 | 51/0/131 | E2 | Chr6 | Intronic | CAGE1 | . | 6p24.3 | |
| HPV16:2623,chr6:8814271 | 37/64/46 | E1 | Chr6 | Intergenic | LOC100506207, TFAP2A | 28593; 1582645 | 6p24.3 | |
| HPV16:5534,chrX:20464412 | 132/168/43 | L2 | ChrX | Intergenic | RPS6KA3, CNKSR2 | 179662; 928004 | Xp22.12 | |
| HPV16:4680,chr6:7326060 | 43/6/22 | L2 | Chr6 | Downstream | CAGE1 | . | 6p24.3 | |
| HPV16:3163,chrX:20462930 | 50/0/21 | E2 | ChrX | Intergenic | RPS6KA3, CNKSR2 | 178180; 929486 | Xp22.12 | |
| HPV16:7619,chr2:99404946 | 5/1/0 | LCR | Chr2 | Intergenic | LOC101927070, KIAA1211L | 16585; 5363 | 2q11.2 | S |
| HPV16:3873,chr2:197526852 | 5/4/0 | E5 | Chr2 | Intronic | CCDC150 | . | 2q33.1 | |
| HPV16:2891,chr6:12645768 | 13/25/12 | E2 | Chr6 | Intergenic | EDN1, PHACTR1 | 348341; 71120 | 6p24.1 | |
| HPV16:3182,chr20:32516399 | 23/0/8 | E2 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 74226; 63895 | 20q11.22 | |
| HPV16:850,chr20:32515476 | 13/2/8 | E7 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 73303; 64818 | 20q11.22 | |
| HPV16:4453,chr20:32472390 | 25/19/4 | L2 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 30217; 107904 | 20q11.22 | |
| HPV16:5744,chr11:103893587 | 37/62/2 | L1 | Chr11 | Intronic | PDGFD | . | 11q22.3 | |
| HPV16:7519,chr2:197519914 | 19/56/0 | LCR | Chr2 | Intronic | CCDC150 | . | 2q33.1 | S |
| HPV16:4489,chr11:31749949 | 17/32/0 | L2 | Chr11 | Intronic | ELP4 | . | 11p13 | S |
| HPV16:2110,chr2:99396966 | 17/25/0 | E1 | Chr2 | Intergenic | LOC101927070, KIAA1211L | 8605; 13343 | 2q11.2 | S |
| HPV16:322,chr20:32486709 | 7/21/0 | E6 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 44536; 93585 | 20q11.22 | S |
| HPV16:1276,chr18:50054 | 5/20/14 | E1 | Chr18 | Intergenic | LOC102723376, ROCK1P1 | 34124; 59011 | 18p11.32 | |
| HPV16:4394,chr12:17224129 | 3/15/2 | L2 | Chr12 | Intergenic | SKP1P2, LINC02378 | 80567; 510628 | 12p12.3 | |
| HPV16:4834,chrX:20461879 | 41/12/0 | L2 | ChrX | Intergenic | RPS6KA3, CNKSR2 | 177129; 930537 | Xp22.12 | S |
| HPV16:1037,chrX:20445300 | 2/11/0 | E1 | ChrX | Intergenic | RPS6KA3, CNKSR2 | 160550; 947116 | Xp22.12 | |
| HPV16:6618,chr20:32506419 | 3/9/12 | L1 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 64246; 73875 | 20q11.22 | |
| HPV16:2638,chr20:32502300 | 4/8/0 | E1 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 60127; 77994 | 20q11.22 | |
| HPV16:1155,chrX:20447276 | 27/8/0 | E1 | ChrX | Intergenic | RPS6KA3, CNKSR2 | 162526; 945140 | Xp22.12 | S |
| HPV16:214,chr6:7242229 | 6/7/0 | E6 | Chr6 | Intronic | RREB1 | . | 6p24.3 | |
| HPV16:4307,chr13:74240744 | 2/6/0 | L2 | Chr13 | Intergenic | LINC00392, KLF12 | 78728; 19405 | 13q22.1 | |
| HPV16:883,chr20:32487936 | 4/5/5 | E1 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 45763; 92358 | 20q11.22 | |
| HPV16:4250,chr2:197550764 | 2/4/0 | L2 | Chr2 | Intronic | CCDC150 | . | 2q33.1 | |
| HPV16:7362chr18:12717 | 8/3/0 | LCR | Chr18 | ncRNA_intronic | LOC102723376 | . | 18p11.32 | |
| HPV16:4405,chr2:99438640 | 1/3/2 | L2 | Chr2 | Exonic | KIAA1211L | . | 2q11.2 | |
| HPV16:462,chr20:30942164 | 8/2/0 | E6 | Chr20 | Intergenic | KIF3B, ASXL1 | 19353; 3983 | 20q11.21 | S |
| HPV16:6558,chr2:99431140 | 3/1/0 | L1 | Chr2 | Intronic | KIAA1211L | . | 2q11.2 | |
| HPV16:7139,chr20:32478733 | 169/0/0 | L1 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 36560; 101561 | 20q11.22 | S |
| HPV16:4276,chr20:32502143 | 51/0/0 | L2 | Chr20 | Intergenic | CHMP4B, RALY-AS1 | 59970; 78151 | 20q11.22 | S |
| HPV16:4029,chr11:103891933 | 21/0/0 | E5 | Chr11 | Intronic | PDGFD | . | 11q22.3 | S |
| HPV16:3312,chr6:17081322 | 8/0/0 | E2 | Chr6 | Intergenic | LOC101928433, STMND1 | 314208; 21167 | 6p22.3 | S |
| HPV16:3295,chr11:31761709 | 6/0/0 | E2 | Chr11 | Intronic | ELP4 | . | 11p13 | S |
| HPV16:5311,chr1:455824 | 6/0/0 | L2 | Chr1 | Intergenic | OR4F16, LOC101928626 | 87227; 106936 | 1p36.33 | |
| HPV16:4027,chr11:103891932 | 4/0/0 | E5 | Chr11 | Intronic | PDGFD | . | 11q22.3 | |
| HPV16:6681,chr10:80475 | 4/0/0 | L1 | Chr10 | Intergenic | NONE, TUBB8 | NONE; 12353 | 10p15.3 | |
| HPV16:1570,chrX:20385416 | 4/0/0 | E1 | ChrX | Intergenic | RPS6KA3, CNKSR2 | 100666; 1007000 | Xp22.12 | |
| HPV16:4508,chr1:143415731 | 3/0/0 | L2 | Chr1 | Intergenic | LOC102723769, MIR6077 | 213492; 257190 | 1q21.1 | |
| HPV16:6840,chr6:171021105 | 3/0/0 | L1 | Chr6 | Intergenic | PDCD2, NONE | 127325; NONE | 6q27 | |
| HPV16:6840,chr1:547221 | 3/0/0 | L1 | Chr1 | Intergenic | OR4F16, LOC101928626 | 178624; 15539 | 1p36.33 | |
| HPV16:6840,chr1:547739 | 3/0/0 | L1 | Chr1 | Intergenic | OR4F16, LOC101928626 | 179142; 15021 | 1p36.33 | |
| HPV16:6305,chr2:197525082 | 3/3/0 | L1 | Chr2 | Intronic | CCDC150 | . | 2q33.1 | |
| HPV16:4730,chr1:10270 | 3/0/0 | L2 | Chr1 | Intergenic | NONE, DDX11L1 | NONE; 1604 | 1p36.33 | |
| HPV16:6929,chr2:99443220 | 2/0/0 | L1 | Chr2 | Intronic | KIAA1211L | . | 2q11.2 | |
| HPV16:1469,chr3:189605104 | 2/0/0 | E1 | Chr3 | Intronic | TP63 | . | 3q28 | |
| HPV16:4730,chrX:155259784 | 2/0/0 | L2 | ChrX | Intergenic | DDX11L16, NONE | 1936; NONE | Xq28 | |
| HPV16:4732,chr2:114360505 | 2/0/0 | L2 | Chr2 | ncRNA_intronic | DDX11L2 | . | 2q13 | |
| HPV16:2621,chr20:3560423 | 2/0/0 | E1 | Chr20 | Intronic | ATRN | . | 20p13 | |
| HPV16:4732,chr18:10186 | 2/0/0 | L2 | Chr18 | Intergenic | NONE, LOC102723376 | NONE; 1889 | 18p11.32 | |
| HPV16:3324,chr6:7328088 | 2/0/0 | E2 | Chr6 | Intronic | CAGE1 | . | 6p24.3 | |
| HPV16:6840,chr1:547835 | 2/0/0 | L1 | Chr1 | Intergenic | OR4F16, LOC101928626 | 179238; 14925 | 1p36.33 | |
| HPV16:4793,chr12:80918599 | 2/0/0 | L2 | Chr12 | Intronic | PTPRQ | . | 12q21.31 | |
| HPV16:3340,chr15:40890192 | 2/0/0 | E2/E4 | Chr15 | Intronic | KNL1 | . | 15q15.1 | |
| HPV16:4732,chr1:10164 | 2/0/0 | L2 | Chr1 | Intergenic | NONE, DDX11L1 | NONE; 1710 | 1p36.33 | |
| HPV16:6899,chr2:72209094 | 2/0/0 | L1 | Chr2 | Intergenic | DYSF, CYP26B1 | 295201; 147273 | 2p13.2 | |
| HPV16:3340,chr20:35719229 | 0/35/0 | E2/E4 | Chr20 | Intronic | RBL1 | . | 20q11.23 | |
| HPV16:3340,chr12:81091809 | 0/96/0 | E2/E4 | Chr12 | Intergenic | PTPRQ, MYF6 | 17841; 9599 | 12q21.31 | |
| HPV16:1355,chr2:99429402 | 0/6/0 | E1 | Chr2 | Intronic | KIAA1211L | . | 2q11.2 | |
| HPV16:4782,chr2:99435835 | 0/6/0 | L2 | Chr2 | Intronic | KIAA1211L | . | 2q11.2 | |
| HPV16:1030,chr9:123681030 | 0/4/0 | E1 | Chr9 | Intronic | TRAF1 | . | 9q33.2 | |
| HPV16:3378,chr17:69506855 | 0/4/0 | E2/E4 | Chr17 | Intergenic | CASC17, LINC02095 | 308535; 511137 | 17q24.3 | |
| HPV16:1515,chr21:39554078 | 0/3/0 | E1 | Chr21 | Intergenic | DSCR8, DSCR10 | 25473; 24172 | 21q22.13 | |
| HPV16:1916,chr16:79637361 | 0/3/0 | E1 | Chr16 | Intergenic | MAF, MAFTRR | 2739; 117848 | 16q23.2 | |
| HPV16:2117,chr1:240419064 | 0/3/0 | E1 | Chr1 | Intronic | FMN2 | . | 1q43 | |
| HPV16:3050,chr17:65126150 | 0/3/0 | E2 | Chr17 | Intronic | HELZ | . | 17q24.2 | |
| HPV16:3337,chr14:46921971 | 0/3/0 | E2/E4 | Chr14 | ncRNA_intronic | LINC00871 | . | 14q21.2 | |
| HPV16:4399,chr2:127164444 | 0/3/0 | L2 | Chr2 | Intergenic | LINC01941, GYPC | 288882; 249067 | 2q14.3 | |
| HPV16:4409,chr3:45985168 | 0/3/0 | L2 | Chr3 | Intronic | CXCR6, FYCO1 | . | 3p21.31 | |
| HPV:16:5685,chr3:56156825 | 0/3/0 | L1 | Chr3 | Intronic | ERC2 | . | 3p14.3 | |
| HPV16:7086,chr2:99457820 | 0/3/0 | L1 | Chr2 | Intronic | KIAA1211L | . | 2q11.2 | |
| HPV16:2724,chr20:30948621 | 0/0/8 | E1 | Chr20 | Intronic | ASXL1 | 20q11.21 | ||
| HPV16:3883,chr3:156990726 | 0/0/4 | E5 | Chr3 | Intronic | VEPH1 | 3q25.31 | ||
| HPV16:3344,chr6:7327990 | 0/89/43 | E2 | Chr6 | Intronic | CAGE1 | . | 6p24.3 | |
| HPV16:1381,chr11:31187618 | 0/3/0 | E1 | Chr11 | Intronic | DCDC1 | . | 11p13 | |
| HPV16:1891,chr20:60384079 | 0/3/0 | E1 | Chr20 | Intronic | CDH4 | . | 20q13.33 | |
| HPV16:2075,chr12:39215471 | 0/3/0 | E1 | Chr12 | Intronic | CPNE8 | . | 12q12 | |
| HPV16:2237,chr4:28262779 | 0/3/0 | E1 | Chr4 | Intergenic | LINC02261,MIR4275 | 978932;558425 | 4p15.1 | |
| HPV16:2716,chr13:74250432 | 1/3/0 | E1 | Chr13 | Intergenic | LINC00392,KLF12 | 88416;9717 | 13q22.1 | |
| HPV16:3340,chr12:81091909 | 0/58/0 | E2/E4 | Chr12 | Intergenic | PTPRQ,MYF6 | 17941;9499 | 12q21.31 | |
| HPV16:2724,chr20:30948899 | 0/11/0 | E1 | Chr20 | Intronic | ASXL1 | . | 20q11.21 | |
| HPV16:3340,chr1:212166417 | 0/27/0 | E2/E4 | Chr1 | Intronic | INTS7 | . | 1q32.3 |
*Breakpoint: each breakpoint was named by combined breakpoint site of HPV genome, chromosome and chromosome location of human breakpoint; Reads Number: N (Nanopore), I (Illumina), Liu (Liu et al.), Nanopore reads number cut-off value is 2, and Illumina reads number cut-off value is 3. There is no cut-off value for integration sites which overlapped by different sequencing platforms. Lane of GeneDetail_refGene listed the distance of integration sites with the nearby genes. S:Sanger Verified.