Table 1. HPV-cellular DNA junctions confirmed by PCR amplification and Sanger sequencing.
| Sample name | #reads | HPV | Cellular sequence | ||
|---|---|---|---|---|---|
| subtype | breakpoint (ORF)a) | breakpointb) | map | ||
| T4 | 4 | HPV16 | 2046 (E1) | 54417043 | 19q13.42 |
| T4 | 5 | HPV16 | 5190 (L2) | 54417038 | 19q13.42 |
| T8 | 2 | HPV16 | 704 (E7) | 59171259 | 17q23.2 |
| T15 | 9 | HPV16 | 3781 (E2) | 73996849 | 13q22.1 |
| T16 | 70 | HPV16 | 2849 (E2) | 17799430 | 7p21.1 |
| T17 | 19 | HPV16 | 2600 (E1) | 53765119 | 19q13.42 |
| T17 | 4 | HPV16 | 3575 (E2/E4) | 240309623 | 2q37.3 |
| T17 | 1 | HPV16 | 4448 (L2) | 240281037 | 2q37.3 |
| T18 | 78 | HPV16 | 1063 (E1) | 74594785 | 4q13.3 |
| T20 | 831 | HPV16 | 2689 (E1) | 123715736 | 10q26.13 |
| T20 | 400 | HPV16 | 2863 (E2) | 1019766 | 10p15.3 |
| T23 | 8 | HPV16 | 850 (E7) | 32515477 | 20q11.22 |
| T23 | 5 | HPV16 | 884 (E1) | 32487936 | 20q11.22 |
| T23 | 14 | HPV16 | 1277 (E1) | 50054 | 18p11.32 |
| T23 | 46 | HPV16 | 2623 (E1) | 8814272 | 6p24.3 |
| T23 | 8 | HPV16 | 2724 (E1) | 30948621 | 20q11.21 |
| T23 | 940 | HPV16 | 2804 (E1/E2) | 32516985 | 20q11.22 |
| T23 | 12 | HPV16 | 2891 (E2) | 12645768 | 6p24.1 |
| T23 | 21 | HPV16 | 3163 (E2) | 20462931 | xp22.12 |
| T23 | 8 | HPV16 | 3182 (E2) | 32516400 | 20q11.22 |
| T23 | 131 | HPV16 | 3328 (E2) | 7328094 | 6p24.3 |
| T23 | 43 | HPV16 | 3344 (E2/E4) | 7327990 | 6p24.3 |
| T23 | 4 | HPV16 | 3883 (E5) | 156990726 | 3q25.31 |
| T23 | 2 | HPV16 | 4393 (L2) | 17224129 | 12p12.3 |
| T23 | 2 | HPV16 | 4405 (L2) | 99438640 | 2q11.2 |
| T23 | 4 | HPV16 | 4453 (L2) | 32472391 | 20q11.22 |
| T23 | 22 | HPV16 | 4681 (L2) | 7326060 | 6p24.3 |
| T23 | 43 | HPV16 | 5535 (L2) | 20464412 | xp22.12 |
| T23 | 2 | HPV16 | 5745 (L1) | 103893590 | 11q22.3 |
| T23 | 12 | HPV16 | 6618 (L1) | 32506420 | 20q11.22 |
| T25 | 5 | HPV16 | 1161 (E1) | 31689429 | 10p11.22 |
| T32 | 23 | HPV16 | 3611 (E2/E4) | 873456 | 9p24.3 |
| T33 | 8 | HPV16 | 958 (E1) | 107223556 | 7q22.3 |
| T33 | 4 | HPV16 | 1558 (E1) | 99425642 | 15q26.3 |
| T33 | 2 | HPV16 | 2744 (E1) | 67500034 | 13q21.32 |
| T33 | 8 | HPV16 | 4911 (L2) | 10702626 | 21p11.2 |
| T34 | 5 | HPV16 | 7 (LCR) | 9283840 | 11p15.4 |
| T34 | 2 | HPV16 | 38 (LCR) | 126566946 | Xq25 |
| T34 | 2 | HPV16 | 1043 (E1) | 9292546 | 11p15.4 |
| T34 | 2 | HPV16 | 1079 (E1) | 128770421 | 8q24.21 |
| T34 | 35 | HPV16 | 1099 (E1) | 128840275 | 8q24.21 |
| T34 | 2 | HPV16 | 1844 (E1) | 25871313 | 5p14.1 |
| T34 | 9 | HPV16 | 2104 (E1) | 128717682 | 8q24.21 |
| T34 | 6 | HPV16 | 2672 (E1) | 64430179 | 4q13.1 |
| T34 | 5 | HPV16 | 2810 (E1/E2) | 128578637 | 8q24.21 |
| T34 | 4 | HPV16 | 3355 (E2/E4) | 126566939 | xq25 |
| T34 | 11 | HPV16 | 3644 (E2) | 128596370 | 8q24.21 |
| T34 | 5 | HPV16 | 3742 (E2) | 9697576 | 11p15.4 |
| T34 | 2 | HPV16 | 5599 (L2/L1) | 25871329 | 5p14.1 |
| T34 | 3 | HPV16 | 5629 (L2/L1) | 128827759 | 8q24.21 |
| T34 | 2 | HPV16 | 5761 (L1) | 9331203 | 11p15.4 |
| T34 | 1 | HPV16 | 7877 (LCR) | 128579990 | 8q24.21 |
| T35 | 4 | HPV16 | 379 (E6) | 129056613 | 8q24.21 |
| T35 | 6 | HPV16 | 738 (E7) | 129040142 | 8q24.21 |
| T35 | 2 | HPV16 | 1362 (E1) | 1806549 | 4p16.3 |
| T35 | 3 | HPV16 | 2941 (E2) | 23578398 | 6p22.3 |
| T35 | 29 | HPV16 | 4963 (L2) | 59909510 | 2p16.1 |
| T35 | 107 | HPV16 | 5609 (L2/L1) | 154556784 | 7q36.2 |
| T35 | 3241 | HPV16 | 5619 (L2/L1) | 129019228 | 8q24.21 |
| T35 | 4 | HPV16 | 7567 (LCR) | 31618653 | 1p35.2 |
| T36 | 4 | HPV16 | 164 (E6) | 22388589 | 11p14.3 |
| T36 | 4 | HPV16 | 2919 (E2) | 85639302 | 2p11.2 |
| T36 | 2 | HPV16 | 3717 (E2) | 85639289 | 2p11.2 |
| T38 | 122 | HPV16 | 384 (E6) | 14288872 | 9p22.3 |
| T38 | 668 | HPV16 | 551 (E6) | 14275445 | 9p22.3 |
| T38 | 1 | HPV16 | 858 (E7) | 15070638 | 20p12.1 |
| T38 | 3 | HPV16 | 1690 (E1) | 14330266 | 9p22.3 |
| T38 | 1 | HPV16 | 1975 (E1) | 14869191 | 20p12.1 |
| T38 | 2 | HPV16 | 1987 (E1) | 14872325 | 20p12.1 |
| T38 | 5 | HPV16 | 2508 (E1) | 15079958 | 20p12.1 |
| T38 | 9 | HPV16 | 3647 (E2) | 14246496 | 9p22.3 |
| T38 | 3 | HPV16 | 4652 (L2) | 14388662 | 9p22.3 |
| T38 | 1 | HPV16 | 7480 (LCR) | 15074857 | 20p12.1 |
| T38 | 1394 | HPV16 | 7708 (LCR) | 14875592 | 20p12.1 |
| T38 | 5 | HPV16 | 7856 (LCR) | 14236572 | 9p22.3 |
| T39 | 19 | HPV16 | 1661 (E1) | 189584107 | 3q28 |
| T39 | 22 | HPV16 | 5300 (L2) | 189584098 | 3q28 |
| T42 | 1 | HPV16 | 697 (E7) | 163224769 | 1q23.3 |
| T42 | 2 | HPV16 | 1356 (E1) | 96471972 | Xq21.33 |
| T42 | 4 | HPV16 | 1728 (E1) | 93013206 | 6q15 |
| T42 | 6 | HPV16 | 1942 (E1) | 150420961 | xq28 |
| T42 | 151 | HPV16 | 2059 (E1) | 94561088 | 6q16.1 |
| T42 | 2 | HPV16 | 2189 (E1) | 147585823 | 7q35 |
| T42 | 4 | HPV16 | 2370 (E1) | 117973872 | 7q31.31 |
| T42 | 2 | HPV16 | 2816 (E2) | 103005957 | 1p21.1 |
| T42 | 499 | HPV16 | 2991 (E2) | 188223631 | 2q32.1 |
| T42 | 4 | HPV16 | 3331 (E2) | 31137921 | 5p13.3 |
| T42 | 2 | HPV16 | 3402 (E2/E4) | 42298926 | 2p21 |
| T42 | 7 | HPV16 | 4279 (L2) | 117974122 | 7q31.31 |
| T42 | 12 | HPV16 | 4879 (L2) | 231434760 | 2q37.1 |
| T42 | 13 | HPV16 | 5045 (L2) | 86378287 | 14q31.3 |
| T43 | 4 | HPV16 | 777 (E7) | 164142942 | 2q24.3 |
| T43 | 36 | HPV16 | 975 (E1) | 73868139 | 13q22.1 |
| T43 | 2 | HPV16 | 3721 (E2) | 45180348 | 2p21 |
| T43 | 30 | HPV16 | 4411 (L2) | 73869942 | 13q22.1 |
| T47 | 2 | HPV16 | 340 (E6) | 10902225 | 19p13.2 |
| T47 | 4 | HPV16 | 3501 (E2/E4) | 62731602 | 17q24.1 |
| T47 | 2 | HPV16 | 3800 (E2) | 31923670 | 6p21.33 |
| T47 | 158 | HPV16 | 3817 (E2) | 57846210 | 6p11.2 |
| SiHa | 201 | HPV16 | 3132 (E2) | 74087562 | 13q22.1 |
| SiHa | 86 | HPV16 | 3384 (E2/E4) | 73788866 | 13q22.1 |
| T9 | 294 | HPV18 | 3782 (E2) | 57925564 | 17q23.1 |
| T31 | 6 | HPV18 | 2918 (E2) | 2539287 | 16p13.3 |
| T44 | 45 | HPV18 | 2233 (E1) | 49741244 | 8q11.21 |
| HeLa | 496 | HPV18 | 2497 (E1) | 128241548 | 8q24.21 |
| HeLa | 702 | HPV18 | 3100 (E2) | 128233367 | 8q24.21 |
| HeLa | 5447 | HPV18 | 5736 (L1) | 128230632 | 8q24.21 |
| HeLa | 211 | HPV18 | 7857 (LCR) | 128234255 | 8q24.21 |
| T11 | 29 | HPV58 | 135 (E6) | 45758413 | 18q21.1 |
| T11 | 129 | HPV58 | 661 (E7) | 66426391 | 11q13.2 |
| T11 | 4 | HPV58 | 1244 (E1) | 53599605 | 20q13.2 |
| T11 | 14 | HPV58 | 2164 (E1) | 64506111 | 4q13.1 |
| T11 | 2 | HPV58 | 2195 (E1) | 53582110 | 20q13.2 |
| T11 | 59 | HPV58 | 3791 (E2) | 47684812 | 15q21.1 |
| T11 | 1259 | HPV58 | 5989 (L1) | 53590867 | 20q13.2 |
| T11 | 461 | HPV58 | 6833 (L1) | 53615729 | 20q13.2 |
| T11 | 127 | HPV58 | 7341 (LCR) | 64506104 | 4q13.1 |
a)
nucleotide position of viral-cellular breakpoints on the HPV genome (Alignment to NC_001526.2 for HPV16, NC_001357.1 for HPV18, and D90400.1 for HPV58);
b)
Cellular nucleotide position of viral-cellular breakpoints on the human genome (Alignment to Hg19 human reference genome)
Abbreviations: T, Tumor; ORF, Open Reading Frame