TABLE 1.
HBV-human junctions in PLC/PRF/5 and Hep3B cells determined by RAISING-sequencing and hybrid capture-sequencing
| Sample | Detection method | No. total reads | HBV junction position | HBV genome | Human chromosome | Human junction position | Human gene | % of total chimeric reads | (Figure 2B) | |
|---|---|---|---|---|---|---|---|---|---|---|
| PLC/PRF/5 cells | RAISING-sequencing | 3804 | 1391 | P, X | Chr5 | 1297478 | (intergenic) | 0.92 | * | → #1 |
| 3577 | 491 | P, S | Chr17 | 82105786 | CCDC57 | 0.87 | ** | → #2 | ||
| 1602 | 1408 | P, X | Chr3 | 131451702 | (intergenic) | 0.39 | *** | → #3 | ||
| 1465 | 817 | P, S | Chr12 | 109573899 | MVK | 0.36 | **** | → #4 | ||
| 935 | 62 | P, S | Chr4 | 180586417 | (intergenic) | |||||
| 475 | 2138 | C | Chr13 | 33088561 | (intergenic) | 0.12 | ***** | |||
| 58 | 257 | P, S | Chr16 | 70170602 | AC009060.1 | |||||
| 31 | 257 | P, S | Chr16 | 69947689 | (intergenic) | |||||
| 9 | 919 | P | Chr5 | 8736559 | (intergenic) | |||||
| 9 | 1719 | X | Chr19 | 16239292 | AP1M1 | |||||
| 7 | 449 | P, S | Chr5 | 78401537 | SCAMP1 | |||||
| 6 | 271 | P, S | Chr11 | 13870025 | AC027779.1 | |||||
| 6 | 926 | P | Chr18 | 3719830 | DLGAP1 | |||||
| 6 | 937 | P | Chr16 | 69957337 | CLEC18A | |||||
| Hybrid capture-sequencing | 57,356 | 491 | P, S | Chr17 | 82105786 | CCDC57 | 0.08 | ** | ||
| 35,788 | 637 | P, S | Chr4 | 180587608 | (intergenic) | |||||
| 24,825 | 2138 | C | Chr13 | 33088561 | (intergenic) | 0.04 | ***** | |||
| 23,527 | 817 | P, S | Chr12 | 109573899 | MVK | 0.03 | **** | |||
| 20,135 | 1408 | P, X | Chr3 | 131451702 | (intergenic) | 0.03 | *** | |||
| 18,677 | 1391 | P, X | Chr5 | 1297478 | (intergenic) | 0.03 | * | |||
| 12,291 | 3081 | P, S | Chr1 | 143222538 | (intergenic) | |||||
| 3128 | 3081 | P, S | Chr1 | 143240684 | (intergenic) | |||||
| 1614 | 3081 | P, S | Chr10 | 41845764 | (intergenic) | |||||
| 513 | 3081 | P, S | Chr1 | 143265918 | (intergenic) | (Figure 2C) | ||||
| Hep3B cells | RAISING-sequencing | 6248 | 2061 | C | Chr13 | 91169307 | (intergenic) | 0.74 | † | → #1 |
| 1431 | 1796 | X | Chr3 | 75917792 | ROBO2 | 0.17 | †† | → #2 | ||
| 344 | 1796 | X | Chr4 | 72824684 | (intergenic) | 0.04 | ††† | |||
| 58 | 1796 | X | Chr11 | 37205841 | (intergenic) | 0.01 | †††† | |||
| 42 | 2061 | C | Chr13 | 91169319 | (intergenic) | |||||
| 8 | 1796 | X | Chr4 | 124126569 | (intergenic) | |||||
| 8 | 861 | P | Chr9 | 26959590 | IFT74 | |||||
| 7 | 1796 | X | Chr5 | 145896541 | GRXCR2 | |||||
| 5 | 1796 | X | Chr10 | 129015069 | (intergenic) | |||||
| 5 | 1796 | X | Chr14 | 42166780 | (intergenic) | |||||
| 5 | 1796 | X | Chr3 | 98232650 | (intergenic) | |||||
| Hybrid capture-sequencing | 72,240 | 1796 | X | Chr3 | 75917792 | ROBO2 | 0.09 | †† | ||
| 64,122 | 2061 | C | Chr13 | 91169307 | (intergenic) | 0.08 | † | |||
| 40,875 | 1796 | X | Chr4 | 72824684 | (intergenic) | 0.05 | ††† | |||
| 16,083 | 1796 | X | Chr11 | 37205841 | (intergenic) | 0.02 | †††† | |||
| 13496 | 1829 | C, X | Chr21 | 7261295 | (intergenic) | |||||
| 4200 | 1829 | C, X | Chr4 | 49118564 | (intergenic) | |||||
| 2641 | 1829 | C, X | ChrY | 56696309 | (intergenic) |
Note: The junctions commonly detected in RAISING-sequencing and hybrid capture-sequencing are indicated by asterisks (*) or daggers (†), and their detection rates of integration events are calculated.
Abbreviation: RAISING, Rapid Amplification of Integration Site without Interference by Genomic DNA contamination.