Table 2.
ID | Pathology | Cytoband | Nucleotide positiona | Assay to determine integration locus | Genesb | Fragile sitesc | % CpG islandsb | Repeat element class (number of events)b | Number of recombination hotspotsb | Number of peaks of open chromatind | |
---|---|---|---|---|---|---|---|---|---|---|---|
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).