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Table 4 Validation of the integration sites in HPV data

From: HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

Sample ID and coverage Affected genes Function of integration site Integration breakpoints in the human genome Integration breakpoints in HBV virus Score Identified by HGT-ID?
145 T (37×) CCNE1 intron chr19: 30303492 1053 87.2 yes
CCNE1 intron chr19: 30303498 1819 87.2 yes
177 T (43×) SENP5 intron chr3: 196625752* 1827* no
180 N (121×) FN1 intron chr2: 216280279 1822 11.9 yes
186 T (36×) KMT2B exon chr19: 36214005 2448 206.2 yes
KMT2B exon chr19: 36214017 1605 206.2 yes
198 T (34×) TERT intron chr5: 1269387 821 137.5 yes
TERT intron chr5: 1269405 1950 137.5 yes
26 T (66×) DUX4 intron chr18: 107920* 670* no
200 T (32×) CCNE1 exon chr19: 30315003 1798 51.4 yes
CCNE1 downstream chr19: 30315365 316 222.751 yes
268 T (34×) CCNE1 upstream chr19: 30298787 1931 155.2 yes
TERT intron chr5: 1291758 3175 134.3 yes
TERT intron chr5: 1292403 354 134.3 yes
43 T (33×) SENP5 intron chr3: 196625710* 1910* no
46 T (32×) TERT upstream chr5: 1295367 751 34.4 yes
70 T (114×) KMT2B exon chr19: 36212331 1931 1015.6 yes
KMT2B exon chr19: 36212311 227 1015.6 yes
71 T (32×) SENP5 intron chr3: 196625776* 417* no
KMT2B intron chr19: 36213141 1884 10 yes
KMT2B intron chr19: 36213136 619 10 yes
95 T (35×) KMT2B exon chr19: 36212564 2240 27.3 yes
  1. Eighteen of 22 previously experimentally validated viral integration sites identified in sequencing data from 13 HBV-positive hepatocellular carcinoma samples using the HGT-ID algorithm. Integration breakpoints of the four missing events (noted with *) were obtained from the original publication [10]