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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]