Re-analysis of hepatitis B virus integration sites reveals potential new loci associated with oncogenesis in hepatocellular carcinoma

doi:10.5501/wjv.v12.i3.209

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World Journal of Virology

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Virol. Jun 25, 2023; 12(3): 209-220
Published online Jun 25, 2023. doi: 10.5501/wjv.v12.i3.209

Table 1 Comparison of hepatitis B virus integration breakpoints among reference genomes

	GRCh38	T2T-CHM13	Original
Tumor
Number of breakpoints	2439	2487	3486
Number of samples	357	355	328
Non-tumor
Number of breakpoints	2759	2874	739
Number of samples	288	288	160

Table 2 Comparison of frequent integration breakpoints in the samples

Gene	GRCh38		Original
Gene	Breakpoints (n)	Samples (n)	Breakpoints (n)	Samples (n)
Tumor
TERT	150	105	160	95
KMT2B	56	33	55	30
DDX11L1	0	0	36	23
CCNA2	12	7	14	8
CCNE1	13	9	14	7
Non-tumor
FN1	97	56	19	17
TERT	12	10	8	3
IQGAP2	7	5	1	1
KMT2B	7	4	5	3

Table 3 Hepatitis B virus integration breakpoints in mitochondrial DNA

Sample	Tumor/Non-tumor	Chromosome	Position	HBV	Quality score
SRR3104746	NT	chrM	5367	1247	6933.33
SRR3105143	NT	chrM	5682	1513	11817.58
SRR3105012	T	chrM	8220	112	2080.04
SRR3104491	NT	chrM	8524	2482	33322.16
SRR3105095	NT	chrM	8694	471	4209.06
SRR3105101	NT	chrM	11079	1559	2937.33
SRR3105143	NT	chrM	11079	1559	14876.83
SRR3105001	NT	chrM	11104	1590	45538.21
SRR3105149	NT	chrM	11104	1590	16156.63
SRR3105251	NT	chrM	11104	1590	2276.31
SRR3105293	NT	chrM	11104	1590	24562.69
SRR3104643	T	chrM	11104	1590	13683.16
SRR3105172	T	chrM	11126	1621	2610.44
SRR3105251	NT	chrM	11130	1625	6793.43
SRR3104939	NT	chrM	11139	1729	30830.54
SRR3105149	NT	chrM	12453	323	2345.03
SRR3104636	NT	chrM	12735	1381	26840.64
SRR3105083	NT	chrM	13273	1755	4230.85
SRR3104696	NT	chrM	13433	363	2963.36
SRR3104643	T	chrM	13964	2809	2222.86
SRR3104823	NT	chrM	14052	1017	1788.18
SRR3105049	NT	chrM	14892	1768	21102.87
SRR3104982	T	chrM	15679	1768	32371.78
SRR3105185	NT	chrM	16319	1788	2013.53

HBV: Hepatitis B virus.

Citation: Kojima R, Nakamoto S, Kogure T, Ma Y, Ogawa K, Iwanaga T, Qiang N, Ao J, Nakagawa R, Muroyama R, Nakamura M, Chiba T, Kato J, Kato N. Re-analysis of hepatitis B virus integration sites reveals potential new loci associated with oncogenesis in hepatocellular carcinoma. World J Virol 2023; 12(3): 209-220
URL: https://www.wjgnet.com/2220-3249/full/v12/i3/209.htm
DOI: https://dx.doi.org/10.5501/wjv.v12.i3.209