Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006409
Fusion event
HBV-SNCAIP integration
Validated
Yes
Detection method
invPCR +Sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1813
Integrated sequence
GACCCCGAGAAGGGTCGTCCGCAGGATTCAGCGCCGACGGGACGTAAACAAAGGACGTCCCGCGCAGGATCCAGTTGGCAGCACAGCCTAGCAGCCATGG| |AAACGATGTATATTTGCGGGATAGGACAACAGAGTTATCAGTCCCGATAATGTTTGCTCCAGACCTGCTGCGAGCAAAACAAGCGGCTAGGAGTTCCGCA
Host Sequence
Chromosome
chr5
Cytoband
q23.2
Reference genome
Start
End
122419019 (Hg38)
Location type
Intron
Target gene
Nearest miRNA
hsa-mir-10397/Upstream/3264303; hsa-mir-103a-1/Downstream/6678669;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/106567, chr5-CpG: 54/Downstream/355825
Upstream sequence
AGAGACTGTGGGAGAGGATGCCAGTGTGGTCCAGCCAGTTTAGTGATGATGAAGAGGGCCCAGATTTCAGAGGGATTGAGGATAAGGACACAGCAGGACT
Downstream sequence
TGGTGCCTGAGCGATGAAGGGCAGGGGTCAAGGAAGGAGAAGGGTCAAGGAAAGAGAATAGTCAAGGATGCCTTGGAGATAGATTGCTTAGGAGACTGCA
Reference
Mason, W. S., et al. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology,2016, 151(5): 986-998 e984.