Basic Information
VIS ID
TVIS20003889
Fusion event
HPV-chr9:q34.11 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E6
Start
7155
Host Sequence
Chromosome
chr9
Cytoband
q34.11
Reference genome
GRCh37/hg19
Start
131855855/129093576 (Hg38)
End
131855855/129093576 (Hg38)
Location type
Intergenic
Nearest miRNA
hsa-let-7a-1/Upstream/700862; hsa-mir-12126/Downstream/776029;
Nearest TSS
ENST00000422679/Upstream/8977; ENST00000434250/Downstream/4278;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/12107, chr9-CpG: 135/Downstream/16769
Nearby gene
CRAT(+649) ;
Upstream sequence
cagccaaatgtgcaactgggtatagggggtctaacaaatgtcttcaggattcaaattgtctctatcatttcttcactctgtttcctttttgttgatgcca
Downstream sequence
CCCACAGTGTTATAGGTCTCATATATAttaggttggtgtaaaagtaattgtggtttttgccatgacttttTTCTCTCTCTCTCTGTCTGTGtatatatat
Reference
Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.
Curate