Basic Information
VIS ID
TVIS20003977
Fusion event
HPV-chr21:q22.3 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
E1
Start
943
Host Sequence
Chromosome
chr21
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
46418875/44998961 (Hg38)
End
46418875/44998961 (Hg38)
Location type
Intergenic
Nearest miRNA
hsa-let-7c/Upstream/1388972; hsa-mir-6815/Downstream/479305;
Nearest TSS
ENST00000624081/Upstream/3776; ENST00000462214/Downstream/5766;
Nearest CpG islands
None/Target, chr21-CpG: 261/Upstream/8215, chr21-CpG: 24/Downstream/2340
Nearby gene
PICSAR(+251) ;
Upstream sequence
CCTGGGCGTGACCAGTGCCCGGACCCCCGACCGGGCAGTACGGCGGCTCTGCGCAAACGTCCCCCCTGCAGGGTCAAGCAGAACTGTGGTCGCTGCCAGG
Downstream sequence
CTGCCTGGCACCTCAGCACCTCGGCCCTCACTGCCCACAGGAATCTGTCAGGAGCCCCACCCCGGCCATGAGCTCGGGGGGCTGGCGCCCCTGGGCTGGG
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