Basic Information
VIS ID
TVIS20004012
Fusion event
HPV-chr13:q13.2 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
E4
Start
3389
Host Sequence
Chromosome
chr13
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
34789996/34215859 (Hg38)
End
34789996/34215859 (Hg38)
Location type
Intergenic
Fragile sites / regions
FRA13A
Nearest miRNA
hsa-mir-2276/Upstream/10053355; hsa-mir-1267/Downstream/5448175;
Nearest TSS
ENST00000623511/Upstream/385107; ENST00000605909/Downstream/132184;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/397503, chr13-CpG: 79/Downstream/726375
Nearby gene
NBEA(-726427) ;
Upstream sequence
GAGTTCAACTACCTGACCAGTTGTTCTTCAGTGAAGAGAACTCACAAAACCTAAAAGACACACATGAAACATATGATTGTGGAAACATTATCAAATGTCA
Downstream sequence
TAAAAATGATAAGTTAAAACCAAGCTATATAAAATTTCTATGATCCAGACACAGAGTAAATTTCCATTGAAATGTTGATCAAGATTCTGCTTGATACAAA
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