Basic Information
VIS ID
TVIS20004253
Fusion event
HPV-chr11:q13.2 integration
Validated
Yes
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AY686584
Region type
LCR
Start
7302
Integrated sequence
GTATGTGCTTGTATGTGCTTGTAAATATTAAGTTGTATGTGTGTTTGTATGTATGGTATAATAAACACGTGTGTATGTGTTTTTAAATGCTTGTGTAACT| |ATTGTGTCATGCAACATAAATAAACTTATTGTTTCAACACCTACTAATTGTGTTGTGGTTATTCATTGTATATAAACTATATTTGCTACATCCTGTTTTT
Host Sequence
Chromosome
chr11
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
66872295/67104824 (Hg38)
End
66872295/67104824 (Hg38)
Fragile sites / regions
FRA11H
Nearest miRNA
hsa-mir-10392/Upstream/59116; hsa-let-7a-2/Downstream/385421;
Nearest TSS
ENST00000527297/Upstream/47935; ENST00000532436/Downstream/14445;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/33103, chr11-CpG: 212/Downstream/12980
Nearby gene
LOC107984341(+7468) ;
Junction sequence
ATATTAAGTTGTATGTGTGTTTGTATGTATGGTATAATAAACACGTGTGTATGTGTTTTTAAATGCTTGTGTAACTA---GCCTGGACAACAGAGTGAGAGTCC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.
Curate