Basic Information
VIS ID
TVIS20004231
Fusion event
HPV-chr13:q22.1 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
Gene
E6
Start
447
Integrated sequence
GTTTGTATGGAACAACATTAGAACAGCAATACAACAAACCGTTGTGTGATTTGTTAATTAGGTGTATTAACTGTCAAAAGCCACTGTGTCCTGAAGAAAA| |GCAAAGACACCTGGACAAAAAGCAAAGATTCCATAATATAAGGGGTCGGTGGACCGGTCGATGTATGTCTTGTTGCAGATCATCAAGAACACGTAGAGAA
Host Sequence
Chromosome
chr13
Cytoband
q22.1
Reference genome
GRCh37/hg19
Start
73620048/73045910 (Hg38)
End
73620048/73045910 (Hg38)
Fragile sites / regions
FRA13B
Nearest miRNA
hsa-mir-1297/Upstream/6827586; hsa-mir-1267/Downstream/4652102;
Nearest TSS
ENST00000623511/Upstream/76271; ENST00000476859/Downstream/9066;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/263436, chr13-CpG: 163/Downstream/12812
Nearby gene
PSMD10P3(-9064) ; KLF5(+9066) ;
Nearest cancer related gene
KLF5(OG, +9066) ;
Junction sequence
TTTGCTTTTTGTCCAGATGTCTTTGCT---CAAAAAAAAAAAAAAAAAAAAAAA
* 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