Basic Information
VIS ID
TVIS20004302
Fusion event
HPV-chrX:p22.2 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
Gene
E6
Start
337
Integrated sequence
TGCTTTTCGGGATTTATGCATAGTATATAGAGATGGGAATCCATATGCTGTATGTGATAAATGTTTAAAGTTTTATTCTAAAATTAGTGAGTATAGACAT| |TATTGTTATAGTTTGTATGGAACAACATTAGAACAGCAATACAACAAACCGTTGTGTGATTTGTTAATTAGGTGTATTAACTGTCAAAAGCCACTGTGTC
Host Sequence
Chromosome
chrX
Cytoband
p22.2
Reference genome
GRCh37/hg19
Start
12054175/12036056 (Hg38)
End
12054175/12036056 (Hg38)
Nearest miRNA
hsa-mir-3690-1/Upstream/717370; hsa-let-7f-2/Downstream/1554236;
Nearest TSS
ENST00000429181/Upstream/267743; ENST00000640291/Downstream/102410;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/277239, chrX-CpG: 71/Downstream/102429
Junction sequence
TATGTAATAGAAGTAAATTATATGCTATCAAAGTACTTTACATGGATCAT---TTATTGTTATAGTGTGTATGGAACAACATTAGAACAGCAATACAACAAACC
* 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.
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