Basic Information
VIS ID
TVIS20004411
Fusion event
HPV-GARS integration
Validated
Yes
Detection method
DIPS-PCR
Data source
Curated
Sample type
Tumor
Disease
Oropharyngeal squamous cell carcinoma (OSCC)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24586376
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
NC_001526.1
Gene
E1
Start
2283
Integrated sequence
CAAATTGTTATGTTTTTAAGGTATCAAGGTGTAGAGTTTATGTCATTTTTAACTGCATTAAAAAGATTTTTGCAAGGCATACCTAAAAAAAATTGCATAT| |TACTATATGGTGCAGCTAACACAGGTAAATCATTATTTGGTATGAGTTTAATGAAATTTCTGCAAGGGTCTGTAATATGTTTTGTAAATTCTAAAAGCCA
Host Sequence
Chromosome
chr7
Cytoband
p15
Reference genome
GRCh37.p5
Start
30661954/30622338 (Hg38)
End
30661954/30622338 (Hg38)
Orient
+
Location type
Exon12
Target gene
GARS
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-93-5p ; hsa-let-7c-5p
Nearest miRNA
hsa-mir-1183/Upstream/332448; hsa-mir-10399/Downstream/2110643;
Nearest TSS
ENST00000635602/Upstream/9; ENST00000465748/Downstream/6152;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/26896, chr7-CpG: 105/Downstream/59418
Upstream sequence
TTGTCTGAATGATTTTGTGGACAGGTGTTTCATCTTGCCTTAAAATCAGCATAAACAGGATCTGGAGTACTGATAGAGAGCTGGCATGGTTTTAAGTTGA
Downstream sequence
TTGAACCCAGTAAGGGAGCAATTGGTAAGGCATATAAGAAGGATGCAAAACTGGTGATGGAGTATCTTGCCATTTGTGATGAGTGCTACATTACAGAAAT
Target sequence
TGATTGATTGTTCTCAGGCTCATTTTCTGAAATACTGAGGCAGTGCTGTAGTTTTGGATTCCTTGACTACTTCATACAAAACAGTCAATGTTGTTCAGT
Reference
Olthof, N. C., et al.Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression.2014, PLoS One 9(2): e88718.
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