| Basic Information ▶ | |
| VISDB ID | TVIS20059763 |
|---|---|
| Fusion Name | HPV-NIHCOLE integration |
| Validated | No |
| Curated Way | Curated |
| Method | High-throughput Viral Integration Detection method |
| Wet Assay | Yes |
| Sample ID | - |
| Sample Name | S106 |
| Sample Type | Tumor |
| Age | 57 = 59; >57 = 50 |
| Gender | - |
| Disease Information ▶ | |
| Disease Name | Oropharyngeal squamous cell carcinoma |
| Disease Abbreviation | OPSCC |
| Cancer | Yes |
| Literature ▶ | |
| PubMed ID | 38279874 |
| Journal | Clinical and Translational Medicine |
| Published Year | 2024 |
| Human Genome ▶ | |
| Human Genome Version Description | GRCh37/hg19 |
| Human Genome RefSeq Accession | GCF_000001405.13 |
| Human Chromosome | chr5 |
| Cytogenetic Band | q21.2 |
| Human Strand | + |
| Human Integration Location Type | intronic |
| Hg19 Start | 103748902 |
| Hg19 End | 103748902 |
| Hg38 Start | 104413201 |
| Hg38 End | 104413201 |
| Junction Sequence | CCCATATTTCCTTTCACTCAGATCCATTTGTCTAGCTTCTACATGCTTGTTCAAATTTGCAACACCACCCAATTTGCTTCCAATCACCTCCATCATCTACCCTATCACATCTATATTTTATCCATTGACTCATACTCATTTG |
| Target Gene ▶ | |
| Target Gene | NIHCOLE, ENSG00000251574 |
| Nearby Gene | - |
| Distance | - |
| Virus Information ▶ | |
| Virus Name | Human Papillomavirus |
| Virus Subtype Name | HPV16 |
| Virus Genome Accession | AF125673 |
| TaxonomyID | 10566 |
| Virus Abbreviation | HPV |
| Virus Genome | Human papillomavirus type 16 isolate 16W12E, complete genome |
| Virus Genome Length | 7904 bp |
| Virus Breakpoint1 | 2190 |
| Virus Breakpoint2 | - |
| Virus Gene Name | HpV16gp3_E1 |
| Virus Region Type | - |
| Integrated Virus Sequence | - |
| ViMIC ID | - |
| Predicted VIS Effect ▶ | |
| Region | intron |
| Impact | intronic_insertion |
| Transcript | Transcript 1: ENST00000731153.1, Transcript 2: ENST00000718094.1, Transcript 3: ENST00000524336.5 |
| Transcript 1 Gene Id | ENSG00000251026.3 |
| Transcript 1 Gene Name | NIHCOLE |
| Transcript 2 Gene Id | ENSG00000251574.9 |
| Transcript 2 Gene Name | ENSG00000251574 |
| Transcript 3 Gene Id | ENSG00000251574.9 |
| Transcript 3 Gene Name | ENSG00000251574 |
| AlphaGenome Analysis | |
| Window | chr5:104347665-104478737 |
| RNA-seq Change (±2kb) | Mean: -4.2547784687485546e-05 | Peak: 0.1396484375 |
| ATAC Change (±2kb) | Mean: -0.0014853818574920297 | Peak: 3.98095703125 |
| Interpretation | RNA-seq: no signal in region (REF≈0, ALT≈0) | Splice sites: no signal in region (REF≈0, ALT≈0) | ATAC: minimal change -3.3% |
| Visualization | |
Center for Precision Health
McWilliams School of Biomedical Informatics at UTHealth Houston
7000 Fannin Street, Suite 600, Houston, TX 77030
Email: Zhongming Zhao, Ph.D