![[feed]](/style/images/feed-icon-14x14.png){kind=icon}
Tools
Tools
Preview |
PDF (Original Article)
- Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
1MB |
![[thumbnail of Supplementary Information]](https://mdc-test.eprints-hosting.org/style/images/fileicons/other.png) |
Other (Supplementary Information)
3MB |
| Item Type: | Article |
|---|---|
| Title: | Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing |
| Creators Name: | Stangl, C., de Blank, S., Renkens, I., Westera, L., Verbeek, T., Valle-Inclan, J.E., Chamorro González, R., Henssen, A.G., van Roosmalen, M.J., Stam, R.W., Voest, E.E., Kloosterman, W.P., van Haaften, G. and Monroe, G.R. |
| Abstract: | Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. Here, we develop FUDGE (FUsion Detection from Gene Enrichment) to accurately and impartially identify fusions. FUDGE couples target-selected and strand-specific CRISPR-Cas9 activity for fusion gene driver enrichment - without prior knowledge of fusion partner or breakpoint-location - to long read nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints within 2 days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay for diagnostic pan-cancer fusion detection. |
| Keywords: | CRISPR-Cas Systems, DNA Sequence Analysis, Gene Fusion, Genetic Testing, High-Throughput Nucleotide Sequencing, Nanopore Sequencing, Neoplasms, Tumor Cell Line |
| Source: | Nature Communications |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 11 |
| Number: | 1 |
| Page Range: | 2861 |
| Date: | 5 June 2020 |
| Official Publication: | https://doi.org/10.1038/s41467-020-16641-7 |
| PubMed: | View item in PubMed |
Repository Staff Only: item control page
