Partner independent fusion gene detection by multiplexed CRISPR Cas9 enrichment and long read Nanopore sequencing (FUDGE)
Targeted long-read nanopore sequencing. 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. To accurately and impartially identify fusions, we developed FUDGE: FUsion Detection from Gene Enrichment. 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 two 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, providing unparalleled opportunity for diagnostic pan-cancer fusion detection.
- 17 samples
- DAC: EGAC00001000432
- Technology: GridION
- NPUNCU DUO:0000018 (version: 2021-02-23)not for profit, non commercial use onlyThis data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
- GRU DUO:0000042 (version: 2021-02-23)general research useThis data use permission indicates that use is allowed for general research use for any research purpose.
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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS00001003964 | Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF00003622143 | bam | 101.4 MB | ||
| EGAF00003622144 | bam | 688.1 MB | ||
| EGAF00003622145 | bam | 430.6 MB | ||
| EGAF00003622146 | bam | 845.8 MB | ||
| EGAF00003622147 | bam | 501.5 MB | ||
| EGAF00003622148 | bam | 50.6 MB | ||
| EGAF00003622149 | bam | 1.6 GB | ||
| EGAF00003622150 | bam | 2.2 GB | ||
| EGAF00003622151 | bam | 1.4 GB | ||
| EGAF00003622152 | bam | 1.2 GB | ||
| EGAF00003622153 | bam | 388.7 MB | ||
| EGAF00003622154 | bam | 172.7 MB | ||
| EGAF00003622155 | bam | 454.5 MB | ||
| EGAF00003622156 | bam | 183.7 MB | ||
| EGAF00003622157 | bam | 609.4 MB | ||
| EGAF00003622158 | bam | 1.5 GB | ||
| EGAF00003622159 | bam | 2.4 GB | ||
| 17 Files (14.7 GB) | ||||