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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.

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DUO:0000018
version: 2021-02-23

not for profit, non commercial use only

This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.

DUO:0000042
version: 2021-02-23

general research use

This data use permission indicates that use is allowed for general research use for any research purpose.

UMCU genetics default access policy to enable re-production of research and re-use of data for scientific purposes.

Please contact the DAC for the most up to date policies.

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 Quality Report
Located in
i
EGAF00003622143 bam 101.4 MB
EGAF00003622144 bam 688.1 MB Report
EGAF00003622145 bam 430.6 MB Report
EGAF00003622146 bam 845.8 MB Report
EGAF00003622147 bam 501.5 MB Report
EGAF00003622148 bam 50.6 MB
EGAF00003622149 bam 1.6 GB Report
EGAF00003622150 bam 2.2 GB Report
EGAF00003622151 bam 1.4 GB Report
EGAF00003622152 bam 1.2 GB Report
EGAF00003622153 bam 388.7 MB Report
EGAF00003622154 bam 172.7 MB Report
EGAF00003622155 bam 454.5 MB Report
EGAF00003622156 bam 183.7 MB Report
EGAF00003622157 bam 609.4 MB Report
EGAF00003622158 bam 1.5 GB Report
EGAF00003622159 bam 2.4 GB Report
17 Files (14.7 GB)