Dataset Information


Ena-DATASET-UMCU-05-05-2020-10:43:09:124-607 - samples

ABSTRACT: 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.

PROVIDER: EGAD00001006111 | EGA |


Similar Datasets

| EGAS00001003964 | EGA
| GSE100769 | GEO
2013-05-31 | E-GEOD-45133 | ArrayExpress
2020-01-16 | PXD013461 | Pride
| GSE111320 | GEO
| GSE56512 | GEO
| GSE94464 | GEO
| EGAS00001002149 | EGA
| EGAS00001003558 | EGA
| GSE80126 | GEO