Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

• Published in: Nature communications Vol. 11; no. 1; p. 2861
• Main Authors: Stangl, Christina, de Blank, Sam, Renkens, Ivo, Westera, Liset, Verbeek, Tamara, Valle-Inclan, Jose Espejo, González, Rocio Chamorro, Henssen, Anton G., van Roosmalen, Markus J., Stam, Ronald W., Voest, Emile E., Kloosterman, Wigard P., van Haaften, Gijs, Monroe, Glen R.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group 05.06.2020; Nature Publishing Group UK; Nature Portfolio
• Subjects: Bioinformatics; Breakpoints; Cancer; CRISPR; Diagnostic systems; Enrichment; Fusion protein; Gene sequencing; Genes; Multiplexing; Nucleotides; Porosity; Target recognition
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-16641-7

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.