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

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.; Monroe, G.R.

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

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Item Type:	Article
Title:	Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing
Creators:	Stangl, C., de Blank, S. ORCID: https://orcid.org/0000-0003-2191-5675, Renkens, I., Westera, L., Verbeek, T., Valle-Inclan, J.E., Chamorro González, R. ORCID: https://orcid.org/0000-0002-5653-7259, Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X, van Roosmalen, M.J., Stam, R.W., Voest, E.E. ORCID: https://orcid.org/0000-0001-8249-9586, Kloosterman, W.P. ORCID: https://orcid.org/0000-0003-3357-4580, van Haaften, G. ORCID: https://orcid.org/0000-0003-3033-0329 and Monroe, G.R. ORCID: https://orcid.org/0000-0002-8653-2643
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

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