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

Christina Stangl; Sam de Blank; Ivo Renkens; Liset Westera; Tamara Verbeek; Jose Espejo Valle-Inclan; Rocio Chamorro González; Anton G. Henssen; Markus J. van Roosmalen; Ronald W. Stam; Emile E. Voest; Wigard P. Kloosterman; Gijs van Haaften; Glen R. Monroe

doi:10.1038/s41467-020-16641-7

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

Christina Stangl
, Sam de Blank
, Ivo Renkens
, Liset Westera
, Tamara Verbeek
, Jose Espejo Valle-Inclan
, Rocio Chamorro González
, Anton G. Henssen
, Markus J. van Roosmalen
, Ronald W. Stam
, Emile E. Voest
, Wigard P. Kloosterman
, Gijs van Haaften
, Glen R. Monroe

Research output: Contribution to journal › Article › peer-review

58 Citations (Scopus)

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.

Original language	English
Article number	2861
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-16641-7
Publication status	Published - 1 Dec 2020

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Stangl, C., de Blank, S., Renkens, I., Westera, L., Verbeek, T., Valle-Inclan, J. E., González, R. C., Henssen, A. G., van Roosmalen, M. J., Stam, R. W., Voest, E. E., Kloosterman, W. P., van Haaften, G., & Monroe, G. R. (2020). Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing. Nature communications, 11(1), Article 2861. https://doi.org/10.1038/s41467-020-16641-7

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title = "Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and 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. 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.",

author = "Christina Stangl and \{de Blank\}, Sam and Ivo Renkens and Liset Westera and Tamara Verbeek and Valle-Inclan, \{Jose Espejo\} and Gonz{\'a}lez, \{Rocio Chamorro\} and Henssen, \{Anton G.\} and \{van Roosmalen\}, \{Markus J.\} and Stam, \{Ronald W.\} and Voest, \{Emile E.\} and Kloosterman, \{Wigard P.\} and \{van Haaften\}, Gijs and Monroe, \{Glen R.\}",

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Stangl, C, de Blank, S, Renkens, I, Westera, L, Verbeek, T, Valle-Inclan, JE, González, RC, Henssen, AG, van Roosmalen, MJ , Stam, RW, Voest, EE, Kloosterman, WP, van Haaften, G & Monroe, GR 2020, 'Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing', Nature communications, vol. 11, no. 1, 2861. https://doi.org/10.1038/s41467-020-16641-7

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AU - Stangl, Christina

AU - de Blank, Sam

AU - Renkens, Ivo

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AU - Verbeek, Tamara

AU - Valle-Inclan, Jose Espejo

AU - González, Rocio Chamorro

AU - Henssen, Anton G.

AU - van Roosmalen, Markus J.

AU - Stam, Ronald W.

AU - Voest, Emile E.

AU - Kloosterman, Wigard P.

AU - van Haaften, Gijs

AU - Monroe, Glen R.

PY - 2020/12/1

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AB - 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.

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IS - 1

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ER -

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

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