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 Name:

Stangl, C. and de Blank, S. and Renkens, I. and Westera, L. and Verbeek, T. and Valle-Inclan, J.E. and Chamorro González, R. and Henssen, A.G. and van Roosmalen, M.J. and Stam, R.W. and Voest, E.E. and Kloosterman, W.P. and van Haaften, G. and Monroe, G.R.

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:

Number:

Page Range:

2861

Date:

5 June 2020