TY - JOUR
T1 - Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing
AU - Stangl, Christina
AU - de Blank, Sam
AU - Renkens, Ivo
AU - Westera, Liset
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.
N1 - Funding Information:
We thank all members of the Kloosterman and van Haaften groups for fruitful discussions and support. The authors thank KWF for supporting C.S. and W.P.K. grant UU 2012-5710. This work was supported by funds from the Utrecht University to implement a single-molecule sequencing facility. We thank the Utrecht Sequencing Facility for the Nanopore Sequencing. The colon cancer samples were kindly provided by Prof Ijzer-mans, Department of Surgery, Erasmus Medical Center Rotterdam, The Netherlands. Miriam Guillen Navarro, Susan Arentsen-Peters, Heathcliff Dorado-Garcia and Victor Bardinet have kindly helped with providing the clinical samples and information.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/6/5
Y1 - 2020/6/5
N2 - 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.
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.
UR - http://www.scopus.com/inward/record.url?scp=85085976317&partnerID=8YFLogxK
U2 - 10.1038/s41467-020-16641-7
DO - 10.1038/s41467-020-16641-7
M3 - Article
C2 - 32504042
AN - SCOPUS:85085976317
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 2861
ER -