Universität zu Köln

Chmielecki, Juliann, Peifer, Martin ORCID: 0000-0002-5243-5503, Jia, Peilin, Socci, Nicholas D., Hutchinson, Katherine, Viale, Agnes, Zhao, Zhongming, Thomas, Roman K. and Pao, William (2010). Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. Nucleic Acids Res., 38 (20). S. 6985 - 6997. OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

Full text not available from this repository.

Abstract

Tyrosine kinase (TK) fusions are attractive drug targets in cancers. However, rapid identification of these lesions has been hampered by experimental limitations. Our in silico analysis of known cancer-derived TK fusions revealed that most breakpoints occur within a defined region upstream of a conserved GXGXXG kinase motif. We therefore designed a novel DNA-based targeted sequencing approach to screen systematically for fusions within the 90 human TKs; it should detect 92% of known TK fusions. We deliberately paired 'in-solution' DNA capture with 454 sequencing to minimize starting material requirements, take advantage of long sequence reads, and facilitate mapping of fusions. To validate this platform, we analyzed genomic DNA from thyroid cancer cells (TPC-1) and leukemia cells (KG-1) with fusions known only at the mRNA level. We readily identified for the first time the genomic fusion sequences of CCDC6-RET in TPC-1 cells and FGFR1OP2-FGFR1 in KG-1 cells. These data demonstrate the feasibility of this approach to identify TK fusions across multiple human cancers in a high-throughput, unbiased manner. This method is distinct from other similar efforts, because it focuses specifically on targets with therapeutic potential, uses only 1.5 mu g of DNA, and circumvents the need for complex computational sequence analysis.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Chmielecki, Juliann UNSPECIFIED UNSPECIFIED UNSPECIFIED Peifer, Martin UNSPECIFIED orcid.org/0000-0002-5243-5503 UNSPECIFIED Jia, Peilin UNSPECIFIED UNSPECIFIED UNSPECIFIED Socci, Nicholas D. UNSPECIFIED UNSPECIFIED UNSPECIFIED Hutchinson, Katherine UNSPECIFIED UNSPECIFIED UNSPECIFIED Viale, Agnes UNSPECIFIED UNSPECIFIED UNSPECIFIED Zhao, Zhongming UNSPECIFIED UNSPECIFIED UNSPECIFIED Thomas, Roman K. UNSPECIFIED UNSPECIFIED UNSPECIFIED Pao, William UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-493843
DOI:	10.1093/nar/gkq579
Journal or Publication Title:	Nucleic Acids Res.
Volume:	38
Number:	20
Page Range:	S. 6985 - 6997
Date:	2010
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1362-4962
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language CELL-LINE; GENE FUSIONS; REARRANGEMENTS; SELECTION; IDENTIFICATION; ACTIVATION; GEFITINIB; RET Multiple languages Biochemistry & Molecular Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/49384