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Nat Biotechnol. 2009 Nov;27(11):1005-11. doi: 10.1038/nbt.1584. Epub 2009 Nov 1.

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

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  • 1Michigan Center for Translational Pathology, Ann Arbor, Michigan, USA.

Abstract

Cancer genomes contain many aberrant gene fusions-a few that drive disease and many more that are nonspecific passengers. We developed an algorithm (the concept signature or 'ConSig' score) that nominates biologically important fusions from high-throughput data by assessing their association with 'molecular concepts' characteristic of cancer genes, including molecular interactions, pathways and functional annotations. Copy number data supported candidate fusions and suggested a breakpoint principle for intragenic copy number aberrations in fusion partners. By analyzing lung cancer transcriptome sequencing and genomic data, we identified a novel R3HDM2-NFE2 fusion in the H1792 cell line. Lung tissue microarrays revealed 2 of 76 lung cancer patients with genomic rearrangement at the NFE2 locus, suggesting recurrence. Knockdown of NFE2 decreased proliferation and invasion of H1792 cells. Together, these results present a systematic analysis of gene fusions in cancer and describe key characteristics that assist in new fusion discovery.

PMID:
19881495
[PubMed - indexed for MEDLINE]
PMCID:
PMC3086882
Free PMC Article

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