RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib

Lilljebjörn, Henrik; Ågerstam, Helena; Orsmark-Pietras, Christina; Rissler, Marianne; Ehrencrona, Hans; Nilsson, Lars; Richter, Johan; Fioretos, Thoas

doi:10.1038/leu.2013.324

Cited by 52 publications

(40 citation statements)

References 14 publications

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“…87 Since this initial study, a complex network of kinase-activating aberrations has been revealed, with many occurring in single patients. 7,93,94 The common feature of these chimeric genes is the fusion of the 3' end of a kinase gene with the 5' portion of so-called activating gene, of which over 30 have now been reported.…”

Section: Kinase Activating Gene Fusionsmentioning

confidence: 99%

New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia

2016

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Section: Kinase Activating Gene Fusionsmentioning

confidence: 99%

New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia

2016

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“…In contrast to our results and those of Panagopoulos et al, 22 a recent study evaluating the reliability of RNA-Seq for detecting clinically relevant fusion genes in leukemias detected all previously known fusions, as well as nine novel ones, with a single algorithm (ChimeraScan). 23 Possibly, the higher admixture of normal cells in solid tumors, such as sarcomas, makes it advisable to use more than one fusion algorithm when searching for gene fusions.…”

Section: Discussionmentioning

confidence: 99%

RNA sequencing of sarcomas with simple karyotypes: identification and enrichment of fusion transcripts

Hofvander

Tayebwa

Nilsson

et al. 2015

Laboratory Investigation

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Gene fusions are neoplasia-associated mutations arising from structural chromosomal rearrangements. They have a strong impact on tumor development and constitute important diagnostic markers. Malignant soft tissue tumors (sarcomas) constitute a heterogeneous group of neoplasms with 450 distinct subtypes, each of which is rare. In addition, there is considerable morphologic overlap between sarcomas and benign lesions. Several subtypes display distinct gene fusions, serving as excellent biomarkers. The development of methods for deep sequencing of the complete transcriptome (RNA-Seq) has substantially improved the possibilities for detecting gene fusions. With the aim of identifying new gene fusions of biological and clinical relevance, eight sarcomas with simple karyotypes, ie, only one or a few structural rearrangements, were subjected to massively parallel paired-end sequencing of mRNA. Three different algorithms were used to identify fusion transcripts from RNA-Seq data. Three novel (KIAA2026-NUDT11, CCBL1-ARL1, and AFF3-PHF1) and two previously known fusions (FUS-CREB3L2 and HAS2-PLAG1) were found and could be verified by other methods. These findings show that RNA-Seq is a powerful tool for detecting gene fusions in sarcomas but also suggest that it is advisable to use more than one algorithm to analyze the output data as only two of the confirmed fusions were reported by more than one of the gene fusion detection software programs. For all of the confirmed gene fusions, at least one of the genes mapped to a chromosome band implicated by the karyotype, suggesting that sarcomas with simple karyotypes constitute an excellent resource for identifying novel gene fusions.

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“…Of further potential clinical relevance, recent studies have found CSF1R to be rearranged in childhood ALLs, 21,23 and in vitro studies using cell lines and human leukemic PreB ALL cells have demonstrated their sensitivity to a CSF1R-specific inhibitor, 22 supporting that CSF1R might be a relevant therapeutic target in childhood ALL.…”

Section: Csf1r Marks Fetal Myeloid-primed B-cell Progenitors 223mentioning

confidence: 99%

“…20 Of particular relevance for our studies, several cases have been reported in which CSF1R is rearranged in childhood PreB B-ALL. [21][22][23] In light of these findings, we investigated the potential expression and role of CSF1R in normal fetal B lymphopoiesis by specifically investigating its expression in the FL CD19…”

Section: Introductionmentioning

confidence: 99%

Macrophage colony-stimulating factor receptor marks and regulates a fetal myeloid-primed B-cell progenitor in mice

Zriwil

Böiers

Wittmann

et al. 2016

Blood

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RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib

Cited by 52 publications

References 14 publications

New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia

New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia

RNA sequencing of sarcomas with simple karyotypes: identification and enrichment of fusion transcripts

Macrophage colony-stimulating factor receptor marks and regulates a fetal myeloid-primed B-cell progenitor in mice

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