FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

Ge, Huanying; Liu, Kejun; Juan, Todd; Fang, Fang; Newman, Matthew; Hoeck, Wolfgang

doi:10.1093/bioinformatics/btr310

Cited by 237 publications

(237 citation statements)

References 25 publications

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“…The software used for detection of fusion transcripts included Fusioncatcher v0.99.4e (https://github.com/ndaniel/fusioncatcher),10 Chimerascan v0.4.5 (https://github.com/genome/chimerascan-vrl),11 FusionMap 31.03.15 (https://omictools.com/fusionmap-tool),12 and TopHat 2.0.9 (https://ccb.jhu.edu/software/tophat/index.shtml). 13 The candidate fusion transcripts obtained by bioinformatic analysis were checked using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) and BLAT (https://genome.ucsc.edu/cgi-bin/hgBlat?command=start).…”

Section: Methodsmentioning

confidence: 99%

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

Agostini

Brunetti

Davidson

et al. 2018

Intl Journal of Cancer

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Formation of fusion genes is pathogenetically crucial in many solid tumors. They are particularly characteristic of several mesenchymal tumors, but may also be found in epithelial neoplasms. Ovarian carcinomas, too, may harbor fusion genes but only few of these were found to be recurrent with a rate ranging from 0.5 to 5%. Because most attempts to find specific and recurrent fusion transcripts in ovarian carcinomas focused exclusively on high‐grade serous carcinomas, the situation in the other carcinoma subgroups remains largely uninvestigated as far as fusion genes are concerned. We performed transcriptome sequencing on a series of 34 samples from ovarian tumors that included borderline, clear cell, mucinous, endometrioid, low‐grade and high‐grade serous carcinomas in search of fusion genes typical of these subtypes. We found a total of 24 novel fusion transcripts. The PCMTDI‐CCNL2 fusion transcript, which involves a member of the cyclin family, was found recurrently involved but only in endometrioid carcinomas (4 of 18 tumors; 22%). We also found three additional fusion transcripts involving genes belonging to the cyclin family: ANXA5‐CCNA2 and PDE4D‐CCNB1 were detected in two endometrioid carcinomas, whereas CCNY‐NRG4 was identified in a clear cell carcinoma. The recurrent involvement of CCNL2 in four fusions and of three other genes of the cyclin family in three additional transcripts hints that deregulation of cyclin genes is important in the pathogenesis of ovarian carcinomas in general but of endometrioid carcinomas particularly.

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Section: Methodsmentioning

confidence: 99%

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

Agostini

Brunetti

Davidson

et al. 2018

Intl Journal of Cancer

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“…To detect fusion transcripts involving amplified genes, we used both ChimeraScan (CS) 19 and FusionMap (FM) 20 (Supplementary Methods). A custom bioinformatics pipeline was implemented to combine SVs with chimeric transcript data and evaluate the occurrence of posttranscriptional events in the genesis of chimeras.…”

Section: Rna-seq Was Performed On 20 Aml-amp Cases and Two Remission mentioning

confidence: 99%

MYC-containing amplicons in acute myeloid leukemia: Genomic structures, evolution, and transcriptional consequences

et al. 2017

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Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of highresolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres. Surprisingly, amplified genes (mainly PVT1) frequently participated in fusion transcripts lacking a corresponding DNA template. We also detected a significant overexpression of the circular RNA of PVT1 (circPVT1) in AML-amp cases versus AML with a normal karyotype. Our results show that 8q24 amplicons in AML are surprisingly plastic DNA structures with an unexpected association to novel fusion transcripts and circular RNAs.

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“…Several computational tools have also been developed for the detection of fusion transcripts using RNA-Seq data, such as MapSplice [51], ShortFuse [52], FusionHunter [44], FusionMap [53], SnowShoes-FTD [54],defuse [55], chimerascan [56], FusionCatcher [57], TopHatFusion [44], BreakFusion [58], EricScript [59], SOAPfuse [60], FusionQ [61] , PRADA [62] and JAFFA [63]. Liu et al [64] performed a large-scale comparative study by applying these above 15 fusion transcript detection pipelines to 3 synthetic data sets and 3 real pairedend RNA-seq studies and developed a meta-caller algorithm to combine three top-performing methods (FusionCatcher, SOAPfusea and JAFFA).…”

Section: Next Generation Sequencing (Ngs): a High-performing Strategymentioning

confidence: 99%

Fusion Genes and their Detection through Next Generation Sequencing in Malignant Hematological Disease and Solid Tumors

Liu¹,

Weng²,

Ming³

et al. 2016

Diagn Pathol Open

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Fusion genes are neoplasia-associated mutations, which play a particularly significant role in tumorgenesis and exhibit great importance for clinical applications in malignant hematological diseases and solid tumors. Simultaneously with copy number variants (CNVs), gene fusions are resulting from balanced and unbalanced chromosomal rearrangements. Thus, understanding the mutagenesis and instability of CNV, as well as the underlying molecular mechanisms of chromosomal rearrangements will improve our comprehension of gene fusions. Recently, next generation sequencing (NGS), especially transcriptome sequencing or RNA-Sequencing (RNA-seq), has become a very useful tool to identify gene alterations in cancer and a powerful approach for investigating the tumorgenesis. However, we are still facing with the challenge of minimizing false positives in results of RNA-seq. Whole-genome sequencing (WGS) is also used for the fusion gene detection, which provides us a more comprehensive and integrative way to detect structural variants. WGS may correct the false-negative results from RNA-seq. Additionally; many computational tools with more sensitivity and specificity have been developed for the detection of fusion transcripts from NGS datas. In the future, multi-omics analysis, third-generation sequencing and liquid-biopsy technique all provide opportunities to comprehensively interpret gene fusions and understand the biology of cancer genomes.

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FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

Abstract: FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for noncommercial use at (http://www.omicsoft.com/fusionmap).

Cited by 237 publications

References 25 publications

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

MYC-containing amplicons in acute myeloid leukemia: Genomic structures, evolution, and transcriptional consequences

Fusion Genes and their Detection through Next Generation Sequencing in Malignant Hematological Disease and Solid Tumors

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