SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

Jia, Wenlong; Qiu, Kunlong; He, Minghui; Song, Pengfei; Zhou, Quan; Zhou, Feng; Yu, Yuan; Zhu, Dandan; Nickerson, Michael L.; Wan, Shengqing; Liao, Xiangke; Zhu, Xinhua; Peng, Shaoliang; Li, Yingrui; Wang, Jun; Guo, Guangwu

doi:10.1186/gb-2013-14-2-r12

Cited by 187 publications

(156 citation statements)

References 37 publications

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“…Detection of fusion transcripts was enabled by SOAPfuse. 44 RNAseq data were also used for the classification of the 2 disease subtypes, GCB and ABC, based on a published set of genes. 45 Information about qPCR is provided in the supplemental Methods.…”

Section: Dna Extraction Wgs and Analysis Of Svmentioning

confidence: 99%

Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas

Γεωργίου

Chen

Berglund

et al. 2016

Blood

179

176

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Key Points• Translocations between PD-L1 and the IGH locus represent a genetic mechanism of PD-L1 overexpression in DLBCL.• Genetic alterations in the PD-L1/PDL-2 locus are mainly associated with the non-GCB subtype of DLBCL.Diffuse large B-cell lymphoma (DLBCL) is one of the most common and aggressive types of B-cell lymphoma. Deregulation of proto-oncogene expression after a translocation, most notably to the immunoglobulin heavy-chain locus (IGH), is one of the hallmarks of DLBCL. Using whole-genome sequencing analysis, we have identified the PD-L1/PD-L2 locus as a recurrent translocation partner for IGH in DLBCL. PIM1 and TP63 were also identified as novel translocation partners for PD-L1/PD-L2. Fluorescence in situ hybridization was furthermore used to rapidly screen an expanded DLBCL cohort. Collectively, a subset of samples was found to be affected by gains (12%), amplifications (3%), and translocations (4%) of the PD-L1/PD-L2 locus. RNA sequencing data coupled with immunohistochemistry revealed that these cytogenetic alterations correlated with increased expression of PD-L1 but not of PD-L2. Moreover, cytogenetic alterations affecting the PD-L1/PD-L2 locus were more frequently observed in the non-germinal center B cell-like (non-GCB) subtype of DLBCL. These findings demonstrate the genetic basis of PD-L1 overexpression in DLBCL and suggest that treatments targeting the PD-1-PD-L1/PD-L2 axis might benefit DLBCL patients, especially those belonging to the more aggressive non-GCB subtype. (Blood. 2016;127(24):3026-3034)

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Section: Dna Extraction Wgs and Analysis Of Svmentioning

confidence: 99%

Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas

Γεωργίου

Chen

Berglund

et al. 2016

Blood

179

176

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“…Several methods/pipelines have been developed to identify chimeric RNAs formed from cancer-related mutations, and these use RNA-seq data derived from a single NGS platform, e.g., TopHatFusion (Kim and Salzberg 2011), FusionSeq (Sboner et al 2010), FusionHunter (Li et al 2011), ChimeraScan (Iyer et al 2011), FusionFinder (Francis et al 2012), Bellerophontes (Abate et al 2012), and SOAPfuse (Jia et al 2013). These methods may also be used to detect trans-splicing candidates.…”

Section: Genome Research 31mentioning

confidence: 99%

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

Chuang

et al. 2013

Genome Res.

167

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Trans-splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans-splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which integrates different types of high-throughput long-/short-read transcriptome sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing. Combining TSscan screening with multiple experimental validation steps revealed that most chimeric RNA products were platformdependent experimental artifacts of RNA sequencing. We successfully identified and confirmed four trans-spliced RNAs, including the first reported trans-spliced large intergenic noncoding RNA (''tsRMST ''). We showed that these trans-spliced RNAs were all highly expressed in human pluripotent stem cells and differentially expressed during hESC differentiation. Our results further indicated that tsRMST can contribute to pluripotency maintenance of hESCs by suppressing lineagespecific gene expression through the recruitment of NANOG and the PRC2 complex factor, SUZ12. Taken together, our findings provide important insights into the role of trans-splicing in pluripotency maintenance of hESCs and help to facilitate future studies into trans-splicing, opening up this important but understudied class of post-transcriptional events for comprehensive characterization.

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“…MSC muscle differentiation and RH30 cell RNA-seq were performed by Axeq. The deep-sequencing data were mapped to human genome version hg19 and analyzed by using the software SOAPfuse (32). The human tissue RNA-seq was analyzed by EricScript (24).…”

Section: Methodsmentioning

confidence: 99%

Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma

Xie

Babiceanu

Kumar

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Gene fusions and fusion products were thought to be unique features of neoplasia. However, more and more studies have identified fusion RNAs in normal physiology. Through RNA sequencing of 27 human noncancer tissues, a large number of fusion RNAs were found. By analyzing fusion transcriptome, we observed close clusterings between samples of same or similar tissues, supporting the feasibility of using fusion RNA profiling to reveal connections between biological samples. To put the concept into use, we selected alveolar rhabdomyosarcoma (ARMS), a myogenic pediatric cancer whose exact cell of origin is not clear. PAX3-FOXO1 (paired box gene 3 fused with forkhead box O1) fusion RNA, which is considered a hallmark of ARMS, was recently found during normal muscle cell differentiation. We performed and analyzed RNA sequencing from various time points during myogenesis and uncovered many chimeric fusion RNAs. Interestingly, we found that the fusion RNA profile of RH30, an ARMS cell line, is most similar to the myogenesis time point when PAX3-FOXO1 is expressed. In contrast, full transcriptome clustering analysis failed to uncover this connection. Strikingly, all of the 18 chimeric RNAs in RH30 cells could be detected at the same myogenic time point(s). In addition, the seven chimeric RNAs that follow the exact transient expression pattern as PAX3-FOXO1 are specific to rhabdomyosarcoma cells. Further testing with clinical samples also confirmed their specificity to rhabdomyosarcoma. These results provide further support for the link between at least some ARMSs and the PAX3-FOXO1-expressing myogenic cells and demonstrate that fusion RNA profiling can be used to investigate the etiology of fusion-gene-associated cancers.rhabdomyosarcoma | gene fusion | chimeric RNA | myogenesis | PAX3-FOXO1

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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

Cited by 187 publications

References 37 publications

Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas

Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma

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