STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

Haas, Brian J.; Dobin, Alexander; Stransky, Nicolas; Ли, Бо; Yang, Xiao; Tickle, Timothy L.; Bankapur, Asma; Ganote, Carrie; Doak, Thomas G.; Pochet, Nathalie; Sun, Jing; Wu, Catherine J.; Gingeras, T; Regev, Aviv

doi:10.1101/120295

Cited by 232 publications

(203 citation statements)

References 43 publications

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“…Sequencing was performed (75 cycles, paired end) with a NextSeq 500/550 High Output V2 kit and an Illumina NextSeq 500 (Illumina). Alignments were performed with the STAR algorithm [11] against the GRCh38 reference genome, and fusion gene assessments were made with STAR-Fusion [12], Fusion-Catcher [10] and FusionMap [13] tools. Expression profiles were extracted from fastq files with Kallisto [14], and transformed as log2(TPM + 2) prior to quantile normalization with the Limma package v 3.32.2 performed in the R environment v3.4.1 [15].…”

Section: Ffpe Rna Sequencingmentioning

confidence: 99%

Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1‐SS18 gene fusion

Alholle

Karanian

Brini

et al. 2018

The Journal of Pathology

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In recent years, undifferentiated small round cell sarcomas (USRCSs) have been divided into a variety of new, rare, sarcoma subtypes, including the group of Ewing-like sarcomas, which have the morphological appearance of Ewing sarcomas, but carry CIC-DUX4, BCOR-CCNB3 and other gene fusions different from the classic EWSR1-ETS gene fusion. Using high-throughput RNA-sequencing (RNA-seq) analyses, we identified a novel recurrent gene fusion, CRTC1-SS18, in two cases of USRCS that lacked any known translocation. RNA-seq results were confirmed by reverse transcription polymerase chain reaction, long-range polymerase chain reaction, and fluorescence in situ hybridization. In vitro, we showed that the cells expressing the gene fusion were morphologically distinct and had enhanced oncogenic potential as compared with control cells. Expression profile comparisons with tumours of other sarcoma subtypes demonstrated that both cases clustered close to EWSR1-CREB1-positive tumours. Moreover, these analyses indicated enhanced NTRK1 expression in CRTC1-SS18-positive tumours. We conclude that the novel gene fusion identified in this study adds a new subtype to the USRCSs with unique gene signatures, and may be of therapeutic relevance. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

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Section: Ffpe Rna Sequencingmentioning

confidence: 99%

Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1‐SS18 gene fusion

Alholle

Karanian

Brini

et al. 2018

The Journal of Pathology

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“…Select events were validated by PCR or FISH. Star Fusion (v0.8.0) and FusionCatcher (v0.99.6a) were used to detect fusion transcripts in RNA‐seq data. Fusion transcript calls were contrasted with DNA SV data and visually verified on DNA level using IGV.…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis reveals recurrent deletion of JAK‐STAT signaling inhibitors HNRNPK and SOCS1 in mycosis fungoides

Torres

Cats

Mei

et al. 2018

Genes Chromosomes & Cancer

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Mycosis fungoides (MF) is the most common cutaneous T‐cell lymphoma (CTCL). Causative genetic alterations in MF are unknown. The low recurrence of pathogenic small‐scale mutations (ie, nucleotide substitutions, indels) in the disease, calls for the study of additional aspects of MF genetics. Here, we investigated structural genomic alterations in tumor‐stage MF by integrating whole‐genome sequencing and RNA‐sequencing. Multiple genes with roles in cell physiology (n = 113) and metabolism (n = 92) were found to be impacted by genomic rearrangements, including 47 genes currently implicated in cancer. Fusion transcripts involving genes of interest such as DOT1L, KDM6A, LIFR, TP53, and TP63 were also observed. Additionally, we identified recurrent deletions of genes involved in cell cycle control, chromatin regulation, the JAK‐STAT pathway, and the PI‐3‐K pathway. Remarkably, many of these deletions result from genomic rearrangements. Deletion of tumor suppressors HNRNPK and SOCS1 were the most frequent genetic alterations in MF after deletion of CDKN2A. Notably, SOCS1 deletion could be detected in early‐stage MF. In agreement with the observed genomic alterations, transcriptome analysis revealed up‐regulation of the cell cycle, JAK‐STAT, PI‐3‐K and developmental pathways. Our results position inactivation of HNRNPK and SOCS1 as potential driver events in MF development.

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“…As such, integrating automated detection tools, e.g. hic_breakfinder [6] and STAR-Fusion [27], with visual heatmap inspection can provide substantial information regarding genomic SVs without any additional cost.…”

Section: Discussionmentioning

confidence: 99%

Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

Jacobson

Grand

Perry

et al. 2018

Preprint

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Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter-and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used Hi-C and RNA-seq to identify and compare large SVs in HL-60 and HL-60/S4 cell lines. Comparisons with previously published karyotypes identified novel SVs in both cell lines. Hi-C was used to characterize the known expansion centered on the MYC locus. The MYC expansion was integrated into known locations in HL-60/S4, and a novel location (chr4) in HL-60. The HL-60 cell line has more within-line structural variation than the HL-60/S4 derivative cell line. Collectively we demonstrate the usefulness of Hi-C and with RNA-seq data for the identification and characterization of SVs.

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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

Abstract: Motivation: Fusion genes created by genomic rearrangements can be potent drivers of tumorigenesis.

Cited by 232 publications

References 43 publications

Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1‐SS18 gene fusion

Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1‐SS18 gene fusion

Genomic analysis reveals recurrent deletion of JAK‐STAT signaling inhibitors HNRNPK and SOCS1 in mycosis fungoides

Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

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