Trusight rna fusion panel

Manufactured by Illumina

Sourced in United States

The TruSight RNA Fusion Panel is a targeted gene enrichment panel designed to detect RNA fusion transcripts. It enables the identification of gene fusions across multiple cancer types. The panel targets known and novel fusion partners, providing comprehensive coverage of fusion genes implicated in various cancers.

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Lab products found in correlation

Expressart ffpe clear rna ready kit, by AMS Biotechnology (32 mentions) Agilent bioanalyzer, by Agilent Technologies (25 mentions) Miseq platform, by Illumina (14 mentions) Rneasy ffpe kit, by Qiagen (7 mentions) Nanodrop 1000, by Qiagen (6 mentions) Qubit rna hs assay kit, by Thermo Fisher Scientific (6 mentions) Miniseq sequencer, by Illumina (5 mentions) Amsbio s expressart ffpe clear rna ready kit, by AMS Biotechnology (4 mentions) Rna seq alignment workflow, by Illumina (4 mentions) Fusionplex custom solid panel, by Illumina (3 mentions) Amsbio s, by AMS Biotechnology (3 mentions) High pure ffpe rna isolation kit, by Roche (3 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions) Rna seq alignment app, by Illumina (2 mentions) Bioanalyzer rna 6000 nano kit, by Agilent Technologies (2 mentions) Rna seq libraries, by Illumina (2 mentions) Miseq v3 platform, by Illumina (2 mentions) High pure ffpet rna isolation kit, by Roche (2 mentions) Trusight rna pan cancer panel, by Illumina (2 mentions) Msk solid fusion, by Illumina (2 mentions)

82 protocols using trusight rna fusion panel

FFPE RNA Sequencing and MSK-IMPACT Profiling

Cited 2 times

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Case #1 was subjected to RNA sequencing. RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using Amsbio’s ExpressArt FFPE Clear RNA Ready kit (Amsbio LLC, Cambridge, MA). Fragment length was assessed with an RNA 6000 chip on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA-sequencing libraries were prepared using 20 to 100 ng total RNA with the TruSight RNA Fusion Panel (Illumina, San Diego, CA)^{18 (link)}. Each sample was subjected to targeted RNA sequencing on an Illumina MiSeq (∼3 million reads per sample). All reads were independently aligned with STAR (version 2.3) and BowTie2 against the human reference genome (hg19) for Manta-Fusion and TopHat-Fusion analysis, respectively.
Case #3 was evaluated using MSK-IMPACT (Integrated Mutational Profiling of Actionable Cancer Targets), a targeted ultra-deep next generation sequencing platform designed to capture all exons and selected introns of 468 cancer-associated genes including oncogenes, tumor suppressor genes, and members of targetable pathways^{19 (link)}.

Argani P., Boyraz B., Oliva E., Matoso A., Gross J., Fridman E., Zhang L., Dickson B.C, & Antonescu C.R. (2022). GLI1 Gene Alterations in Neoplasms of the Genitourinary and Gynecologic Tract. The American journal of surgical pathology, 46(5), 677-687.

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FFPE RNA Extraction and Fusion Gene Detection

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Briefly, for each case scrolls (3–4 at 10 microns) were cut from formalin-fixed paraffin-embedded tissue into Eppendorf tubes. RNA was extracted using the ExpressArt FFPE Clear RNA Ready kit (Amsbio, Cambridge, MA). RNA-seq libraries were prepared using 20-100 ng total RNA with the TruSight RNA Fusion Panel (Illumina, San Diego, CA), an enrichment-based assay that targets 507 known fusion-associated genes. Each sample was sequenced with 76 base-pair paired-end reads on an Illumina MiSeq at 8 samples per flow cell (~3 million reads per sample). The results were analyzed using the STAR aligner and Manta fusion caller as well as the JAFFA fusion caller utilizing BOWTIE2 aligner.(15 (link), 16 (link))
The mRNA expression levels of NUTM1, and the respective fusion partners, were evaluated and compared to those of other samples analyzed on the same targeted RNA sequencing platform.

Dickson B.C., Sung Y.S., Rosenblum M.K., Reuter V.E., Harb M., Wunder J.S., Swanson D, & Antonescu C.R. (2018). NUTM1 GENE FUSIONS CHARACTERIZE A SUBSET OF UNDIFFERENTIATED SOFT TISSUE AND VISCERAL TUMORS. The American journal of surgical pathology, 42(5), 636-645.

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Targeted RNA Sequencing for Gene Fusions

Cited 3 times

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In a smaller subset of cases the gene fusion was determined either by RT-PCR (n=20), karyotype (n=2), MSK-IMPACT assay (n=27), or targeted RNA sequencing (n=12), as previously described^{16 –18}. Targeted RNA sequencing was performed either by using an Archer™ FusionPlex™ platform^{19 (link),20 (link)} or a TruSight RNA Fusion Panel (Illumina, San Diego, CA) on an Illumina MiSeq platform^{21 (link)}, using standard protocols. Reads were independently aligned with STAR (version 2.3) against the human reference genome (hg19) and analyzed by STAR-Fusion.

Tsuda Y., Zhang L., Meyers P., Tap W.D., Healey J.H, & Antonescu C.R. (2020). The Clinical Heterogeneity of Round Cell Sarcomas with EWSR1/FUS Gene Fusions. Impact of Gene Fusion Type on Clinical Features and Outcome. Genes, chromosomes & cancer, 59(9), 525-534.

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Targeted RNA Sequencing of FFPE Samples

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Four cases were analyzed by targeted RNA sequencing, using RNA extracted from FFPE tissue with the Amsbio’s ExpressArt FFPE Clear RNA Ready kit (Amsbio LLC, Cambridge, MA). The fragment length was assessed with an RNA 6000 chip on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA-seq libraries were prepared using 20 to 100 ng total RNA with the TruSight RNA Fusion Panel (Illumina, San Diego, CA). Targeted RNA sequencing was performed on an Illumina MiSeq platform. Reads were independently aligned with STAR (version 2.3) against the human reference genome (hg19) and analyzed by STAR-Fusion.

Suurmeijer A.J., Dickson B.C., Swanson D., Sung Y.S., Zhang L, & Antonescu C.R. (2020). Variant WWTR1 Gene Fusions in Epithelioid Hemangioendothelioma – A Genetic Subset Associated with Cardiac Involvement. Genes, chromosomes & cancer, 59(7), 389-395.

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mRNA Profiling of BCOR, NTRK, and NTF3 in Round Cell Sarcomas

Cited 2 times

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The mRNA levels of BCOR, NTRK1/2/3, and NTF3 expression were evaluated in round cell sarcomas with BCOR ITD, BCOR fusions, or YWHAE fusions using RNA sequencing (RNAseq) data and compared to other sarcoma types available on the same platforms. Datasets from 2 RNAseq platforms were analyzed including 10 cases studied on whole transcriptome sequencing (6 BCOR ITD, 2 BCOR-CCNB3, 1 BCOR-MAML3, and 1 YWHAE-NUTM2B) and 7 cases tested on targeted RNAseq using the TruSight RNA Fusion Panel (Illumina, San Diego, CA) (1 BCOR ITD, 3 BCOR-CCNB3, 2 KMT2D-BCOR, and 1 BCOR-CHD9), as previously described.[1 (link), 2 (link)] Whole transcriptome sequencing data was also analyzed for NTRK3 expression at the exon level. Control groups of other sarcomas with available data in each dataset included: Ewing sarcoma (n=1), CIC-DUX4 sarcomas (n=9), and OFMT with ZC3H7B-BCOR fusion (n=1) in whole transcriptome sequencing and synovial sarcoma (n=1) and SFT (n=4) in the targeted TruSight RNA Fusion Panel. In addition, one infantile fibrosarcoma with an EML4-NTRK3 fusion with targeted RNAseq data was also included as reference for the enhanced level of NTRK3 mRNA upregulation.

Kao Y.C., Sung Y.S., Argani P., Swanson D., Alaggio R., Tap W., Wexler L., Dickson B.C, & Antonescu C.R. (2020). NTRK3 Overexpression in Undifferentiated Sarcomas with YWHAE and BCOR Genetic Alterations. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 33(7), 1341-1349.

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FFPE RNA Sequencing for Fusion Analysis

Cited 1 time

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RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using Amsbio’s ExpressArt FFPE Clear RNA Ready kit (Amsbio LLC, Cambridge, MA). One case was tested on the TruSight RNA Fusion Panel (Illumina, San Diego, CA), using 100 ng total RNA for RNA-sequencing libraries preparation.^{9 (link)} Fragment length was assessed with an RNA 6000 chip on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). The sample was subjected to targeted RNA sequencing on an Illumina MiSeq at eight samples per flow cell (~3 million reads per sample). All reads were independently aligned with STAR (version 2.3) and BowTie2 against the human reference genome (hg19) for Manta-Fusion and TopHat-Fusion analysis, respectively. The second case was tested by Anchored Multiplex RNA sequencing assay using the Archer FusionPlex Solid tumor Kit (Archer, Boulder, CO).^{10 (link)} Anchored Multiplex polymerase chain reaction amplicons were sequenced on Illumina MiSeq, and the data were analyzed using the Archer software.

Antonescu C.R., Agaram N.P., Sung Y.S., Zhang L, & Dickson B.C. (2020). Undifferentiated round cell sarcomas with novel SS18-POU5F1 fusions. Genes, chromosomes & cancer, 59(11), 620-626.

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Detecting RNA Fusions in FFPE Tissue

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RNA was isolated from formalin-fixed paraffin-embedded (FFPE) tissue sections using RNeasy FFPE Kit of Qiagen (Hilden, Germany) and quantified spectrophotometrically using NanoDrop-1000 (Waltham, United States). Molecular analysis was performed using the TruSight RNA Fusion Panel (Illumina, Inc., San Diego, CA, USA) with 500 ng RNA as input according to the manufacturer`s protocol. Libraries were sequenced on a MiSeq (Illumina, Inc., San Diego, CA, USA) with > 3 million reads per case, and sequences were analyzed using the RNA-Seq Alignment workflow, version 2.0.1 (Illumina, Inc., San Diego, CA, USA). The RNA-Seq alignment app (Illumina) was employed to call fusions by using the TopHat-Fusion algorithm. Additionally, the Integrative Genomics Viewer (IGV), version 2.2.13 (Broad Institute, REF) was used for data visualization of fusions.

Agaimy A., Haller F., Renner A., Niedermeyer J., Hartmann A, & French C.A. (2022). Misleading Germ Cell Phenotype in Pulmonary NUT Carcinoma Harboring the ZNF532-NUTM1 Fusion. The American journal of surgical pathology, 46(2), 281-288.

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FFPE RNA Sequencing and Fusion Assay

Cited 2 times

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Formalin-fixed paraffin-embedded tissue sections (either scrolls [3–4 at 10 microns] or tissue scraped from glass slides [4–5 at 4 microns] were obtained from each case. RNA extraction was performed with the ExpressArt FFPE Clear RNA Ready kit (Amsbio, Cambridge, MA). Libraries were prepared using 20–100 ng total RNA with the TruSight RNA Fusion Panel (Illumina, San Diego, CA), an enrichment-based assay targeting 507 fusion-associated genes. RNA sequencing (RNA-seq) was performed with 76 base-pair paired-end reads on an Illumina MiSeq at 8 samples per flow cell (~3 million reads per sample). The results were analyzed using both the STAR aligner and Manta fusion caller, and the BOWTIE2 aligner and JAFFA fusion caller (10 (link), 11 (link)).
Archer™ FusionPlex™ technology was used to develop the MSK-Solid Fusion assay, which is a clinical molecular diagnostic essay performed in a CLIA-accredited laboratory utilizing multiplex polymerase chain reaction (PCR) to detect oncogenic fusion transcripts involving 62 genes as described previously (12 (link)).

Dickson B.C., Antonescu C.R., Demicco E.G., Leong I., Anderson N.D., Swanson D., Zhang L., Fletcher C.D, & Hornick J.L. (2021). Hybrid Schwannoma-Perineurioma Frequently Harbors VGLL3 Rearrangement. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 34(6), 1116-1124.

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NGS-based Kinase Gene Fusion Identification

Cited 5 times

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Kinase gene fusions were identified in eight cases by NGS-based methods, including by whole transcriptome sequencing (n = 4), anchored multiplex RNA sequencing (Archer Dx) (n = 2), targeted RNA sequencing with TruSight RNA Fusion Panel (Illumina, San Diego, California) (n = 1), and FoundationOne CDx (n = 1). RNA was extracted from frozen tissues for whole transcriptome sequencing and from formalin-fixed paraffin-embedded (FFPE) tissues for the other platforms. The sequencing and analysis process were as reported previously.^{3 (link),4 (link),7 (link),9 (link),10 (link),12 (link)}

Kao Y.C., Suurmeijer A.J., Argani P., Dickson B.C., Zhang L., Sung Y.S., Agaram N.P., Fletcher C.D, & Antonescu C.R. (2020). Soft tissue tumors characterized by a wide spectrum of kinase fusions share a lipofibromatosis-like neural tumor pattern. Genes, chromosomes & cancer, 59(10), 575-583.

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mRNA Profiling of BCOR, NTRK, and NTF3 in Round Cell Sarcomas

Cited 2 times

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