NGS-based Kinase Gene Fusion Identification

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)}

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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.

Publication 2020

TruSight RNA Fusion Panel

Embedded paraffin Formalin Frozen Gene fusions Kinase Tissues

Corresponding Organization : Memorial Sloan Kettering Cancer Center

Other organizations : Taipei Medical University-Shuang Ho Hospital, Taipei Medical University, University Medical Center Groningen, University of Groningen, Johns Hopkins Medicine, Johns Hopkins University, Mount Sinai Hospital, Brigham and Women's Hospital

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Variable analysis

independent variables

NGS-based methods, including whole transcriptome sequencing, anchored multiplex RNA sequencing (Archer Dx), targeted RNA sequencing with TruSight RNA Fusion Panel (Illumina, San Diego, California), and FoundationOne CDx

dependent variables

Identification of kinase gene fusions

control variables

RNA extraction from frozen tissues for whole transcriptome sequencing and from formalin-fixed paraffin-embedded (FFPE) tissues for the other platforms
Sequencing and analysis process as reported previously in the cited references

controls

No positive or negative controls were explicitly mentioned in the provided information.

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