Abstract 2436
Background
RNA sequencing (RNA-Seq) assay has been widely used for transcript level gene quantification and fusion detection for research use in fresh frozen samples. Clinical use of RNA is complicated by the common use of formalin-fixed paraffin-embedded (FFPE) tissue storage, which can cause low yield and RNA degradation. We evaluate the feasibility, quality, and analytical performance of RNA-Seq on clinical FFPE tumor samples for gene fusion detection.
Methods
Total RNA was extracted from FFPE tumor samples and/or adjacent normal samples. Ribosomal RNA depletion, cDNA synthesis, and library preparation were used to prepare next-generation sequencing (NGS) libraries that were sequenced on Illumina HiSeq X instrument. Sequencing data were analyzed and annotated with an in-house developed pipeline. A set of experimental and data quality control parameters were set up.
Results
The assay identified all the positive fusions from RNA reference material with 15 NTRK fusions spiked-in and ALK, RET, NTRK1 and FGFR3 fusions from 5 positive cell lines. The assay Limit of Detection was tested by diluting RNA from ALK fusion positive cell H2228C to fusion-negative cell line. Gene fusions were generally detectable down to 10% dilutions for all fusion types and as little as 5% for some fusion types. RNA-Seq assay detected 10 of 12 gene fusions detected by DNA based NGS assay, for a sensitivity of 83%. No false-positive gene fusions were identified in 28 tumor specimens that were negative for fusions, for a specificity of 100%. The assay also identified 6 novel fusions in 3 tumor specimens, which had been confirmed by RT-PCR and Sanger sequencing. Good intra-assay and inter assay reproducibility was observed with complete concordance for the presence or absence of gene fusions in 3 samples and 6 replicates. We observed 81% success rate on whole transcriptome RNA-Seq process for more than 100 FFPE samples.
Conclusions
RNA-Seq assay can help identify gene fusions in patients with cancer, which is a good supplement for DNA based NGS assay, especially for novel fusion detection or fusion breakpoints which are hard to design probes for DNA samples. These patients may in turn benefit from approved and investigational fusion related targeted therapies.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
3DMed Inc.
Funding
3DMed Inc.
Disclosure
H. Dong: Full / Part-time employment: 3DMed Inc. C. Wang: Full / Part-time employment: 3DMed Inc. Q. Xu: Full / Part-time employment: 3DMed Inc. Y. Guo: Full / Part-time employment: 3DMed Inc. Y. Chen: Full / Part-time employment: 3DMed Inc. B. Li: Full / Part-time employment: 3DMed Inc. S. Liu: Full / Part-time employment: 3DMed Inc. C. Chen: Full / Part-time employment: 3DMed Inc. L. Xiong: Full / Part-time employment: 3DMed Inc. F. Li: Full / Part-time employment: 3DMed Inc. All other authors have declared no conflicts of interest.
Resources from the same session
1242 - Monalizumab in combination with cetuximab in patients (pts) with recurrent or metastatic (R/M) head and neck cancer (SCCHN) previously treated or not with PD-(L)1 inhibitors (IO): 1-year survival data.
Presenter: Roger Cohen
Session: Poster Display session 3
Resources:
Abstract
4703 - Updated results of a phase II study evaluating accelerator-based boron neutron capture therapy (AB-BNCT) with borofalan(10B) (SPM-011) in recurrent squamous cell carcinoma (R-SCC-HN) and recurrent and locally advanced non-SCC (R/LA-nSCC-HN) of the head and neck
Presenter: Katsumi Hirose
Session: Poster Display session 3
Resources:
Abstract
3638 - Phase 3 KEYNOTE-048 Study of First-Line (1L) Pembrolizumab (P) for Recurrent/Metastatic (R/M) Head and Neck Squamous Cell Carcinoma (HNSCC): Asia vs Non-Asia Subgroup (subgrp) Analysis
Presenter: Makoto Tahara
Session: Poster Display session 3
Resources:
Abstract
2954 - Integrated data review evaluating safety, pharmacokinetics (PK) and immunogenicity of RM-1929 photoimmunotherapy (PIT) in subjects with locoregional, recurrent head and neck squamous cell carcinoma (rHNSCC).
Presenter: Jennifer Johnson
Session: Poster Display session 3
Resources:
Abstract
3629 - First line versus second line immunotherapy in recurrent/metastatic squamous cell carcinoma of the head and neck
Presenter: Caroline Even
Session: Poster Display session 3
Resources:
Abstract
767 - Sensitizing HRAS overexpressing head and neck squamous cell carcinoma (HNSCC) to chemotherapy
Presenter: Theodoros Rampias
Session: Poster Display session 3
Resources:
Abstract
4985 - A Single-Arm, Open-Label, Multicenter, Phase IIIb Clinical Trial with Nivolumab in Subjects with Recurrent or Metastatic Platinum-refractory Squamous Cell Carcinoma of the Head and Neck.
Presenter: Paolo Bossi
Session: Poster Display session 3
Resources:
Abstract
1564 - Long-term Results of Phase 2 Trial of Reduced Modified Clinical Target Volume in Low-risk Nasopharyngeal Carcinoma Treated with Intensity Modulated Radiotherapy
Presenter: Jingjing Miao
Session: Poster Display session 3
Resources:
Abstract
3356 - To compare two oral mucosa contouring methods in predicting acute oral mucocitis in nasopharyngeal carcinoma treated with helical tomotherapy
Presenter: Yuan-Yuan Chen
Session: Poster Display session 3
Resources:
Abstract
1984 - Induction chemotherapy (IC) followed by concurrent chemoradiotherapy (CCRT) in nasopharyngeal carcinoma (NPC)
Presenter: Gizem Kaval
Session: Poster Display session 3
Resources:
Abstract