Abstract 4149: Targeted RNA-Capseq provides new insight into clinical fusion detection
Authors: Jin Gu , Wang Chunyang , Zhang Xiaoyan , Yin Chunming , Yang Quanyu , Yang Jie , Wei Linlin , Zheng Qiaosong , Ma Tonghui , Li Tao 
Published: September 2020

Background: The precise genotyping-diagnosis of sarcomas, which is critical to clinical treatment and management, remains challenge due to the various types and overlapping morphologies of this cancer. Gene fusion is not only an important molecular biological characterization of sarcoma, but also a key and widely used diagnostic object. Yet, thus far, the conventional methods, e.g. FISH and RT-PCR, for detecting fusion genes in the clinic have some technical limitations. They lack multiplex capabilities and cannot be used for discovering novel fusions, while novel fusions can help for the precise classification of sarcoma. Therefore, it is urgent to develop more efficient methods, such as lncRNA-seq, to detect fusion genes in sarcoma patients. Here, we developed a RNA-Capseq panel that is more economical than lncRNA-seq and could exert its outstanding function in detecting various fusions, including novel fusions, in sarcomas.

Methods: We developed a RNA-Capseq panel targeting 395 cancer genes to detect gene fusions. Six cell lines (NCI-H2228, REH, THP1, N-A010, N-A057, N-A119) of lung cancer or hematological tumor with known fusion genes were subjected to the targeted RNA-Capseq panel. The FFPE samples from 10 patients with unknown type of sarcoma were assessed by the targeted RNA-Capseq panel and lncRNA-seq (as control method), and then verified by FISH. The paired frozen tissue of those patients were also evaluated synchronously.

Results: All well-known fusion landscapes in six tested cell lines, such as EML4-ALK, and SLC34A2-ROS1, were successfully recaptured by the targeted RNA-Capseq panel. Across the entire FFPE cohort, fusion genes were detected in 8 out of 10 (80%) patient samples by both the targeted RNA-Capseq panel and lncRNA-seq. Among them, PAX3-FOXO1, SS18-SSX1 and COL1A1-PDGFB were respectively identified in 1, 1 and 5 patients, all of which were successfully validated by FISH. These positive fusions were helpful in diagnosing their sarcoma patients, one case of rhabdomyosarcoma, one of synovial sarcoma, and five of dermatofibrosarcoma protuberans, which were consistent with the clinical pathological classification. Moreover, the targeted RNA-Capseq panel, as well as lncRNA-Seq, also identified two novel fusion genes ATIC-XRCC5 and ELN-MAGI2 that were not detected by FISH, but further verified in the paired frozen tissues. Compared with lncRNA-seq, it could pinpoint fusions under a relatively small amount of data, which makes it more affordable and accessible. It was also highly possible to identify fusions in case of low tumor purity or poor RNA quality. Conclusions:

Compared to FISH and RT-PCR, the 395-gene targeted RNA-Capseq panel can detect more fusion genes at one time and discover novel fusion subtypes. The 395-gene targeted RNA-Capseq panel is promising in the diagnosis of sarcoma patients in the clinic.

Citation Format: Gu Jin, Chunyang Wang, Xiaoyan Zhang, Chunming Yin, Quanyu Yang, Jie Yang, Linlin Wei, Qiaosong Zheng, Tonghui Ma, Tao Li. Targeted RNA-Capseq provides new insight into clinical fusion detection [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4149.