RAISING is a high-performance method for identifying random transgene integration sites

• DOI: 10.1038/s42003-022-03467-w
• Publication Date: 2022-06-02T10:07:35Z
• Authors: Yusaku Wada; Tomoo Sato; Hiroo Hasegawa; Takahiro Matsudaira; Naganori Nao; Ariella L. G. Col...; Tomohiko Tasaka; Shunsuke Yamauchi; Tomohiro Okagawa; Haruka Momose; Michikazu Tanio; Madoka Kuramitsu; Daisuke Sasaki; Nariyoshi Matsumoto; Naoko Yagishita; Junji Yamauchi; Natsumi Araya; Kenichiro Tanabe; Makoto Yamagishi; Makoto Nakashima; Shingo Nakahata; Hidekatsu Iha; Masao Ogata; Masamichi Muramatsu; Yoshitaka Imaizumi; Kaoru Uchimaru; Yasushi Miyazaki; Satoru Konnai; Katsunori Yanagihara; Kazuhiro Morishita; Toshiki Watanabe; Yoshihisa Yamano; Masumichi Saito
• Keywords: Sanger sequencing

Abstract Both natural viral infections and therapeutic interventions using vectors pose significant risks of malignant transformation. Monitoring for clonal expansion infected cells is important detecting cancer. Here we developed a novel method tracking clonality via the detection transgene integration sites. RAISING (Rapid Amplification Integration Sites without Interference by Genomic DNA contamination) sensitive, inexpensive alternative to established methods. Its compatibility with Sanger sequencing combined our CLOVA (Clonality Value) software critical those access expensive high throughput sequencing. We analyzed samples from 688 individuals retrovirus HTLV-1, which causes adult T-cell leukemia/lymphoma (ATL) model method. defined value identifying ATL patients 100% sensitivity 94.8% specificity, longitudinal analysis also demonstrates usefulness risk assessment. Future studies will confirm broad applicability technology, especially in emerging gene therapy sector.