biostudies-literatureWada YMEXT | Japan Society for the Promotion of ScienceNIAMS NIH HHS535https://www.ebi.ac.uk/biostudies/studies/S-EPMC9163355biostudies-literatureUnknown5(1)Both natural viral infections and therapeutic interventions using viral vectors pose significant risks of malignant transformation. Monitoring for clonal expansion of infected cells is important for detecting cancer. Here we developed a novel method of tracking clonality via the detection of transgene integration sites. RAISING (Rapid Amplification of Integration Sites without Interference by Genomic DNA contamination) is a sensitive, inexpensive alternative to established methods. Its compatibility with Sanger sequencing combined with our CLOVA (Clonality Value) software is critical for those without access to expensive high throughput sequencing. We analyzed samples from 688 individuals infected with the retrovirus HTLV-1, which causes adult T-cell leukemia/lymphoma (ATL) to model our meCommunications biologyRAISING is a high-performance method for identifying random transgene integration sites.PMC9163355T32 AR060719JP 17H03594JP 16H06277 CoBiATasaka TTanio MMiyazaki YSaito MNao NHasegawa HMuramatsu MYagishita NWada YImaizumi YYamagishi MIha HOgata MNakashima MYanagihara KYamauchi SKonnai SWatanabe TKuramitsu MYamauchi JAraya NMorishita KNakahata SSato TColer-Reilly ALGOkagawa TTanabe KYamano YMatsudaira TSasaki DMomose HMatsumoto NUchimaru KfalseRAISING is a high-performance method for identifying random transgene integration sites.Both natural viral infections and therapeutic interventions using viral vectors pose significant risks of malignant transformation. Monitoring for clonal expansion of infected cells is important for detecting cancer. Here we developed a novel method of tracking clonality via the detection of transgene integration sites. RAISING (Rapid Amplification of Integration Sites without Interference by Genomic DNA contamination) is a sensitive, inexpensive alternative to established methods. Its compatibility with Sanger sequencing combined with our CLOVA (Clonality Value) software is critical for those without access to expensive high throughput sequencing. We analyzed samples from 688 individuals infected with the retrovirus HTLV-1, which causes adult T-cell leukemia/lymphoma (ATL) to model our me2022-01-01T00:00:00Z2022 Jun2025-05-29T22:27:18.348Z2024-11-09T13:59:59.146ZS-EPMC91633553565494610.1038/s42003-022-03467-w