RAISING is a high-performance method for identifying random transgene integration sites.
Yusaku WadaTomoo SatoHiroo HasegawaTakahiro MatsudairaNaganori NaoAriella L G Coler-ReillyTomohiko TasakaShunsuke YamauchiTomohiro OkagawaHaruka MomoseMichikazu TanioMadoka KuramitsuDaisuke SasakiNariyoshi MatsumotoNaoko YagishitaJunji YamauchiNatsumi ArayaKenichiro TanabeMakoto YamagishiMakoto NakashimaShingo NakahataHidekatsu IhaMasao OgataMasamichi MuramatsuYoshitaka ImaizumiKaoru UchimaruYasushi MiyazakiSatoru KonnaiKatsunori YanagiharaKazuhiro MorishitaToshiki WatanabeYoshihisa YamanoMasumichi SaitoPublished in: Communications biology (2022)
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 method. We defined a clonality value identifying ATL patients with 100% sensitivity and 94.8% specificity, and our longitudinal analysis also demonstrates the usefulness of ATL risk assessment. Future studies will confirm the broad applicability of our technology, especially in the emerging gene therapy sector.
Keyphrases
- gene therapy
- risk assessment
- human health
- high throughput sequencing
- sars cov
- induced apoptosis
- loop mediated isothermal amplification
- papillary thyroid
- bone marrow
- acute myeloid leukemia
- drinking water
- nucleic acid
- copy number
- cross sectional
- label free
- childhood cancer
- single molecule
- current status
- gene expression
- squamous cell
- case control
- lymph node metastasis
- pi k akt