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Updated: Sep 21, 2025

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

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Published on: June 14, 2017

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

Yusaku Wada¹, Tomoo Sato^2,3, Hiroo Hasegawa^4,5

¹Biotechnological Research Support Division, FASMAC Co., Ltd, Atsugi, Kanagawa, 243-0021, Japan.

Communications Biology

|June 2, 2022

Summary

A new method, RAISING, tracks cancer development by detecting viral DNA integration sites. This inexpensive technique accurately identifies adult T-cell leukemia/lymphoma (ATL) and aids in risk assessment.

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Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Area of Science:

Virology
Oncology
Molecular Biology

Background:

Viral infections and gene therapies carry risks of malignant transformation.
Monitoring infected cell clonal expansion is crucial for early cancer detection.

Purpose of the Study:

To develop a novel, sensitive, and inexpensive method for tracking cellular clonality by detecting transgene integration sites.
To assess the utility of this method in identifying adult T-cell leukemia/lymphoma (ATL) and evaluating ATL risk.

Main Methods:

Developed RAISING (Rapid Amplification of Integration Sites without Interference by Genomic DNA contamination) for detecting transgene integration sites.
Utilized Sanger sequencing and CLOVA (Clonality Value) software for analysis.
Analyzed samples from 688 individuals infected with HTLV-1.

Main Results:

The RAISING method demonstrated high sensitivity and specificity in identifying ATL patients.
A defined clonality value achieved 100% sensitivity and 94.8% specificity for ATL detection.
Longitudinal analysis confirmed the method's utility in ATL risk assessment.

Conclusions:

RAISING offers a cost-effective and sensitive alternative for tracking clonality, particularly for researchers without access to high-throughput sequencing.
The method shows significant promise for early cancer detection and risk assessment in viral infections and gene therapy.
Further studies are warranted to confirm the broad applicability of RAISING in gene therapy and other fields.