Detection and quantification of DNA double-strand breaks by genomic and imaging methods: a critical appraisal of capabilities and limitations

Abstract

DNA double-strand breaks (DSBs) are the most genotoxic form of DNA damage. Unrepaired DSBs may cause loss of chromosome fragments at mitosis, while incorrectly repaired DSBs can cause chromosome aberrations and other adverse effects, leading to cell cycle arrest, senescence, cell death, or neoplastic transformation. Detecting and quantifying DSBs is important in studies of genome instability, aging, and cancer. Methods of detecting and quantifying DSBs fall into two broad categories: imaging-based methods, used to detect and localize DNA breaks in individual cells, and genomic methods, a new category utilizing massively parallel DNA sequencing to map DSBs genome-wide in a cell population. Imaging and genomic methods yield fundamentally different information. This review focuses on a critical evaluation of the capabilities and limitations of genomic and imaging methods for the detection and quantification of DSBs. It explains why the class of genomic methods, where quantification is based on counting the detected unique DSBs and the number of cells in the sample, results in inaccurate assessment of the average number of DSBs per cell and how this problem can be solved. We also discuss complementarity of genomic and imaging methods and potential directions of their future development.