Chapter 13 - CometChip: Single-Cell Microarray for High-Throughput Detection of DNA Damage

DNA damage promotes cancer, and ironically, at high doses DNA damaging agents are also often used to treat cancer. Despite its importance, most assays for DNA damage are very low throughput, as little has been done to introduce engineering principles. Here, we present a novel platform for high throughput analysis of DNA damage in human cells. Based upon the well-established single cell gel electrophoresis assay (a.k.a. the comet assay), the Comet Chip enables robust, high throughput and objective DNA damage quantification. Single cells are captured by gravity into an agarose microwell array. Arrayed cells can then be directly assayed, or challenged with exposure to DNA damaging agents prior to analysis. The microarray maximizes real estate and normalizes distribution, enabling analysis of 96 samples of widely varying cell concentrations to be processed in parallel. The platform is compatible with both the alkaline conditions (detecting single strand breaks, abasic sites and alkali sensitive sites) and neutral conditions (detecting double strand breaks). Analysis of 96 samples in parallel greatly reduces sample-to-sample variation and can be completed in one day. Through integration of biological and engineering principles, the Comet Chip provides the necessary throughput and sensitivity for a wide variety of applications in epidemiological studies, in the clinic and in drug development.