Speaker
Description
Proton therapy for cancer treatment is a rapidly growing field as increasing evidence suggests it induces more complex damage in DNA than photons [1]. Accurate comparison between the two requires quantification of the damage caused, one method being the comet assay [2]. The program discussed here, based on neural network architecture, aims to speed up analysis of comet assay images and provide accurate assessment of the DNA damage levels apparent in them.
The comet assay is an established technique in which DNA strand breaks are spread out via an electric field, creating a comet-like object. The elongation and intensity of the comet tail indicate the level of damage incurred. Many methods to measure damage exist, from “by eye” ranking systems to computer software, which can be time consuming [2]. They result in analysing only a small fraction of images, which is a problem addressed by this program.
The neural network performs object detection and localisation using instance segmentation. Rather than extracting features to distinguish if and where an object is, instance segmentation incorporates the bounding-box method with pixel-wise classification, aiming to sort pixels into one of two classes: comet or background. The identified comet instances are then saved as masks, with a minimum identification accuracy of 90%. The purpose is to provide accurate comet detection in order to perform measurements of the comet tail length and tail DNA fraction, some common features used to measure DNA damage following a comet assay [3].
Further, modelling of the comet assay process is underway to provide a better understanding of the relationship between the assay images and the underlying level of DNA damage.
References
[1] Swati Girdhani, Rainer Sachs, and Lynn Hlatky. “Biological Effects of Proton Radiation: What We Know
and Don’t Know”. In: Radiation Research 179.3 (2013). PMID: 23373900, pp. 257–272. doi:10.1667/RR2839.1. Eprint: https://doi.org/10.1667/RR2839.1. url:https://doi.org/10.1667/RR2839.1
[2] Andrew R. Collins. “The comet assay for DNA damage and repair”. In: Molecular Biotechnology 26.3 (Apr. 2004), p. 249. issn: 1559-0305. doi:10.1385/MB:26:3:249.
[3] T. S. Kumaravel et al. “Comet Assay measurements: a perspective”. In: Cell Biology and Toxicology 25.1 (Feb. 2009), pp. 53–64. issn: 1573-6822.doi: 10.1007/s10565-007-9043-9. url:https://doi.org/10.1007/s10565-007-9043-9
