A new Standard DNA damage (SDD) data format

• Published in: arXiv.org 2022-01
• Main Authors: Schuemann, J, McNamara, A, Warmenhoven, J W, Henthorn, N T, Kirkby, K, Merchant, M J, Ingram, S, Paganetti, H, Held, K D, Ramos-Mendez, J, Faddegon, B, Perl, J, Goodhead, D, Plante, I, Rabus, H, Nettelbeck, H, Friedland, W, Kundrat, P, Ottolenghi, A, Baiocco, G, Barbieri, S, Dingfelder, M, Incerti, S, Villagrasa, C, Bueno, M, Bernal, M A, Guatelli, S, Sakata, D, Brown, J M C, Francis, Z, Kyriakou, I, Lampe, N, Ballarini, F, Ca-rante, M P, Davidkova, M, Štepán, V, Jia, X, Cucinotta, F A, Schulte, R, Stewart, R, Carlson, D, Galer, S, Kuncic, Z, LaCombe, S, Milligan, J, Cho, S H, Inaniwa, T, Sato, T, Durante, M, Prise, K, McMahon, S J
• Format: Article
• Language: English
• Subjects: Biological effects; Biological models (mathematics); Chains; Chemical reactions; Damage assessment; Damage patterns; DNA damage; DNA repair; Format; Modelling; Radiation; Radiation damage; Radiation effects; Repair; Simulation; Standard data
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.2201.11849

Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular components to form observable endpoints. One hurdle is the difficulty faced by members of different research groups in directly comparing results. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modelling chain. The modelling chain typically consists of track structure Monte Carlo simulations of the physics interactions creating direct damages to the DNA; followed by simulations of the production and initial reactions of chemical species causing indirect damages. After the DNA damage induction, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. We propose a new Standard data format for DNA Damage to unify the interface between the simulation of damage induction and the biological modelling of cell repair processes. Such a standard greatly facilitates inter model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation induced DNA damage and the resulting observable biological effects.