NSF Award
9904842
Algorithms for Computing Chromosome Aberration Frequencies.<br/><br/><br/>This project will develop computer algorithms for analyzing chromosome aberrations produced by ionizing radiation during the G1 phase of the cell cycle. Such aberrations are rearrangements of chromosomes, caused by interactions of DNA double strand breaks (DSBs). They are informative about radiation damage pathways as modulated by DNA repair and misrepair, and about chromatin structure at large scales, up to the full size of a mammalian chromosome. Their importance is in fact interdisciplinary, bridging the fields of radiobiology and cytogenetics, with information valuable for biodosimetry, risk estimation, chromosome structure, and the understanding of radiation-induced cell killing.<br/><br/>A very rich, colorful variety of chromosome aberrations can be observed using chromosome painting (fluorescent in situ hybridization -- i.e. FISH), which has revolutionized aberration work. Often current experimental results are so complex. involving dozens of different aberration categories, that mathematical analysis and computer calculations are essential for interpreting the data. The present project has two aims. The first aim is to analyze quantitatively the recombinational repair ("one-hit") molecular model of aberration formation. In contrast to older (breakage-and-rejoining or Revell) models, the recombinational repair model considers that radiation-produced DSBs lead to additional, enzymatically -produced breaks. If correct, the model has important implications for almost all areas of radiobiology.<br/><br/>Preliminary studies by the PI suggest that the model may be contradicted by current FISH data sets because the predicted frequency of visibly complex chromosome aberrations appears to exceed that observed. To be decisive the analysis needs more quantitative detail, obtainable only by Monte Carlo simulations. The project will develop the Monte Carlo algorithms, test the recombinational repair model with recent FISH data, and compare it to the breakage-and-rejoining model, which has hitherto been found generally consistent with experiments. In addition to a plethora of data for human cells, data on other genomes are now available and will be included to get a broad spectrum of comparative radisosensitivities, taking advantage of the fact that the aberration simulation software uses just two adjustable parameters (the number of reactive DSBs per unit dose per unit genomic size, and the number of DSB interaction sites), which can be compared meaningfully among different genomes.<br/><br/>The second project aim is to incorporate recent pulsed-field gel electrophoresis data on DSB clustering along chromatin, and related computations, into algorithms for estimating the formation probabilities of various intrachanges (i.e. 1-chromosome aberrations). Previous studies have indicated that radiation-produced intrachanges are unexpectedly frequent and are biologically important. Clustering of DSBs along chromatin has a strong influence on intrachanges, which can be estimated quantitatively by appropriate equations and simulations. Under this aim aberration data, and also published mutation data dealing mainly with radiation-produced large deletions, will be compared to estimates obtained from the intrachange algorithms developed.<br/><br/>The proposed data analysis tools are comparatively inexpensive. They can supply much-needed coherence to aberration data, interrelate different empirical assays, and will help guide new experiments or critical rexaminations of extant data sets in laboratories world-wide.
