Author: James T. Van Leuven; Martina M. Ederer; Katelyn Burleigh; LuAnn Scott; Randall A. Hughes; Vlad Codrea; Andrew D. Ellington; Holly Wichman; Craig Miller
Title: FX174 Attenuation by Whole Genome Codon Deoptimization Document date: 2020_2_11
ID: mpb4fy16_20
Snippet: Ultimately, our goal was to correlate changes in genomic properties ( e.g. codon preference) to changes in viral fitness. The most straightforward method of analysis would be to regress the two measurements, and indeed the fitness of deoptimized variants was linearly correlated to CAI (R 2 =0.36, p=2E-16, fig. 6a ). However, it is worth noting that the data points used in this regression were not independent because the deoptimized fragments were.....
Document: Ultimately, our goal was to correlate changes in genomic properties ( e.g. codon preference) to changes in viral fitness. The most straightforward method of analysis would be to regress the two measurements, and indeed the fitness of deoptimized variants was linearly correlated to CAI (R 2 =0.36, p=2E-16, fig. 6a ). However, it is worth noting that the data points used in this regression were not independent because the deoptimized fragments were combined to achieve higher levels of deoptimization. Our combinometic method of making variants also allowed us to correct for the cumulative fitness effect of combined fragments by The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.10.942847 doi: bioRxiv preprint fitness effect of about -2. This background subtraction approach corrected for the non-independence of data points in regressions between change in fitness from WT and change in CAI from WT.
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