Revisions to the fission rate estimates made in Baker et al., Cell Reports, 2014
In this Jupyter Notebook we explore the effects of revisions to the ‘Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human Colon’ paper. In the manuscript, data from Formalin-Fixed Paraffin-Embedded (FFPE) samples, rather than the fresh-frozen tissue described in the manuscript, was mistakenly included. We have identified a mistake in the calculation of the correction factor for chance collision of independent CCO- clones. Further, in the original estimate of the fission rate from the patch size data, singleton crypts were omitted from the analysis to account for local spatial variations in the fission rate, but this was not reported. We explore differences in the estimates of the fission rate addressing these issues, and provide all the raw data to facilitate further analysis by others.
We show that the inclusion of the FFPE data does not significantly alter the mean fission rates of the patient cohort, whereas the revised correction significantly lowers the estimated mean fission rates (for normal patients the original estimate of the mean fission rate was 0.028 divisions/year/crypt, whilst the revised estimate for these patients is 0.009 divisions/year/crypt)