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Updated: Feb 18, 2026

Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9
Published on: January 3, 2015
The independent loss model with ordered insertions for the evolution of CRISPR spacers
F Baumdicker1, A M I Huebner1, P Pfaffelhuber1
1Department of Mathematical Stochastics, Albert-Ludwigs-University of Freiburg, Germany.
Abstract:
Today, the CRISPR (clustered regularly interspaced short palindromic repeats) region within bacterial and archaeal genomes is known to encode an adaptive immune system. We rely on previous results on the evolution of the CRISPR arrays, which led to the ordered independent loss model, introduced by Kupczok and Bollback (2013). When focusing on the spacers (between the repeats), new elements enter a CRISPR array at rate θ at the leader end of the array, while all spacers present are lost at rate ρ along the phylogeny relating the sample. Within this model, we compute the distribution of distances of spacers which are present in all arrays in a sample of size n. We use these results to estimate the loss rate ρ from spacer array data for n=2 and n=3.
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