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Reconstruction of MC1R evolution over the molecular phylogeny in PAML shows that these mutations were derived in terminal lineages.
Distinct from the previous cases, these mutations were derived from a population-based study of EC and CRC patients whose tumours showed MSI, the main hallmark of HNPCC.
Mouse fibroblasts carrying pathogenic mtDNA mutations were derived from the mouse L929 cell line, which has fixed several mutations over long-term culture.
MSH6 missense mutations were derived from a project comprising altogether 2000 colorectal and EC cases newly diagnosed in the main hospitals of the Columbus metropolitan area in central Ohio (population 1.5 million).
However, 32 of these mutations were derived from one case with closely spaced germline alleles that did not allow us to distinguish between a −1 or +1 repeat unit mutation and hence were scored as 'other' mutations.
It was unfortunately not possible to pool our data with nucleotide mutation frequency data obtained in various other published evolution experiments, where either input virus sequences were unknown and mutation counts were inferred by maximum likelihood or parsimony based approaches [ 17, 18, 28], or where observed mutations were derived only from small portions of the virus genome [ 66].
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U2OS HIF-1α (344–826 V5) also with N416R, M561A and M568A mutations was derived and cultured using described protocols [ 12].
When data on APC and K-ras mutations are derived from the study by Smith et al. [ 9], similar results, although not statistically significant, could be obtained.
The number of possible synonymous and non-synonymous mutations was derived by examining the longest annotated coding transcript per gene (transcript length based upon Ensembl Biomart described above).
Interestingly, though the writing of mutations was derived independently from the same fact, we can now see that it helps us understand the physical basis of convergence.
pL101Btrp, used to screen for termination-altering mutations, was derived from pL101 [a gift from Linda Hyman, Tulane University (Hyman et al. 1991)].
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