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These relevant features are gene essentiality score (GARP score), mRNA expression intensity (RMA score), DNA copy number, mutation occurrence and closeness centrality in the PPI network.
STATA Version 8.2 (Stata Corp., College Station, TX) was used to analyze estimates of the effect of prophylaxis on mutation occurrence and estimates of the effect of mutation on treatment outcome.
We compared our results with those of [ 25], leading to conclusions very similar to theirs: very slight influence of marker density on the mapping accuracy, mapping accuracy increasing with sample size, QTL effect, number of generations since mutation occurrence, and effective size.
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For example, the Bateman-Mukai technique assumes a Poisson distribution of mutation occurrence in the genome, and that mutations at different loci underlying the trait are in gamatic phase equilibrium.
The highest scoring features are GARP score for gene essentiality, RMA intensity for mRNA expression, row chromosomal copy number for DNA copy number, mutation occurrence for somatic mutation pattern and closeness centrality for network-topological property.
Importantly, differences have been found in the specific TP53 mutation occurrence in breast cancer types and grades, as well as in the survival of patients bearing particular hotspot mutations (discussed in part IV).
The area of mutation occurrence is restricted mainly to Europe and parts of Asia.
The CAI values were used to calculate the difference before and after the mutation occurrence as follows: ΔCAI of a given synonymous mutation equals CAI value after the synonymous mutational event minus the CAI value before the mutation occurred.
However, these parameters are poorly known, in large part because of the difficulty of designing and interpreting experiments to examine the rare and intrinsically stochastic process of mutation occurrence.
ORFs of 341 pF1K clones were PCR-cloned using PrimeStar HS or KOD plus high-fidelity DNA polymerases, as described in Section 2. All ORF clones obtained by PCR cloning were sequence-verified and we found that the PCR mutation occurrence rate was less than 5 × 10−5 mutations per residue under the conditions employed in this study.
However, mechanisms of mutation occurrence may not be as straightforward as we have wished, and the results of in-depth analyses suggested a possibility of Lamarckian contributions [66 73].
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