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To provide greater depth of insight into the operative mutational processes, we incorporated the sequence context in which mutations occurred, by considering the bases immediately 5′ and 3′ to each mutated base.
To provide further insight into the underlying mutational processes, we incorporated the sequence context in which mutations occurred by considering the bases immediately 5′ and 3′ to each mutated base, giving 96 possible trinucleotide contexts for a mutation.
We then examined the sequence context in which these mutations occurred by examining the bases immediately 5′ and 3′ to the mutated bases.
Most mutations occurred by passage 5 and all mutations were observed by passage 15.
The reversal of BRCA2-inactivating point mutations occurred by short deletions that are potentially fostered by BRCA2 dysfunction itself.
To see the effect of variation of mutation rates across samples, we change the sample ID in which mutations occurred by sampling a new sample ID under two different distributions namely, moderate sample variation and high sample variation.
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This possibly suggests a partial overlapping spectrum of genetic alteration underlying these different pancreatic cancer subtypes unless these are mutations occurring by chance.
The odds of 20 random identical mtDNA mutations occurring by chance in two separate tumors localized in the opposite lungs of the same patient were calculated as [ genome size)×(mutations)]×[ genome size)×(mutations)] i.e. [16,499∶1×20]×[16,499∶1×20] = 6.9×1010∶1 [27].
The trees are not expected to provide accurate renditions of the phylogenies as they are by necessity constrained by limitations imposed by the nature of the data (very short sequences, convergence in a scenario of emerging drug resistance, recombination, critical mutations occurring by insertion and deletion), and are based on thousands of short fragments with some experimental error.
Recent work has demonstrated that this class of mutations occurs by over-activation of the cytosine deaminase APOBEC3B [ 16, 17].
Tumorigenesis starts if inactivation of the second, normal PTCH allele by either loss-of-heterozygosity or point mutation occurs by chance in a single cell (two-hit mutagenesis).
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