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The number of false-positive calls is also markedly reduced (>10-fold), and our panel design allows for distinction between true mutations and deamination artifacts.
With direct cloning it is impossible to distinguish between true mutations and mutations that occurred during replication of the plasmid.
With PCR amplification first, any errors that take place during the PCR will be included in the pool of cloned molecules, thereby making it impossible to distinguish between true mutations and PCR errors.
However, the strategies applied in these studies often included previous mapping of the mutation to a smaller genomic region and/or resequencing of large numbers of candidate mutations to distinguish between true mutations and sequence errors.
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Actually, the problem of discriminating between true mutations that have occurred during evolution and sequencing errors (in the reference sequence or in the new sequence data) is a challenging task.
During this experiment we detected both true mutations and mtDNA contamination.
Upon cloning, polymerase errors cannot be distinguished from true mutations and may give an overestimation of mutation load.
However, errors produced by most sequencing protocols complicate distinguishing between true biological mutations and technical artifacts that confound detection of rare mutations and rare individual genome variants.
The use of populations of mtDNA detects only high frequency variants within the population, while cloning makes it difficult to distinguish between mutations (hereafter, true mutations) in the starting genomes and those introduced during the construction and selection of clones.
The average between the true mutation proportions of each technical replicate was used to provide a rough estimation of the total number of each type of mutation.
We only counted frameshift mutations and nonsense mutations of ASXL1 gene as true mutations in this study as previously reported.
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