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Although the procedure is conceptually simple, technical difficulties arise due to inhomogeneous samples, existence of competing subclonal populations, and systematic and non-systematic errors introduced by the sequencing technologies.
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One explanation for this could be tumor heterogeneity, which would render mutations present in small subset of cells undetectable by the sequencing technology used.
To exclude false positives introduced by the sequencing technology or the mapping algorithm used, results were confirmed with Sanger sequencing.
Apart from the aforementioned problems, the analysis of metagenomic data sets can also be influenced by the sequencing technology used.
This specifies relative abundance of each gene variation between RNA samples and also measurement error estimated by the sequencing technology.
Also we demonstrated in the Pacific Biosciences experiments that the choice of assembly method should be informed by the sequencing technology and desired result.
Technical replicates from the same library are typically not necessary, due to the high technical reproducibility achieved by the sequencing technology [ 17].
Although the output created by this tool is now valid, if the user has selected the wrong presumed input variant, it is possible for the resultant score values not to reflect the values intended by the sequencing technology.
We use high credibility intervals derived from that distribution to decide between the competing variant present/absent hypotheses and distinguish alleles existing in the sample from variants introduced as artifacts by the sequencing technology.
Based on these considerations we can assume that our results should not be affected too much by problems with the sequencing technology.
However, the mutation detection levels are limited by the error rate of the sequencing technology as well as by the availability of variant-calling algorithms with high statistical power and low false positive rates.
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