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Seven mutations were missing in SIFT prediction for BS292.
We examined the approximate ancestry graph for this sample (Supplementary Fig. A7) to determine why other mutations were missing from the tree output by AncesTree.
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As expected, many single nucleotide mutations were missed in aCGH.
By using in silico phylogenetic approaches, they found that on average at least five mutations were missed per sample.
On the other hand, it cannot completely be excluded that the causal mutations were missed by sequencing and are still presented in targeted regions.
However, since the DHPLC mutation detection rate is not 100% for each gene, it cannot be ruled out that some mutations were missed.
However, the two additional steps detected only seven mutations, and it is therefore likely that no more than one or two mutations were missed.
The difficulty of interpreting this is compounded by the real possibility that driver mutations were missed or misclassified as passengers because of their rarity.
Recall as a measure how many sequenced mutations were missed in the aCGH analysis was defined as the number of mutations that were found by both approaches divided by the total number of mutations in aCGH.
Our analysis of position-dependency yielded similar results than [ 32, 33], albeit a number of mutations were missed even though there were probes with a mutation in their middle region in aCGH.
Imputation reduces the amount of sequencing and data storage required, though the study found that fewer null mutations were detected in the imputed data set suggesting that some mutations were missed in these individuals.
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