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For example, in 1 article, no mutations were found in the frequently mutated region of TP53 (exons 4 to 9), but the 3 analyzed cases (2 YSTs and 1 IT) contained less than 10%TP53-positiveTP53-positive.
Another frequently mutated region of Merlin is in α1CTD, where 8 missense mutations have been identified.
Furthermore, sequencing across the mutated region of genomic DNA derived from SW480 cells revealed that the expected mutation was present (data not shown)).
We have now designed five different PTM constructs targeted to the mutated region of zebrafish nebulin.
Comparison of the mutated region of the UN-7 and PNG-1 protein sequence with the same region from other filamentous fungi shows the strong conservation of the mutated residues in other organisms.
The mutated region of the DN-hTERT is conserved in zebrafish TERT (Figure S1), and we therefore generated a DN zTERT accordingly (catalytically inactive zTERT; CD-zTERT) by substituting the aspartic acid and valine residues at positions 682 and 683 with alanine and isoleucine residues, respectively.
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Observable levels of private mutations are likely to be deceptively low, especially in vivo, as two mitigating processes occur: viruses that accrue substantial mutational burdens are defective and are lost from the population, and recombination can act to preserve the population for at least a time by recombining non-lethally mutated regions of viral genomes.
The iterative remapping stage uses successively identified high confidence variant sequences as additional reference allele fragments to enhance alignment of reads to highly mutated regions of the genome.
10.7554/eLife.04531.009 Figure 2. Codon pair scores and numbers of CpG and UpA dinucleotides in native (WT) and mutated regions of E7.
Sequence a random set of plasmids in the mutated region to rule out sequence bias.
Our Deep-Drilling with iterative Mapping (DDiMAP) method retains variant allele patterns to aid in single nucleotide variation detection and generation of additional reference alleles, with remapping increasing coverage of highly mutated regions to capture data critical to heterogeneity analysis and enhancing sensitivity.
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