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The researchers found that they could detect even slight genetic changes, charting a two- to threefold increase in mutations at low exposures to ENU.
However, most infants with wild-type HIV had persistent NVP-R mutations at low frequencies (86%; median clonal frequency of 3.1%; range 1.2%–12.8%), with similar rates and mutation patterns for both intervention groups (Table 4).
Regardless of the list that is used to define mutations associated with transmitted resistance, the occurrence of polymorphic resistance-related mutations at low levels among some sequences studied is highly probable.
They found evidence of natural occurrence of all four resistance mutations at low levels and the cut-off values for detection of high-confidence minority resistance mutations (transmitted or acquired) were determined to be 0.5%, 1.0%, 1.0% and 0.7%, respectively.
The ability to detect mutations at low fractions is largely affected by the quality of FFPE samples.
Clonal heterogeneity may be a feature of DCLK1, as we and others [ 25, 50] observed mutations at low allelic fractions.
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The resulting higher accurate detection of somatic mutations at low-allelic fraction increases utility in cancer molecular diagnostics.
Here, we present Mutascope, a software dedicated to the detection of mutations at low-allelic fraction from amplicon sequencing of matched tumor-normal samples pairs.
When applied to the mutations at low-allelic fraction in the MIX samples, these filters increase the sensitivity and positive predictive value (Fig. 1f and Supplementary Discussion).
The classification of the 162 somatic mutations at low-allelic fraction (0.01 0.1) by Mutascope was more accurate than other standard tools (area under the curve: 0.97— Fig. 1c).
It is often difficult to distinguish driver mutations from passenger mutations when the mutations occur at low frequency.
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