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Plasma Fluorescence Scanning and Fecal Porphyrin Analysis for the Diagnosis of Variegate Porphyria: Precise Determination of Sensitivity and Specificity with Detection of Protoporphyrinogen Oxidase Mutations as a Reference Standard.
First, our analysis validated the use of the disease-causing mutations as a reference for functionality as approximately 92% of these mutations not only passed the functionality threshold of SIFT and had a high Conservation Index (8.4 ± 1.8) but also passed at least one additional test either MutPred or Panther (fig. 1 C).
Except lin(bh25) and unc sy5415), all other loci were uniquely assigned to linkage groups by standard 2-factor mapping using known mutations that serve as reference (Table 6, also see [ 21]).
Mutation frequencies, as well as z-scores when a reference set is available, can be exported to text files for further analysis in other programs.
Variant annotation was performed using ANNOVAR [ 21] to remove synonymous mutations and RefSeq genes used as reference to coordinate the mutations.
For the unpolarized MK data, the estimate of the proportion of amino acid substitutions fixed by positive selection is calculated using synonymous mutations as a neutral reference class, following Fay et al. (2002) and excluding singletons.
When using infections with a double mutation in the dhfr gene as reference group, we did not observe any association between the presence of additional mutations in the dhfr or dhps genes and the prevalence or density of submicroscopic gametocytes.
The reference to ?the improbability of random mutation as a driving factor in genetic change? is a stock creationist canard contravened by decades of scientific research.
Firstly, the coordinates of mutations on reference genes (such as NM_012469, c.2185C>T) were converted to the corresponding coordinates on human reference genome hg19 (UCSC, such as chr20 62658491), whose genomic coordinates were retrieved by UCSC Genome Browser (22).
Mutation analysis is often used as reference to evaluate other criteria due to the high quality of its results in spite of its higher costs [22, 32].
