By assuming that the vast majority of observed mutations were single nucleotide changes within a codon, each mutation was assigned to the NS (nonsynonymous) or S (synonymous) class of mutations, and the average z-score of each class was computed for every codon.
Thus, The PSS feature value for a missense mutation is assigned as the 436-dimension vector.
Depending on the banding pattern, the mutation is assigned to one of the four individual DNAs.
The SSM feature value for a missense mutation is assigned as the element (i, j) of scoring mutation matrix.
Because the assignment of genes to mutations is done based on co-occurrences, sometimes a mutation is assigned to several genes.
The entire mtDNA sequence of the Chinese proband carrying the 4435A>G mutation was assigned to an Asian mitochondrial haplogroup by using the nomenclature of mitochondrial haplogroups.
GEMA_r01.java has several advanced features already build in including the availability of multiple environment option where each mutation is assigned a selection coefficient vector with coordinates representing scalar s values specific for each environment.
Another case with an FLT3 mutation was assigned to early T-ALL, but the immunophenotype did not fulfil the criteria of an ETP-ALL due to a weak CD8 expression.
Second, each slc mutation was assigned to one chromosome by cosegregation analyses (Anders et al. 2008), further refining the number of candidate SNPs to 3 ± 2 per mutant genome.
A0 is binary: if any mutation occurs in a given gene in a particular sample or if the given gene is in a statistically significant variation region of the particular sample, which is determined by GISTIC [ 50], then the mutation is assigned the number 1; if these criteria are not met then 0 is assigned.
