The study design aimed to identify candidate genetic variants associated to CM by comparing a group of CM patients with a group of severe malaria patients that did not exhibit CM.
Most of the variants seemed to have evolved from their antecedent temporal variants with a varying number of nucleotide changes, as illustrated by comparing variant 2004 to variant 2002.
For each of the two exomes, putative ENU mutations were identified by comparing variant calls from a mutant with variant calls from a control exome.
Efficacy of RIG was determined by comparing the variant calls produced by RIG from publicly available Arabidopsis WGS data against a collection of known variants from Sanger sequence data and variants present in the Gramene database (build 43; accessed January 2015) (Nordborg et al. 2005; Cao et al. 2011; Schmitz et al. 2013; Monaco et al. 2014).
For both MommeD12 and MommeD38, putative ENU-induced substitution or indel variants within the linked intervals were identified by comparing exome variant calls generated from the two mutant lines with control exomes.
Rather than predefining some specific set of annotations as informative about variant consequences, an alternative approach is to attempt to learn informative annotations, or combinations of annotations, by comparing known functional variants with variants for which there is no direct evidence of functional consequences.
The corresponding SNPs and insertion deletions (indels) were identified by comparing the resulting variant calls to the custom reference genome sequence using the Alpheus software [ 14] with the parameters: variant allele frequency ≥10%%, variant unique reads ≥2 and average base quality score ≥20 in the given accession, and either no variant allele or any allele present in the other accession(s).
By comparing the variants of these genes in the ancient skeletons with those in 60 modern-day Ukrainians, as well as a larger sample of 246 modern genomes from the surrounding region, the team found that the frequency of variants related to lighter skin and hair, as well as blue eyes, increased significantly between the ancient and modern populations.
Thus further knowledge about tumor-related mutations in PIK3CA might be gained by comparing those variants to orthologs in other species as well as paralogs of related kinases.
The lower AUC for SuRFR, however, is likely to represent the lowest estimate of SuRFR's performance, as by comparing regulatory variants with control variants matched by distance to TSS, we are effectively removing position from consideration.
