In contrast to the 1000 genomes project, the genotype calls from the 5000 exomes project were publicly available only in a collapsed form as genotype frequencies for European Americans and African Americans and not as separate variant sets for each sample.
Thus, there is evidence for three independent variants in SLC2A9 that influence urate levels in Europeans and for a separate variant in East Asians.
Here, the performance of the model was tracked by systematically varying the threshold for separating variants from invariants from 0 to 1 in increments of 0.01.
In addition, no significant difference could be found between the cases and controls for any of the four separate variants (Table 5).
For example, if a GWAS analysis deals sequentially with one million separate variant-disease associations, it is perfectly acceptable to model one of those associations in isolation.
For example, the alternative splicing of Fibulin-1 transcripts results in four separate variants termed -1A to -1D, which differ at the C-terminus of the protein.
PhyloWGS separates variants into simple somatic mutations (SSMs) and copy number variations (CNVs).
Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL.
A prior odds and SIFT model contains only prior odds of genes, SIFT effect and a separate intercept for each variant class.
For comparison against existing methods we also quantified the performance of SIFT on the same data set, with or without gene-specific priors: A prior odds and SIFT model contains only prior odds of genes, SIFT effect and a separate intercept for each variant class.
