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The stark contrast between the mutations present and the mutations that physicians could respond to motivates a re-structure of the bioinformatics workflow that concentrates variants that lead to known clinical consequences.
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We first consider expanding the list of known variants by concentrating variant-discovery in cases.
In this study we concentrated on variants with a minor allele frequency >0.5 with the intention of studying common variants of this gene.
To efficiently identify those with significant biological functions, a practical strategy is to concentrate on variants located in important sequence regions such as gene regulatory regions.
Further it has been shown that non-coding variants concentrated around regions of the genome marked by DNase I hypersensitive sites (DHS) are enriched in traits [ 46].
Unlike previous studies that have concentrated on genetic variants that regulate multiple genes within a pathway (Stegle et al. 2012), we focus here on discovering associations between gene expression and age.
Additional work in this area concentrated on computing variants of edit distance either on whole sequences with tandem arrays or on two tandem arrays using different sets of evolutionary operations [ 12- 14].
Whereas somatic mutations impairing the activity of TP53 tend to accumulate in the DNA-binding domain and the tetramerization domain of the TF, tolerated germline variants concentrate in the N-terminal and C-terminal portions of the protein, outside its most important structural and functional features.
Initial computational analysis of exome sequence data concentrated on filtering variants according to their population frequency, predicted pathogenicity and the presence of rare predicted-pathogenic mutations in multiple unrelated individuals with a certain rare disease ('intersection' strategy; Boycott et al., 2013; Robinson et al., 2011).
When the detection of variants is concentrated among cases, it is not valid to compare the resulting counts to those obtained by probing only for those same alleles among controls.
Due to the small population of the study, we concentrated on common allele variants, and for that reason SNPs with a reported Caucasian minor allele frequency (MAF) of <5% were excluded, and only SNPs in the HapMap were investigated.
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