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On the basis of Tukey's model, we propose a novel but computationally simple generalized test of association that can simultaneously capture both the main effects of the variants within a genomic region and their interactions with the variants in another region or with an environmental exposure.
Sieh and Whittemore then created a statistical computer model using that data to calculate a woman's risk for breast cancer: however many cancer-related genes a woman has, multiplied by the effects of the variants.
The potential functional effects of the variants were predicted using Ensembl SNP Effect Predictor (http://www.ensembl.org/) and FastSNP [25].
The analysis of associations with quantitative traits was restricted to non-diabetics to avoid diabetes status or treatment masking potential effects of the variants on these phenotypic traits.
Third, we calculated the effects of the variants on TF motif prediction scores (JASPAR).
However, further studies will be needed to determine the functional effects of the variants.
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No functional effects of the variant have been reported.
If the effects of the variant are highly deleterious to carriers, or even lethal, the variant is purged from the population by strong purifying selection.
41 The upper right quadrant of figure 1 indicates those variants where all three in silico prediction tools are concordant in ascribing detrimental effects of the variant.
Effects of the variant CYP17 genotype on risk have been investigated in a number of studies, with some corroborative results and some conflicting results.
Finally, we tested the effect of the variants on SH2B1 enhancement of NGF-induced neurite outgrowth.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com