Varanto: variant enrichment analysis and annotation.

SUMMARY: Genome-wide association studies (GWAS) aim to identify associations of genetic variations such as single-nucleotide polymorphisms (SNPs) to a specific trait or a disease. Identifying common themes such as pathways, biological processes and diseases associations is needed to further explore and interpret these results. Varanto is a novel web tool for annotating, visualizing and analyzing human genetic variations using diverse data sources. Varanto can be used to query a set of input variations, retrieve their associated variation and gene level annotations, perform annotation enrichment analysis and visualize the results. AVAILABILITY AND IMPLEMENTATION: Varanto web app is developed with R and implemented as Shiny app with PostgreSQL database and is freely available at http://bioinformatics.uef.fi/varanto. Source code for the tool is available at https://github.com/oqe/varanto. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Metabolic Profiling of High Egg Consumption and the Associated Lower Risk of Type 2 Diabetes in Middle-Aged Finnish Men.

SCOPE: Higher egg intake was previously associated with a lower risk of developing type 2 diabetes (T2D) in the prospective, population-based Kuopio Ischaemic Heart Disease Risk Factor Study (KIHD) in eastern Finland. Potential compounds that can explain this association are explored using nontargeted LC-MS-based metabolic profiling. METHODS AND RESULTS: Two hundred and thirty-nine baseline serum samples from the KIHD are analyzed in four groups: subjects with higher (mean intake one egg per day) or lower (mean intake two eggs per week) egg intake who developed T2D (cases) or remained heatlhy (controls) during the mean follow-up of 19.3 years. Different serum profiles of subjects who had either higher or lower egg intakes, and of those who developed type 2 diabetes or remained healthy, are observed. The higher baseline tyrosine level predicts higher odds of T2D (OR 1.94; 95% CI 1.45, 2.60; p < 0.001; FDR 0.023) along with an unknown hexose-containing compound (OR 2.13; 95% CI 1.57, 2.88; p < 0.001; FDR 0.005). Certain predominant metabolites in T2D cases are correlated positively with ones in the lower-egg-intake group and negatively with ones in the higher-egg-intake group. CONCLUSION: Our current findings may underline some potential metabolites that can explain how egg intake is associated with a lower risk of T2D.