PT - JOURNAL ARTICLE AU - Julian Hecker AU - Anna Maaser AU - Dmitry Prokopenko AU - Heide Loehlein Fier AU - Christoph Lange TI - Reporting correct p-values in VEGAS analyses AID - 10.1101/101014 DP - 2017 Jan 01 TA - bioRxiv PG - 101014 4099 - http://biorxiv.org/content/early/2017/01/18/101014.short 4100 - http://biorxiv.org/content/early/2017/01/18/101014.full AB - VEGAS (versatile gene-based association study) is a popular methodological framework to perform gene-based tests based on summary statistics from single-variant analyses. The approach incorporates linkage disequilibrium information from reference panels to account for the correlation of test statistics. The gene-based test can utilize three different types of tests. In 2015, the improved framework VEGAS2, using more detailed reference panels, was published. Both versions provide user-friendly web- and offline-based tools for the analysis. However, the implementation of the popular top-percentage test is erroneous in both versions. The p-values provided by VEGAS2 are deflated/anti-conservative. Based on real data examples, we demonstrate that this can increase substantially the rate of false positive findings and can lead to inconsistencies between different test options. We also provide code that allows the user of VEGAS to compute correct p-values.