Reporting Correct p Values in VEGAS Analyses. (27th March 2017)

• Record Type: Journal Article
• Authors: Hecker, Julian; Maaser, Anna; Prokopenko, Dmitry; Fier, Heide Loehlein; Lange, Christoph
• Is Part Of: Twin research and human genetics. Volume 20:Number 3(2017)
• Page Start: 257
• Page End: 259
• Publication Date: 2017-03-27
• Subjects: VEGAS, -- VEGAS2, -- gene-based test, -- p values; Twins -- Periodicals; Multiple birth -- Periodicals; 618.25
• DOI: 10.1017/thg.2017.16
• Languages: English
• ISSNs: 1832-4274

Abstract

Abstract : 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.