Related Experiment Video
Updated: Jul 3, 2026
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
Published on: July 1, 2020
PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for
1Department of Statistics, The University of Auckland, Auckland, New Zealand. b.browning@auckland.ac.nz
Background:
Large-scale genetic association studies can test hundreds of thousands of genetic markers for association with a trait. Since the genetic markers may be correlated, a Bonferroni correction is typically too stringent a correction for multiple testing. Permutation testing is a standard statistical technique for determining statistical significance when performing multiple correlated tests for genetic association. However, permutation testing for large-scale genetic association studies is computationally demanding and calls for optimized algorithms and software. PRESTO is a new software package for genetic association studies that performs fast computation of multiple-testing adjusted P-values via permutation of the trait.
Results:
PRESTO is an order of magnitude faster than other existing permutation testing software, and can analyze a large genome-wide association study (500 K markers, 5 K individuals, 1 K permutations) in approximately one hour of computing time. PRESTO has several unique features that are useful in a wide range of studies: it reports empirical null distributions for the top-ranked statistics (i.e. order statistics), it performs user-specified combinations of allelic and genotypic tests, it performs stratified analysis when sampled individuals are from multiple populations and each individual's population of origin is specified, and it determines significance levels for one and two-stage genotyping designs. PRESTO is designed for case-control studies, but can also be applied to trio data (parents and affected offspring) if transmitted parental alleles are coded as case alleles and untransmitted parental alleles are coded as control alleles.
Conclusion:
PRESTO is a platform-independent software package that performs fast and flexible permutation testing for genetic association studies. The PRESTO executable file, Java source code, example data, and documentation are freely available at http://www.stat.auckland.ac.nz/~browning/presto/presto.html.
Related Concept Videos
01:24Testing a Claim about Population Proportion
There are two methods of testing a claim about a population proportion: (1) Using the sample proportion from the data where a binomial distribution is approximated to the normal distribution and (2) Using the binomial probabilities calculated from the data.
The first method uses normal distribution as an approximation to the binomial distribution. The requirements are as follows: sample size is large...
01:10Bonferroni Test
The means of different samples are first paired in all possible combinations.
The null hypothesis of the...
01:08Fisher's Exact Test
01:21Friedman Two-way Analysis of Variance by Ranks
01:16Statistical Inference Techniques in Hypothesis Testing: Parametric Versus Nonparametric Data
Parametric statistics, as the name suggests, assumes that data follow a specific distribution, often a normal distribution. This assumption enables robust hypothesis testing and estimation. Parametric methods, like the Student's t-test or Goodness-of-fit test, are frequently employed in biostatistics due to their robustness. For instance, comparing...
01:09Statistical Methods to Analyze Parametric Data: Student t-Test and Goodness-of-Fit Test
The Student's t-test is a statistical test that examines if there is a statistically significant difference between the means of two groups. This test is instrumental when dealing with data...